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Harmsen MM, Ackerschott B, de Smit H. Serum immunoglobulin or albumin binding single-domain antibodies that enable tailored half-life extension of biologics in multiple animal species. Front Immunol 2024; 15:1346328. [PMID: 38352869 PMCID: PMC10862077 DOI: 10.3389/fimmu.2024.1346328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
Single-domain antibody fragments (sdAbs) can be isolated from heavy-chain-only antibodies that occur in camelids or the heavy chain of conventional antibodies, that also occur in camelids. Therapeutic application of sdAbs is often complicated by their low serum half-life. Fusion to sdAb that bind to long-lived serum proteins albumin or IgG can prolong serum half-life of fusion partners. Such studies mostly focused on human application. For half-life prolongation in multiple animal species novel species cross-reacting sdAb are needed. We here describe the isolation from immunized llamas of sdAbs G6 and G13 that bound IgG of 9-10 species analysed, including horse, dog, cat, and swine, as well as sdAb A12 that bound horse, dog, swine and cat albumin. A12 bound albumin with 13 to 271 nM affinity dependent on the species. G13 affinity was difficult to determine by biolayer interferometry due to low and heterogeneous signals. G13 and G6 compete for the same binding domain on Fab fragments. Furthermore, they both lack the hallmark residues typical of camelid sdAbs derived from heavy-chain antibodies and had sequence characteristics typical of human sdAbs with high solubility and stability. This suggests they are derived from conventional llama antibodies. They most likely bind IgG through pairing with VL domains at the VH-VL interface rather than a paratope involving complementarity determining regions. None of the isolated sdAb interfered with FcRn binding to albumin or IgG, and thus do not prevent endosomal albumin/IgG-sdAb complex recycling. Fusions of albumin-binding sdAb A12 to several tetanus neurotoxin (TeNT) binding sdAbs prolonged the terminal serum half-life in piglets to about 4 days, comparable to authentic swine albumin. However, G13 conferred a much lower half-life of 0.84 days. Similarly, in horse, G13 prolonged half-life to only 1.2 days whereas A12 fused to two TeNT binding domains (T6T16A12) had a half-life of 21 days. The high half-life of T6T16A12, which earlier proved to be a highly potent TeNT antitoxin, further supports its therapeutic value. Furthermore, we have identified several additional sdAbs that enable tailored half-life extension of biologicals in multiple animal species.
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Affiliation(s)
- Michiel M. Harmsen
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, Netherlands
| | | | - Hans de Smit
- Research and Development, Smivet B.V., Wijchen, Netherlands
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2
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Levi R, Dvorkin S, Louzoun Y. Shared bias in H chain V-J pairing in naive and memory B cells. Front Immunol 2023; 14:1166116. [PMID: 37790930 PMCID: PMC10543446 DOI: 10.3389/fimmu.2023.1166116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction H chain rearrangement in B cells is a two-step process where first DH binds JH, and only then VH is joined to the complex. As such, there is no direct rearrangement between VH and JH. Results Nevertheless, we here show that the VHJH combinations frequency in humans deviates from the one expected based on each gene usage frequency. This bias is observed mainly in functional rearrangements, and much less in out-of-frame rearrangements. The bias cannot be explained by preferred binding for DH genes or a preferred reading frame. Preferred VH JH combinations are shared between donors. Discussion These results suggest a common structural mechanism for these biases. Through development, thepreferred VH JH combinations evolve during peripheral selection to become stronger, but less shared. We propose that peripheral Heavy chain VH JH usage is initially shaped by a structural selection before the naive B cellstate, followed by pathogen-induced selection for host specific VH-JH pairs.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
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3
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Structural mechanism of Fab domain dissociation as a measure of interface stability. J Comput Aided Mol Des 2023; 37:201-215. [PMID: 36918473 PMCID: PMC10049950 DOI: 10.1007/s10822-023-00501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023]
Abstract
Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs). We describe the Fab dissociation mechanisms, showing a separation in the VH-VL and in the CH1-CL domains. We found that the depths of the minima in the free energy curve, corresponding to the bound states, correlate with the experimentally determined melting temperatures. Additionally, we provide a detailed structural description of the dissociation mechanism and identify key interactions in the CDR loops and in the CH1-CL interface that contribute to stabilization. The dissociation of the VH-VL or CH1-CL domains can be represented by conformational changes in the bend angles between the domains. Our findings elucidate the melting process of antigen binding fragments and highlight critical residues in both the variable and constant domains, which are also strongly germline dependent. Thus, our proposed mechanisms have broad implications in the development and design of new and more stable antigen binding fragments.
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4
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Ralph DK, Matsen FA. Inference of B cell clonal families using heavy/light chain pairing information. PLoS Comput Biol 2022; 18:e1010723. [PMID: 36441808 PMCID: PMC9731466 DOI: 10.1371/journal.pcbi.1010723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 12/08/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package.
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Affiliation(s)
- Duncan K. Ralph
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Frederick A. Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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5
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Di Rienzo L, Milanetti E, Ruocco G, Lepore R. Quantitative Description of Surface Complementarity of Antibody-Antigen Interfaces. Front Mol Biosci 2021; 8:749784. [PMID: 34660699 PMCID: PMC8514621 DOI: 10.3389/fmolb.2021.749784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/14/2021] [Indexed: 11/29/2022] Open
Abstract
Antibodies have the remarkable ability to recognise their cognate antigens with extraordinary affinity and specificity. Discerning the rules that define antibody-antigen recognition is a fundamental step in the rational design and engineering of functional antibodies with desired properties. In this study we apply the 3D Zernike formalism to the analysis of the surface properties of the antibody complementary determining regions (CDRs). Our results show that shape and electrostatic 3DZD descriptors of the surface of the CDRs are predictive of antigen specificity, with classification accuracy of 81% and area under the receiver operating characteristic curve (AUC) of 0.85. Additionally, while in terms of surface size, solvent accessibility and amino acid composition, antibody epitopes are typically not distinguishable from non-epitope, solvent-exposed regions of the antigen, the 3DZD descriptors detect significantly higher surface complementarity to the paratope, and are able to predict correct paratope-epitope interaction with an AUC = 0.75.
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Affiliation(s)
- Lorenzo Di Rienzo
- Center for Life Nano and Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nano and Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano and Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
| | - Rosalba Lepore
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
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6
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Zhao P, Guo S, Zhong Z, Yang S, Xia X. Quantitative characterization of the B cell receptor repertoires of human immunized with commercial rabies virus vaccine. Hum Vaccin Immunother 2021; 17:2538-2546. [PMID: 34559619 PMCID: PMC8475592 DOI: 10.1080/21645515.2021.1893576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/03/2021] [Accepted: 02/16/2021] [Indexed: 02/05/2023] Open
Abstract
Humoral immunity is crucial for an efficient host immune response against rabies virus (RABV) infection. But the B cell receptor (BCR) repertoire in human after RABV vaccine immunization remained unclear. To study the BCR repertoires in peripheral blood mononuclear cells (PBMCs) of human immunized with rabies virus vaccine. In this study, we conducted BCR complementarity determining region 3 (CDR3) repertoires in 4 healthy volunteers before and after immunization with RABV vaccine by high-throughput sequencing. The bioinformatics analysis process was performed. The results showed that RABV vaccination changed the BCR diversity and the usage of V/J gene segments, as well as V-J pairing. B cell clone expansion was induced by the vaccination and sequences of high expand CDR3 aa clones were identified. To the best of our knowledge, we firstly quantitative characterized B cell receptor repertoire of human immunized with c rabies virus vaccine. It might provide us with new insights into B cell receptor condition after RABV vaccination.
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Affiliation(s)
- Pingsen Zhao
- Department of Laboratory Medicine, Yuebei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Yuebei People’s Hospital, Shaoguan Municipal Quality Control Center for Laboratory Medicine, Shaoguan, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People’s Hospital, Shantou University Medical College, Shaoguan, China
- CONTACT Pingsen Zhao ; Department of Laboratory Medicine, Yuebei People’s Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan512025, P. R. China
| | - Sharula Guo
- Department of Infection Control, Yuebei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Zhixiong Zhong
- Center for Precision Medicine, Meizhou People’s Hospital, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Songtao Yang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xianzhu Xia
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
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van den Brand M, Rijntjes J, Möbs M, Steinhilber J, van der Klift MY, Heezen KC, Kroeze LI, Reigl T, Porc J, Darzentas N, Luijks JACW, Scheijen B, Davi F, ElDaly H, Liu H, Anagnostopoulos I, Hummel M, Fend F, Langerak AW, Groenen PJTA. Next-Generation Sequencing-Based Clonality Assessment of Ig Gene Rearrangements: A Multicenter Validation Study by EuroClonality-NGS. J Mol Diagn 2021; 23:1105-1115. [PMID: 34186174 DOI: 10.1016/j.jmoldx.2021.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Ig gene (IG) clonality analysis has an important role in the distinction of benign and malignant B-cell lymphoid proliferations and is mostly performed with the conventional EuroClonality/BIOMED-2 multiplex PCR protocol and GeneScan fragment size analysis. Recently, the EuroClonality-NGS Working Group developed a method for next-generation sequencing (NGS)-based IG clonality analysis. Herein, we report the results of an international multicenter biological validation of this novel method compared with the gold standard EuroClonality/BIOMED-2 protocol, based on 209 specimens of reactive and neoplastic lymphoproliferations. NGS-based IG clonality analysis showed a high interlaboratory concordance (99%) and high concordance with conventional clonality analysis (98%) for the molecular conclusion. Detailed analysis of the individual IG heavy chain and kappa light chain targets showed that NGS-based clonality analysis was more often able to detect a clonal rearrangement or yield an interpretable result. NGS-based and conventional clonality analysis detected a clone in 96% and 95% of B-cell neoplasms, respectively, and all but one of the reactive cases were scored polyclonal. We conclude that NGS-based IG clonality analysis performs comparable to conventional clonality analysis. We provide critical parameters for interpretation and discuss a first step toward a quantitative scoring approach for NGS clonality results. Considering the advantages of NGS-based clonality analysis, including its high sensitivity and possibilities for accurate clonal comparison, this supports implementation in diagnostic practice.
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Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Markus Möbs
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Julia Steinhilber
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Michèle Y van der Klift
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kim C Heezen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tomas Reigl
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Jakub Porc
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Nikos Darzentas
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic; Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jeroen A C W Luijks
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frédéric Davi
- Hematology Department, Hospital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - Hesham ElDaly
- Histopathology Department, Coventry University Hospitals National Health Service Trust, Coventry, United Kingdom; Clinical Pathology Department, Cairo University, Cairo, Egypt
| | - Hongxiang Liu
- Haematopathology and Oncology Diagnostics Service, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom
| | | | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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8
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DutaFabs are engineered therapeutic Fab fragments that can bind two targets simultaneously. Nat Commun 2021; 12:708. [PMID: 33514724 PMCID: PMC7846786 DOI: 10.1038/s41467-021-20949-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
We report the development of a platform of dual targeting Fab (DutaFab) molecules, which comprise two spatially separated and independent binding sites within the human antibody CDR loops: the so-called H-side paratope encompassing HCDR1, HCDR3 and LCDR2, and the L-side paratope encompassing LCDR1, LCDR3 and HCDR2. Both paratopes can be independently selected and combined into the desired bispecific DutaFabs in a modular manner. X-ray crystal structures illustrate that DutaFabs are able to bind two target molecules simultaneously at the same Fv region comprising a VH-VL heterodimer. In the present study, this platform is applied to generate DutaFabs specific for VEGFA and PDGF-BB, which show high affinities, physico-chemical stability and solubility, as well as superior efficacy over anti-VEGF monotherapy in vivo. These molecules exemplify the usefulness of DutaFabs as a distinct class of antibody therapeutics, which is currently being evaluated in patients. Bispecific antibodies can bind to two distinct targets though the fusion of two different Fv regions. In this study, the authors develop DutaFabs that present two separated and independent antigen binding sites within the same Fv region, giving rise to bispecific Fab fragments.
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9
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Zarei B, Javidan Z, Fatemi E, Rahimi Jamnani F, Khatami S, Khalaj V. Targeting c-Met on gastric cancer cells through a fully human fab antibody isolated from a large naive phage antibody library. Daru 2020; 28:221-235. [PMID: 32193747 PMCID: PMC7238820 DOI: 10.1007/s40199-020-00334-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The aberrant Hepatocyte growth factor (HGF)/ mesenchymal-epithelial transition factor (c-Met) signaling pathway in various malignancies and its correlation with tumor invasion and poor prognosis has validated c-Met as a compelling therapeutic target. Up to now, several monoclonal antibodies and small molecule inhibitors targeting c-Met have been introduced with different outcomes, none are yet clinically approved. Toward the generation of novel fully human anti-c-Met molecules, we generated a large naïve Fab antibody library using phage display technology, which subsequently screened for novel Fabs against c-Met. METHODS A phage library, with a functional size of 5.5 × 1010 individual antibody clones, was prepared using standard protocols and screened for c-Met-specific Fabs by successive rounds of panning. A panel of Fabs targeting c-Met were isolated, from which four clones were selected and further characterized by DNA sequencing. The c-Met binding ability of our selected Fabs was evaluated by c-Met ELISA assay and flow cytometry techniques. RESULTS Among the confirmed anti-c-Met Fabs, clone C16, showed the highest affinity (Kaff: 0.3 × 109 M-1), and 63% binding to MKN45 cells (a human gastric adenocarcinoma cell-line) as compared to c-Met negative T47D cell-line (9.03%). CONCLUSION Together, our study presents a single-pot antibody library, as a valuable source for finding a range of antigen-specific Fab antibodies, and also, a fully human, high affinity and specific anti c-Met Fab antibody, C16, which has the potential of developing as a therapeutic or chemotherapeutic delivery agent for killing c-Met-positive tumor cells.
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Affiliation(s)
- Bahareh Zarei
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Javidan
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elnaz Fatemi
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research,
Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Shohreh Khatami
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Khalaj
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
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10
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Chiu ML, Goulet DR, Teplyakov A, Gilliland GL. Antibody Structure and Function: The Basis for Engineering Therapeutics. Antibodies (Basel) 2019; 8:antib8040055. [PMID: 31816964 PMCID: PMC6963682 DOI: 10.3390/antib8040055] [Citation(s) in RCA: 237] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Antibodies and antibody-derived macromolecules have established themselves as the mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure–function relationships of antibodies provides a platform for protein engineering that has been exploited to generate a wide range of biologics for a host of therapeutic indications. In this review, our basic understanding of the antibody structure is described along with how that knowledge has leveraged the engineering of antibody and antibody-related therapeutics having the appropriate antigen affinity, effector function, and biophysical properties. The platforms examined include the development of antibodies, antibody fragments, bispecific antibody, and antibody fusion products, whose efficacy and manufacturability can be improved via humanization, affinity modulation, and stability enhancement. We also review the design and selection of binding arms, and avidity modulation. Different strategies of preparing bispecific and multispecific molecules for an array of therapeutic applications are included.
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Affiliation(s)
- Mark L. Chiu
- Drug Product Development Science, Janssen Research & Development, LLC, Malvern, PA 19355, USA
- Correspondence:
| | - Dennis R. Goulet
- Department of Medicinal Chemistry, University of Washington, P.O. Box 357610, Seattle, WA 98195-7610, USA;
| | - Alexey Teplyakov
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
| | - Gary L. Gilliland
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
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11
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Ren J, Nettleship JE, Harris G, Mwangi W, Rhaman N, Grant C, Kotecha A, Fry E, Charleston B, Stuart DI, Hammond J, Owens RJ. The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus. Mol Immunol 2019; 112:123-130. [PMID: 31100550 PMCID: PMC6677920 DOI: 10.1016/j.molimm.2019.04.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/10/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
The Fab structures of two cattle antibodies (B4 and B13) that neutralise bRSV have been solved. The light chain plays a critical role in the folding and positioning of CDR H3 of the heavy chains. The H3 loop plays a dominant role in antigen-binding.
Cattle antibodies have unusually long CDR3 loops in their heavy chains (HCs), and limited light chain (LC) diversity, raising the question of whether these mask the effect of LC variation on antigen recognition. We have investigated the role of the LC in the structure and activity of two neutralizing cattle antibodies (B4 and B13) that bind the F protein of bovine respiratory syncytial virus (bRSV). Recombinant Fab fragments of B4 and B13 bound bRSV infected cells and showed similar affinities for purified bRSV F protein. Exchanging the LCs between the Fab fragments produced hybrid Fabs: B13* (B13 HC/B4 LC) and B4* (B4 HC/B13 LC). The affinity of B13* to the F protein was found to be two-fold lower than B13 whilst the binding affinity of B4* was reduced at least a hundred-fold compared to B4 such that it no longer bound to bRSV infected cells. Comparison of the structures of B4 and B13 with their LC exchanged counterparts B4* and B13* showed that paratope of the HC variable domain (VH) of B4 was disrupted on pairing with the B13 LC, consistent with the loss of binding activity. By contrast, B13 H3 adopts a similar conformation when paired with either B13 or B4 LCs. These observations confirm the expected key role of the extended H3 loop in antigen-binding by cattle antibodies but also show that the quaternary LC/HC subunit interaction can be crucial for its presentation and thus the LC variable domain (VL) is also important for antigen recognition.
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Affiliation(s)
- Jingshan Ren
- The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Joanne E Nettleship
- The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK; Research Complex at Harwell, R92 Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Gemma Harris
- Research Complex at Harwell, R92 Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - William Mwangi
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Nahid Rhaman
- The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK; Research Complex at Harwell, R92 Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Clare Grant
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Abhay Kotecha
- The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Elizabeth Fry
- The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Bryan Charleston
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - David I Stuart
- The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - John Hammond
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Raymond J Owens
- The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK; Research Complex at Harwell, R92 Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
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12
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Leighton PA, Morales J, Harriman WD, Ching KH. V(D)J Rearrangement Is Dispensable for Producing CDR-H3 Sequence Diversity in a Gene Converting Species. Front Immunol 2018; 9:1317. [PMID: 29951062 PMCID: PMC6008532 DOI: 10.3389/fimmu.2018.01317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022] Open
Abstract
An important characteristic of chickens is that the antibody repertoire is based on a single framework, with diversity found mainly in the CDRs of the light and heavy chain variable regions. Despite this apparent limitation in the antibody repertoire, high-affinity antibodies can be raised to a wide variety of targets, including those that are highly conserved. Transgenic chickens have previously been generated that express a humanized antibody repertoire, with a single framework that incorporates diversity by the process of gene conversion, as in wild-type chickens. Here, we compare the sequences and antibodies that are generated purely by gene conversion/somatic hypermutation of a pre-rearranged heavy chain, with the diversity obtained by V(D)J rearrangement followed by gene conversion and somatic hypermutation. In a gene converting species, CDR-H3 lengths are more variable with V(D)J rearrangement, but similar levels of amino acid diversity are obtainable with gene conversion/somatic hypermutation alone.
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Koelsch KA, Cavett J, Smith K, Moore JS, Lehoux SD, Jia N, Mather T, Quadri SMS, Rasmussen A, Kaufman CE, Lewis DM, Radfar L, Scordino TA, Lessard CJ, Kurien BT, Cummings RD, James JA, Sivils KL, Farris AD, Scofield RH. Evidence of Alternative Modes of B Cell Activation Involving Acquired Fab Regions of N-Glycosylation in Antibody-Secreting Cells Infiltrating the Labial Salivary Glands of Patients With Sjögren's Syndrome. Arthritis Rheumatol 2018; 70:1102-1113. [PMID: 29457375 DOI: 10.1002/art.40458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 02/13/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To better understand the role of B cells, the potential mechanisms responsible for their aberrant activation, and the production of autoantibodies in the pathogenesis of Sjögren's syndrome (SS), this study explored patterns of selection pressure and sites of N-glycosylation acquired by somatic mutation (acN-glyc) in the IgG variable (V) regions of antibody-secreting cells (ASCs) isolated from the minor salivary glands of patients with SS and non-SS control patients with sicca symptoms. METHODS A novel method to produce and characterize recombinant monoclonal antibodies (mAb) from single cell-sorted ASC infiltrates was applied to concurrently probe expressed genes (all heavy- and light-chain isotypes as well as any other gene of interest not related to immunoglobulin) in the labial salivary glands of patients with SS and non-SS controls. V regions were amplified by reverse transcription-polymerase chain reaction, sequenced, and analyzed for the incidence of N-glycosylation and selection pressure. For specificity testing, the amplified regions were expressed as either the native mAb or mutant mAb lacking the acN-glyc motif. Protein modeling was used to demonstrate how even an acN-glyc site outside of the complementarity-determining region could participate in, or inhibit, antigen binding. RESULTS V-region sequence analyses revealed clonal expansions and evidence of secondary light-chain editing and allelic inclusion, of which neither of the latter two have previously been reported in patients with SS. Increased frequencies of acN-glyc were found in the sequences from patients with SS, and these acN-glyc regions were associated with an increased number of replacement mutations and lowered selection pressure. A clonal set of polyreactive mAb with differential framework region 1 acN-glyc motifs was also identified, and removal of the acN-glyc could nearly abolish binding to autoantigens. CONCLUSION These findings support the notion of an alternative mechanism for the selection and proliferation of some autoreactive B cells, involving V-region N-glycosylation, in patients with SS.
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Affiliation(s)
- Kristi A Koelsch
- University of Oklahoma Health Sciences Center, Oklahoma Medical Research Foundation, and Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
| | - Joshua Cavett
- University of Oklahoma Health Sciences Center, Oklahoma Medical Research Foundation, and Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
| | | | - Jacen S Moore
- University of Oklahoma Health Sciences Center, Oklahoma Medical Research Foundation, and Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
| | - Sylvain D Lehoux
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Nan Jia
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Tim Mather
- Oklahoma Medical Research Foundation, Oklahoma City
| | - Syed M S Quadri
- University of Oklahoma Health Sciences Center and Oklahoma Medical Research Foundation, Oklahoma City
| | | | - C Erick Kaufman
- University of Oklahoma Health Sciences Center, Oklahoma City
| | - David M Lewis
- University of Oklahoma College of Dentistry, Oklahoma City
| | - Lida Radfar
- University of Oklahoma College of Dentistry, Oklahoma City
| | | | - Christopher J Lessard
- University of Oklahoma Health Sciences Center and Oklahoma Medical Research Foundation, Oklahoma City
| | - Biji T Kurien
- University of Oklahoma Health Sciences Center, Oklahoma Medical Research Foundation, and Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
| | - Richard D Cummings
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Judith A James
- University of Oklahoma Health Sciences Center and Oklahoma Medical Research Foundation, Oklahoma City
| | - Kathy L Sivils
- University of Oklahoma Health Sciences Center and Oklahoma Medical Research Foundation, Oklahoma City
| | - A Darise Farris
- University of Oklahoma Health Sciences Center and Oklahoma Medical Research Foundation, Oklahoma City
| | - R Hal Scofield
- University of Oklahoma Health Sciences Center, Oklahoma Medical Research Foundation, and Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
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Adler AS, Bedinger D, Adams MS, Asensio MA, Edgar RC, Leong R, Leong J, Mizrahi RA, Spindler MJ, Bandi SR, Huang H, Tawde P, Brams P, Johnson DS. A natively paired antibody library yields drug leads with higher sensitivity and specificity than a randomly paired antibody library. MAbs 2018; 10:431-443. [PMID: 29376776 PMCID: PMC5916548 DOI: 10.1080/19420862.2018.1426422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Deep sequencing and single-chain variable fragment (scFv) yeast display methods are becoming more popular for discovery of therapeutic antibody candidates in mouse B cell repertoires. In this study, we compare a deep sequencing and scFv display method that retains native heavy and light chain pairing with a related method that randomly pairs heavy and light chain. We performed the studies in a humanized mouse, using interleukin 21 receptor (IL-21R) as a test immunogen. We identified 44 high-affinity binder scFv with the native pairing method and 100 high-affinity binder scFv with the random pairing method. 30% of the natively paired scFv binders were also discovered with the randomly paired method, and 13% of the randomly paired binders were also discovered with the natively paired method. Additionally, 33% of the scFv binders discovered only in the randomly paired library were initially present in the natively paired pre-sort library. Thus, a significant proportion of “randomly paired” scFv were actually natively paired. We synthesized and produced 46 of the candidates as full-length antibodies and subjected them to a panel of binding assays to characterize their therapeutic potential. 87% of the antibodies were verified as binding IL-21R by at least one assay. We found that antibodies with native light chains were more likely to bind IL-21R than antibodies with non-native light chains, suggesting a higher false positive rate for antibodies from the randomly paired library. Additionally, the randomly paired method failed to identify nearly half of the true natively paired binders, suggesting a higher false negative rate. We conclude that natively paired libraries have critical advantages in sensitivity and specificity for antibody discovery programs.
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Affiliation(s)
- Adam S Adler
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Daniel Bedinger
- b Carterra Inc. , 825 N 300 W, Suite C309, Salt Lake City , UT USA
| | - Matthew S Adams
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Michael A Asensio
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Robert C Edgar
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Renee Leong
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Jackson Leong
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Rena A Mizrahi
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Matthew J Spindler
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | | | - Haichun Huang
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - Pallavi Tawde
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - Peter Brams
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - David S Johnson
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
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15
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On being the right size: antibody repertoire formation in the mouse and human. Immunogenetics 2017; 70:143-158. [DOI: 10.1007/s00251-017-1049-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/04/2017] [Indexed: 01/01/2023]
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16
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Teplyakov A, Obmolova G, Malia TJ, Luo J, Muzammil S, Sweet R, Almagro JC, Gilliland GL. Structural diversity in a human antibody germline library. MAbs 2016; 8:1045-63. [PMID: 27210805 PMCID: PMC4968113 DOI: 10.1080/19420862.2016.1190060] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. The CDR conformations for the most part are tightly clustered, especially for the ones with shorter lengths. The longer CDRs with tandem glycines or serines have more conformational diversity than the others. CDR H3, despite having the same amino acid sequence, exhibits the largest conformational diversity. About half of the structures have CDR H3 conformations similar to that of the parent; the others diverge significantly. One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. The stem regions of 14 of the variant pairs are in the ‘kinked’ conformation, and only 2 are in the extended conformation. The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. Two of 16 structures showed particularly large variations in the tilt angles when compared with the other pairings. The structures and their analyses provide a rich foundation for future antibody modeling and engineering efforts.
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Affiliation(s)
| | - Galina Obmolova
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Thomas J Malia
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Jinquan Luo
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Salman Muzammil
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Raymond Sweet
- a Janssen Research & Development LLC, Spring House , PA , USA
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17
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DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, Georgiou G. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires. Proc Natl Acad Sci U S A 2016; 113:E2636-45. [PMID: 27114511 PMCID: PMC4868480 DOI: 10.1073/pnas.1525510113] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19(+)CD20(+)CD27(-) IgM-naive B cells, >120,000 antibody clusters from CD19(+)CD20(+)CD27(+) antigen-experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ-Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease.
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Affiliation(s)
- Brandon J DeKosky
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Oana I Lungu
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Daechan Park
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Erik L Johnson
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Wissam Charab
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | | | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology University of Texas at Austin, Austin, TX 78712
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712; Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
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18
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Kuroda D, Gray JJ. Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking. Bioinformatics 2016; 32:2451-6. [PMID: 27153634 DOI: 10.1093/bioinformatics/btw197] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 04/03/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATIONS Characterizing protein-protein interfaces and the hydrogen bonds is a first step to better understand proteins' structures and functions toward high-resolution protein design. However, there are few large-scale surveys of hydrogen bonds of interfaces. In addition, previous work of shape complementarity of protein complexes suggested that lower shape complementarity in antibody-antigen interfaces is related to their evolutionary origin. RESULTS Using 6637 non-redundant protein-protein interfaces, we revealed peculiar features of various protein complex types. In contrast to previous findings, the shape complementarity of antibody-antigen interfaces resembles that of the other interface types. These results highlight the importance of hydrogen bonds during evolution of protein interfaces and rectify the prevailing belief that antibodies have lower shape complementarity. CONTACT jgray@jhu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, 142-8555, Japan
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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19
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Chen HS, Hou SC, Jian JW, Goh KS, Shen ST, Lee YC, You JJ, Peng HP, Kuo WC, Chen ST, Peng MC, Wang AHJ, Yu CM, Chen IC, Tung CP, Chen TH, Ping Chiu K, Ma C, Yuan Wu C, Lin SW, Yang AS. Predominant structural configuration of natural antibody repertoires enables potent antibody responses against protein antigens. Sci Rep 2015. [PMID: 26202883 PMCID: PMC5378893 DOI: 10.1038/srep12411] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Humoral immunity against diverse pathogens is rapidly elicited from natural antibody repertoires of limited complexity. But the organizing principles underlying the antibody repertoires that facilitate this immunity are not well-understood. We used HER2 as a model immunogen and reverse-engineered murine antibody response through constructing an artificial antibody library encoded with rudimentary sequence and structural characteristics learned from high throughput sequencing of antibody variable domains. Antibodies selected in vitro from the phage-displayed synthetic antibody library bound to the model immunogen with high affinity and specificities, which reproduced the specificities of natural antibody responses. We conclude that natural antibody structural repertoires are shaped to allow functional antibodies to be encoded efficiently, within the complexity limit of an individual antibody repertoire, to bind to diverse protein antigens with high specificity and affinity. Phage-displayed synthetic antibody libraries, in conjunction with high-throughput sequencing, can thus be designed to replicate natural antibody responses and to generate novel antibodies against diverse antigens.
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Affiliation(s)
- Hong-Sen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Shin-Chen Hou
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhih-Wei Jian
- 1] Genomics Research Center, Academia Sinica, Taipei, Taiwan 115 [2] Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan 112 [3] Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan 115
| | - King-Siang Goh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - San-Tai Shen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhong-Jhe You
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Wen-Chih Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Shui-Tsung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Ming-Chi Peng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chih Yuan Wu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
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20
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Wiehe K, Easterhoff D, Luo K, Nicely NI, Bradley T, Jaeger FH, Dennison SM, Zhang R, Lloyd KE, Stolarchuk C, Parks R, Sutherland LL, Scearce RM, Morris L, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Sinangil F, Phogat S, Michael NL, Kim JH, Kelsoe G, Montefiori DC, Tomaras GD, Bonsignori M, Santra S, Kepler TB, Alam SM, Moody MA, Liao HX, Haynes BF. Antibody light-chain-restricted recognition of the site of immune pressure in the RV144 HIV-1 vaccine trial is phylogenetically conserved. Immunity 2014; 41:909-18. [PMID: 25526306 DOI: 10.1016/j.immuni.2014.11.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/20/2014] [Indexed: 01/21/2023]
Abstract
In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition. Structure determination of an unmutated ancestor antibody demonstrated that the V2 binding site was preconfigured for ED motif-mediated recognition prior to maturation. Thus, light chain usage for recognition of the site of immune pressure in the RV144 trial is highly conserved across species. These data indicate that the HIV-1 K169-recognizing ED motif has persisted over the diversification between rhesus macaques and humans, suggesting an evolutionary advantage of this antibody recognition mode.
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Affiliation(s)
- Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
| | - David Easterhoff
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan I Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Frederick H Jaeger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - S Moses Dennison
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christina Stolarchuk
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Richard M Scearce
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, SA and the Centre for the AIDS Programme of Research in South Africa (CAPRISA)
| | - Jaranit Kaewkungwal
- Department of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Sorachai Nitayaphan
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand
| | | | - Supachai Rerks-Ngarm
- Department of Disease Control, Ministry of Public Health, Nonthaburi 11000, Thailand
| | | | - Sanjay Phogat
- Global Solutions for Infectious Diseases, South San Francisco, CA 94080, USA
| | - Nelson L Michael
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jerome H Kim
- US Military Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Harvard University School of Medicine, Boston, MA 02215, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
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21
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Rogosch T, Kerzel S, Dey F, Wagner JJ, Zhang Z, Maier RF, Zemlin M. IgG4 and IgE transcripts in childhood allergic asthma reflect divergent antigen-driven selection. THE JOURNAL OF IMMUNOLOGY 2014; 193:5801-8. [PMID: 25385824 DOI: 10.4049/jimmunol.1401409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The physiologic function of the "odd" Ab IgG4 remains enigmatic. IgG4 mediates immunotolerance, as, for example, during specific immunotherapy of allergies, but it mediates tissue damage in autoimmune pemphigus vulgaris and "IgG4-related disease." Approximately half of the circulating IgG4 molecules are bispecific owing to their unique ability to exchange half-molecules. Better understanding of the interrelation between IgG4 and IgE repertoires may yield insight into the pathogenesis of allergies and into potential novel therapies that modulate IgG4 responses. We aimed to compare the selective forces that forge the IgG4 and IgE repertoires in allergic asthma. Using an IgG4-specific RT-PCR, we amplified, cloned, and sequenced IgG4 H chain transcripts of PBMCs from 10 children with allergic asthma. We obtained 558 functional IgG4 sequences, of which 286 were unique. Compared with previously published unique IgE transcripts from the same blood samples, the somatic mutation rate was significantly enhanced in IgG4 transcripts (62 versus 83%; p < 0.001), whereas fewer IgG4 sequences displayed statistical evidence of Ag-driven selection (p < 0.001). On average, the hypervariable CDRH3 region was four nucleotides shorter in IgG4 than in IgE transcripts (p < 0.001). IgG4 transcripts in the circulation of children with allergic asthma reflect some characteristics of classical Ag-driven B2 immune responses but display less indication of Ag selection than do IgE transcripts. Although allergen-specific IgG4 can block IgE-mediated allergen presentation and degranulation of mast cells, key factors that influence the Ag-binding properties of the Ab differ between the overall repertoires of circulating IgG4- and IgE-expressing cells.
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Affiliation(s)
- Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Sebastian Kerzel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, 93053 Regensburg, Germany; and
| | - Friederike Dey
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | | | - Zhixin Zhang
- Department of Pathology and Microbiology, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198
| | - Rolf F Maier
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany;
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22
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Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected]. Nat Protoc 2014; 9:2771-83. [PMID: 25375991 DOI: 10.1038/nprot.2014.189] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antibodies (or immunoglobulins) are crucial for defending organisms from pathogens, but they are also key players in many medical, diagnostic and biotechnological applications. The ability to predict their structure and the specific residues involved in antigen recognition has several useful applications in all of these areas. Over the years, we have developed or collaborated in developing a strategy that enables researchers to predict the 3D structure of antibodies with a very satisfactory accuracy. The strategy is completely automated and extremely fast, requiring only a few minutes (∼10 min on average) to build a structural model of an antibody. It is based on the concept of canonical structures of antibody loops and on our understanding of the way light and heavy chains pack together.
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Houimel M. The analysis of VH and VL genes repertoires of Fab library built from peripheral B cells of human rabies virus vaccinated donors. Hum Immunol 2014; 75:745-55. [PMID: 24862931 DOI: 10.1016/j.humimm.2014.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 02/04/2023]
Abstract
A human combinatorial Fab antibody library was generated from immune repertoire based on peripheral B cells of ten rabies virus vaccinated donors. The analysis of random Fab fragments from the unselected library presented some bias of V gene usage towards IGHV-genes and IGLV-gen families. The screening of the Fab library on rabies virus allowed specific human Fab antibody fragments characterized for their gene encoding sequences, binding and specificities to RV. Genetic analysis of selected Fabs indicated that the IGHV and IGLV differ from the germ-line sequence. At the level of nucleotide sequences, the IGHV and IGLV domains were found to share 74-92% and 90-96% homology with sequences encoded by the corresponding human germ-line genes respectively. IGHV domains are characterized most frequently by IGHV3 genes, and large proportions of the anti-RV heavy chain IGHV domains are obtained following a VDJ recombination process that uses IGHD3, IGHD2, IGHD1 and IGHD6 genes. IGHJ3 and IGHJ4 genes are predominantly used in RV-Fab. The IGLV domains are dominated by IGKV1, IGLV1 and IGLV3 genes. Numerous somatic hypermutations in the RV-specific IGHV are detected, but only limited amino acid replacement in most of the RV-specific IGLV particularly in those encoded by J proximal IGLV or IGKV genes are found. Furthermore, IGHV3-IGKV1, IGHV3-IGVL1, and IGHV3-IGLV3 germ-line family pairings are preferentially enriched after the screening on rabies virus.
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Affiliation(s)
- Mehdi Houimel
- Laboratoire d'Epidémiologie et de Microbiologie Vétérinaire, Institut Pasteur de Tunis, Tunisia; Université Tunis El Manar, Tunis, Tunisia.
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24
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Tucci FA, Broering R, Lutterbeck M, Schlaak JF, Küppers R. Intrahepatic B-cell follicles of chronically hepatitis C virus-infected individuals lack signs of an ectopic germinal center reaction. Eur J Immunol 2014; 44:1842-50. [DOI: 10.1002/eji.201344378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/05/2014] [Accepted: 03/04/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Felicia A. Tucci
- Institute of Cell Biology (Cancer Research); University of Duisburg-Essen; Essen Germany
| | - Ruth Broering
- Department of Gastroenterology and Hepatology; University of Duisburg-Essen; University Hospital; Essen Germany
| | - Melanie Lutterbeck
- Department of Gastroenterology and Hepatology; University of Duisburg-Essen; University Hospital; Essen Germany
| | - Joerg F. Schlaak
- Department of Gastroenterology and Hepatology; University of Duisburg-Essen; University Hospital; Essen Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research); University of Duisburg-Essen; Essen Germany
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Essen Germany
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25
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Teplyakov A, Luo J, Obmolova G, Malia TJ, Sweet R, Stanfield RL, Kodangattil S, Almagro JC, Gilliland GL. Antibody modeling assessment II. Structures and models. Proteins 2014; 82:1563-82. [PMID: 24633955 DOI: 10.1002/prot.24554] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/23/2014] [Accepted: 03/06/2014] [Indexed: 12/12/2022]
Abstract
To assess the state-of-the-art in antibody structure modeling, a blinded study was conducted. Eleven unpublished Fab crystal structures were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. In the first round, each participant submitted three non-ranked complete Fv models for each target. In the second round, CDR-H3 modeling was performed in the context of the correct environment provided by the crystal structures with CDR-H3 removed. In this report we describe the reference structures and present our assessment of the models. Some of the essential sources of errors in the predictions were traced to the selection of the structure template, both in terms of the CDR canonical structures and VL/VH packing. On top of this, the errors present in the Protein Data Bank structures were sometimes propagated in the current models, which emphasized the need for the curated structural database devoid of errors. Modeling non-canonical structures, including CDR-H3, remains the biggest challenge for antibody structure prediction.
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Affiliation(s)
- Alexey Teplyakov
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania, 19477
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26
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Abate AR, Hung T, Sperling RA, Mary P, Rotem A, Agresti JJ, Weiner MA, Weitz DA. DNA sequence analysis with droplet-based microfluidics. LAB ON A CHIP 2013; 13:4864-9. [PMID: 24185402 PMCID: PMC4090915 DOI: 10.1039/c3lc50905b] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based assay. Using probes of different sequences, we interrogate a target DNA molecule for polymorphisms. With a larger probe set, additional polymorphisms can be interrogated as well as targets of arbitrary sequence.
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Affiliation(s)
- Adam R Abate
- University of California, San Francisco - Bioengineering and Therapeutic Sciences, San Francisco, California, USA
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27
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Butler J, Wertz N, Sun X. Antibody repertoire development in fetal and neonatal piglets. XIV. Highly restricted IGKV gene usage parallels the pattern seen with IGLV and IGHV. Mol Immunol 2013; 55:329-36. [DOI: 10.1016/j.molimm.2013.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/04/2013] [Accepted: 03/13/2013] [Indexed: 01/17/2023]
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28
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Jackson KJL, Kidd MJ, Wang Y, Collins AM. The shape of the lymphocyte receptor repertoire: lessons from the B cell receptor. Front Immunol 2013; 4:263. [PMID: 24032032 PMCID: PMC3759170 DOI: 10.3389/fimmu.2013.00263] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Both the B cell receptor (BCR) and the T cell receptor (TCR) repertoires are generated through essentially identical processes of V(D)J recombination, exonuclease trimming of germline genes, and the random addition of non-template encoded nucleotides. The naïve TCR repertoire is constrained by thymic selection, and TCR repertoire studies have therefore focused strongly on the diversity of MHC-binding complementarity determining region (CDR) CDR3. The process of somatic point mutations has given B cell studies a major focus on variable (IGHV, IGLV, and IGKV) genes. This in turn has influenced how both the naïve and memory BCR repertoires have been studied. Diversity (D) genes are also more easily identified in BCR VDJ rearrangements than in TCR VDJ rearrangements, and this has allowed the processes and elements that contribute to the incredible diversity of the immunoglobulin heavy chain CDR3 to be analyzed in detail. This diversity can be contrasted with that of the light chain where a small number of polypeptide sequences dominate the repertoire. Biases in the use of different germline genes, in gene processing, and in the addition of non-template encoded nucleotides appear to be intrinsic to the recombination process, imparting "shape" to the repertoire of rearranged genes as a result of differences spanning many orders of magnitude in the probabilities that different BCRs will be generated. This may function to increase the precursor frequency of naïve B cells with important specificities, and the likely emergence of such B cell lineages upon antigen exposure is discussed with reference to public and private T cell clonotypes.
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Affiliation(s)
- Katherine J. L. Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marie J. Kidd
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yan Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Phage display antibodies for diagnostic applications. Biologicals 2013; 41:209-16. [DOI: 10.1016/j.biologicals.2013.04.001] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/29/2013] [Accepted: 04/02/2013] [Indexed: 11/23/2022] Open
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30
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Schwimmer LJ, Huang B, Giang H, Cotter RL, Chemla-Vogel DS, Dy FV, Tam EM, Zhang F, Toy P, Bohmann DJ, Watson SR, Beaber JW, Reddy N, Kuan HF, Bedinger DH, Rondon IJ. Discovery of diverse and functional antibodies from large human repertoire antibody libraries. J Immunol Methods 2013; 391:60-71. [DOI: 10.1016/j.jim.2013.02.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 12/12/2012] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
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31
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Tiller T, Schuster I, Deppe D, Siegers K, Strohner R, Herrmann T, Berenguer M, Poujol D, Stehle J, Stark Y, Heßling M, Daubert D, Felderer K, Kaden S, Kölln J, Enzelberger M, Urlinger S. A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties. MAbs 2013; 5:445-70. [PMID: 23571156 DOI: 10.4161/mabs.24218] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.
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32
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Bentley CA, Bazirgan OA, Graziano JJ, Holmes EM, Smider VV. Arrayed antibody library technology for therapeutic biologic discovery. Methods 2013; 60:91-8. [DOI: 10.1016/j.ymeth.2013.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 02/08/2013] [Accepted: 02/11/2013] [Indexed: 01/20/2023] Open
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33
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Finlay WJJ, Almagro JC. Natural and man-made V-gene repertoires for antibody discovery. Front Immunol 2012; 3:342. [PMID: 23162556 PMCID: PMC3498902 DOI: 10.3389/fimmu.2012.00342] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 10/27/2012] [Indexed: 01/15/2023] Open
Abstract
Antibodies are the fastest-growing segment of the biologics market. The success of antibody-based drugs resides in their exquisite specificity, high potency, stability, solubility, safety, and relatively inexpensive manufacturing process in comparison with other biologics. We outline here the structural studies and fundamental principles that define how antibodies interact with diverse targets. We also describe the antibody repertoires and affinity maturation mechanisms of humans, mice, and chickens, plus the use of novel single-domain antibodies in camelids and sharks. These species all utilize diverse evolutionary solutions to generate specific and high affinity antibodies and illustrate the plasticity of natural antibody repertoires. In addition, we discuss the multiple variations of man-made antibody repertoires designed and validated in the last two decades, which have served as tools to explore how the size, diversity, and composition of a repertoire impact the antibody discovery process.
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Abstract
Antibodies are key molecules of the adaptive immune response and are now a major class of biopharmaceuticals. Pairing of heavy and light chains is one of the ways of generating antibody diversity and, while little is known about mechanisms governing V(H)/V(L) pairing, previous studies have suggested that the germline source from which chains are paired is random. By selecting paired antibody protein sequences from human and mouse antibodies from the KabatMan database and mapping them onto their corresponding germline sequences, we find that pairing preferences do exist in the germline, but only for a small proportion of germline gene segments; others are much more promiscuous showing no preferences. The closest equivalent human and mouse gene families were identified and pairing preferences compared. This work may impact on the ability to generate more stable antibodies for use as biopharmaceuticals.
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Affiliation(s)
- Narayan Jayaram
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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35
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Location and length distribution of somatic hypermutation-associated DNA insertions and deletions reveals regions of antibody structural plasticity. Genes Immun 2012; 13:523-9. [PMID: 22717702 PMCID: PMC3449029 DOI: 10.1038/gene.2012.28] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Following the initial diversity generated by V(D)J recombination, somatic hypermutation is the principal mechanism for producing further antibody repertoire diversity in antigen-experienced B cells. While somatic hypermutation typically results in single nucleotide substitutions, the infrequent incorporation of genetic insertions and deletions has also been associated with the somatic hypermutation process. We used high throughput antibody sequencing to determine the sequence of thousands of antibody genes containing somatic hypermutation-associated insertions and deletions (SHA indels), which revealed significant differences between the location of SHA indels and somatic mutations. Further, we identified a cluster of insertions and deletions in the antibody framework 3 region which corresponds to the hypervariable region 4 (HV4) in T cell receptors. We propose that this HV4-like region, identified by SHA indel analysis, represents a region of under-appreciated affinity maturation potential. Finally, through analysis of both location and length distribution of SHA indels, we have determined regions of structural plasticity within the antibody protein.
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36
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Thomson CA, Wang Y, Jackson LM, Olson M, Wang W, Liavonchanka A, Keleta L, Silva V, Diederich S, Jones RB, Gubbay J, Pasick J, Petric M, Jean F, Allen VG, Brown EG, Rini JM, Schrader JW. Pandemic H1N1 Influenza Infection and Vaccination in Humans Induces Cross-Protective Antibodies that Target the Hemagglutinin Stem. Front Immunol 2012; 3:87. [PMID: 22586427 PMCID: PMC3347682 DOI: 10.3389/fimmu.2012.00087] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/04/2012] [Indexed: 02/02/2023] Open
Abstract
Most monoclonal antibodies (mAbs) generated from humans infected or vaccinated with the 2009 pandemic H1N1 (pdmH1N1) influenza virus targeted the hemagglutinin (HA) stem. These anti-HA stem mAbs mostly used IGHV1-69 and bound readily to epitopes on the conventional seasonal influenza and pdmH1N1 vaccines. The anti-HA stem mAbs neutralized pdmH1N1, seasonal influenza H1N1 and avian H5N1 influenza viruses by inhibiting HA-mediated fusion of membranes and protected against and treated heterologous lethal infections in mice with H5N1 influenza virus. This demonstrated that therapeutic mAbs could be generated a few months after the new virus emerged. Human immunization with the pdmH1N1 vaccine induced circulating antibodies that when passively transferred, protected mice from lethal, heterologous H5N1 influenza infections. We observed that the dominant heterosubtypic antibody response against the HA stem correlated with the relative absence of memory B cells against the HA head of pdmH1N1, thus enabling the rare heterosubtypic memory B cells induced by seasonal influenza and specific for conserved sites on the HA stem to compete for T-cell help. These results support the notion that broadly protective antibodies against influenza would be induced by successive vaccination with conventional influenza vaccines based on subtypes of HA in viruses not circulating in humans.
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Affiliation(s)
- C A Thomson
- The Biomedical Research Centre, University of British Columbia Vancouver, BC, Canada
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37
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B cell receptor light chain repertoires show signs of selection with differences between groups of healthy individuals and SLE patients. Mol Immunol 2012; 51:273-82. [PMID: 22516082 DOI: 10.1016/j.molimm.2012.03.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 03/01/2012] [Accepted: 03/22/2012] [Indexed: 02/06/2023]
Abstract
We have developed a microarray to study the expression of L-chain V genes (V(L) genes) in healthy and SLE patient peripheral κ- and λ-sorted B cells. In all repertoires tested, one V(L) gene accounts for over 10% of all gene V(L) expression, consistent with positive selection acting on L-chains. While a few V(L) genes were highly expressed in all individuals, most V(L) genes were expressed at different levels. Some V(L) genes (5 out of a total of 78) were not detected. We attribute their absence from the repertoire to negative selection. Positive selection and negative selection were also found in SLE repertoires, but expression of V(L) genes was different; the differences point to less regulation of V(L) gene repertoires in SLE. Our data shows that V(L) gene expression is variable and supports a model where the L-chain repertoire is generated by both positive and negative selection on L-chains.
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Abstract
Antibodies make up the largest, growing segment of protein therapeutics in the pharmaceutical and biotechnology industries. The development or engineering of therapeutic antibodies is based to a large extent on our knowledge of antibody structure and requires sophisticated methods that continue to evolve. In this chapter, after a review of what is known about the structure and functional properties of antibodies, the current, state-of-the-art antibody engineering methods are described. These methods include antibody humanization, antigen-affinity optimization, Fc engineering for modulated effector function and extended half-life, and engineering for improved stability and biophysical properties. X-ray crystallographic structures of antibody fragments and their complexes can play a critical role in guiding and, in some cases, accelerating these processes. These approaches represent guidelines for developing antibody therapeutics with the desired affinity, effector function, and biophysical properties.
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Creation of the large and highly functional synthetic repertoire of human VH and Vκ domain antibodies. Methods Mol Biol 2012; 911:39-63. [PMID: 22886245 DOI: 10.1007/978-1-61779-968-6_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This protocol describes a method for creation of a highly diverse and functional synthetic phage-displayed repertoire of fully human domain antibodies (dAbs). The repertoire is based on two human frameworks (one VH and one Vκ) that express well in bacteria and are frequently used in human antibodies. To achieve this, we first build dAb libraries, containing full synthetic diversity at key positions in the complementarity-determining regions (CDRs). We then use an antigen-independent preselection of this primary dAb repertoire on generic ligands of the VH and the Vκ scaffolds (namely, the bacterial superantigens, protein A and L) to enrich for folded dAbs. Finally, the CDRs of these preselected dAbs are randomly recombined to further expand genetic diversity. The resulting phage repertoire is in excess of 10(10) clones and is largely populated by correctly folded (over 50%) functional dAbs.
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40
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Verma S, Aitken R. Somatic hypermutation leads to diversification of the heavy chain immunoglobulin repertoire in cattle. Vet Immunol Immunopathol 2011; 145:14-22. [PMID: 22070825 DOI: 10.1016/j.vetimm.2011.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 10/02/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
Abstract
The availability of unique variable (VH), diversity (D), and joining (JH) gene segments in the vertebrate germline determines the extent to which a primary immunoglobulin (Ig) repertoire can be generated through combinatorial rearrangement. Although bovine D segments possess unusual properties, the diversity of the primary Ig heavy chain (IgH) repertoire in cattle is restricted by the dominance of a single family of germline VH genes of limited number and diversity. Cattle therefore must employ other diversification strategies in order to generate a functional IgH repertoire, the main candidates being gene conversion and somatic hypermutation. In considering these possibilities, we predicted that if somatic hypermutation was active during B lymphocyte development, the process would introduce nucleotide substitutions to the VDJ exon and also non-coding region lying downstream of the rearranged JH segment. In contrast, our expectation was that gene conversion would show a greater tendency to confine modification to the IgH coding sequence, leaving intron regions substantially unmodified. An analysis of rearranged IgH sequences from cattle of different ages revealed that the diversification of germline sequences could be observed in very young calves and that substitution frequency increased with age. The age-dependent accumulation of mutations was particularly apparent in the second IgH complementarity-determining region (CDR2). Single base substitutions were found to predominate, with purines targeted more frequently than pyrimidines and transitions favoured over transversions. In non-coding regions, mutations were detected at a normalised frequency that was indistinguishable from that observed in CDR2. These data are consistent with a process of IgH diversification driven predominantly by somatic hypermutation.
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Affiliation(s)
- Subhash Verma
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
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41
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Ghiotto F, Marcatili P, Tenca C, Calevo MG, Yan XJ, Albesiano E, Bagnara D, Colombo M, Cutrona G, Chu CC, Morabito F, Bruno S, Ferrarini M, Tramontano A, Fais F, Chiorazzi N. Mutation pattern of paired immunoglobulin heavy and light variable domains in chronic lymphocytic leukemia B cells. Mol Med 2011; 17:1188-95. [PMID: 21785810 DOI: 10.2119/molmed.2011.00104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/13/2011] [Indexed: 12/13/2022] Open
Abstract
B-cell chronic lymphocytic leukemia (CLL) patients display leukemic clones bearing either germline or somatically mutated immunoglobulin heavy variable (IGHV ) genes. Most information on CLL immunoglobulins (Igs), such as the definition of stereotyped B-cell receptors (BCRs), was derived from germline unmutated Igs. In particular, detailed studies on the distribution and nature of mutations in paired heavy- and light-chain domains of CLL clones bearing mutated Igs are lacking. To address the somatic hyper-mutation dynamics of CLL Igs, we analyzed the mutation pattern of paired IGHV-diversity-joining (IGHV-D-J ) and immunoglobulin kappa/lambda variable-joining (IGK/LV-J ) rearrangements of 193 leukemic clones that displayed ≥ 2% mutations in at least one of the two immunoglobulin variable (IGV ) genes (IGHV and/or IGK/LV ). The relationship between the mutation frequency in IGHV and IGK/LV complementarity determining regions (CDRs) and framework regions (FRs) was evaluated by correlation analysis. Replacement (R) mutation frequency within IGK/LV chain CDRs correlated significantly with mutation frequency of paired IGHV CDRs in λ but not κ isotype CLL clones. CDRs of IGKV-J rearrangements displayed a lower percentage of R mutations than IGHVs. The frequency/pattern of mutations in kappa CLL Igs differed also from that in κ-expressing normal B cells described in the literature. Instead, the mutation frequency within the FRs of IGHV and either IGKV or IGLV was correlated. Notably, the amount of diversity introduced by replaced amino acids was comparable between IGHVs and IGKVs. The data indicate a different mutation pattern between κ and λ isotype CLL clones and suggest an antigenic selection that, in κ samples, operates against CDR variation.
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Affiliation(s)
- Fabio Ghiotto
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
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42
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Malia TJ, Obmolova G, Almagro JC, Gilliland GL, Teplyakov A. Crystal structure of human germline antibody 3-23/B3. Mol Immunol 2011; 48:1586-8. [PMID: 21605907 DOI: 10.1016/j.molimm.2011.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 04/22/2011] [Indexed: 10/18/2022]
Abstract
The human antibody repertoire is dominated by a few combinations of germline sequences, with the genes 3-23 for the heavy chain and B3 for the light chain being among the most frequently used. Despite this fact, there was no experimental structure of the antibody composed of 3-23 and B3. The crystal structure of the Fab fragment of the synthetic antibody composed of the 3-23 and B3 germline sequences was determined to provide a template for antibody modeling. The antigen-binding loops were found in the canonical conformations. Comparison to the other structures where either 3-23 or B3 is paired with a different chain reveals a significant deviation in the orientation of the variable domains.
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Affiliation(s)
- Thomas J Malia
- Centocor R&D, Inc., 145 King of Prussia Road, Radnor, PA 19087, USA
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43
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Abstract
Monoclonal antibodies (mAbs) are arguably the most significant class of biologics for use as pharmaceuticals and diagnostics. Many technological concepts exist for the generation and identification of therapeutically relevant mAbs, including the isolation and cloning of immunoglobulin (Ig) encoding genes from single B-lineage cells. This review summarizes various single B cell approaches and describes their use for the discovery of mAbs with potential therapeutic values or in basic research.
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Affiliation(s)
- Thomas Tiller
- Max Planck Institute for Infection Biology, D-10117 Berlin, Germany.
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Integrated mimicry of B cell antibody mutagenesis using yeast homologous recombination. Mol Biotechnol 2011; 47:57-69. [PMID: 20645027 DOI: 10.1007/s12033-010-9312-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Antibody affinity maturation proceeds in vivo via a combination of point mutations, insertions, deletions, and combinatorial shuffling of light chains or portions of the heavy chain, thereby reducing the probability of trapping in local affinity optima in sequence space. In vivo homologous recombination in yeast can be exploited to mimic the broad spectrum of mutational types deployed by B cells, incorporating both receptor revision and receptor editing together with polymerase-directed point mutagenesis. This method was used to effect a 10,000-fold affinity improvement in an anti-peptide single-chain antibody in three rounds of mutagenesis and screening, and a 1,000-fold affinity improvement in an anti-protein single-chain antibody in a single round. When recombinational mutagenesis (CDR or chain shuffling) was directly compared to error-prone PCR, the recombinational approach yielded greater affinity improvement with substantially reduced divergence from germline sequences, demonstrating an advantage of simultaneously testing a broad range of mutational strategies.
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45
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Levin M, Tan LW, Baker L, Wormald PJ, Greiff L, Ohlin M. Diversity of immunoglobulin E-encoding transcripts in sinus mucosa of subjects diagnosed with non-allergic fungal eosinophilic sinusitis. Clin Exp Allergy 2011; 41:811-20. [PMID: 21561493 DOI: 10.1111/j.1365-2222.2011.03724.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The role of allergy in the aetiopathogenesis of chronic rhinosinusitis (CRS) remains controversial. For example, in some cases with sinus fungal infections allergy can be demonstrated by standard tests. In other cases, such signs can be absent despite elevated levels of IgE-positive cells in sinus tissue and the presence of IgE and eosinophils in the sinus mucous. OBJECTIVE To define the nature of molecular diversity in antibodies of the IgE isotype at the site of local inflammation in subjects diagnosed with non-allergic fungal eosinophilic sinusitis (NAFES). METHODS The local occurrence and sequence characteristics of IgE-encoding transcripts in NAFES patients were investigated and compared with sequences found in subjects diagnosed with CRS featuring systemic allergy. These sequences have also been compared with other reported IgE-encoding transcriptomes. Results IGHV genes derived from major subgroups 1, 3, 4 and 5 and a diverse set of IGHD and IGHJ genes were shown to create the IgE repertoire in patients diagnosed with NAFES and CRS. The average lengths of the third hypervariable loop in these populations were 15.8 and 14.6 residues. The sequences showed evidence of extensive somatic hypermutation (mutation frequency: NAFES, 6.4 ± 3.2%; CRS, 7.0 ± 4.4%) with substitutions targeted to complementarity-determining regions. These sequence collections thus show extensive similarities to those found in other polyclonal Ig repertoires including those encoding IgE. CONCLUSION AND CLINICAL RELEVANCE We conclude that sinus IgE-encoding transcripts in subjects diagnosed with NAFES show evidence of conventional IgE responses and we suggest that allergens with characteristics of classical antigens should be investigated for a role in the local response occurring in NAFES. This investigation illustrates that assessment of local immunity might be an important diagnostic tool in conditions like NAFES with no systemic signs of allergy to identify or rule out an allergic component of the patient's disease.
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Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
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46
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Thomson CA, Little KQ, Reason DC, Schrader JW. Somatic diversity in CDR3 loops allows single V-genes to encode innate immunological memories for multiple pathogens. THE JOURNAL OF IMMUNOLOGY 2011; 186:2291-8. [PMID: 21228346 DOI: 10.4049/jimmunol.0904092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The human Ab response to many common pathogens is oligoclonal, with restricted usage of Ig V-genes. Intriguingly, the IGVK3-11 and IGVH3-30 V-genes are repeatedly paired in protective Abs against the 23F polysaccharide of Streptococcus pneumoniae, as well as against the gB envelope protein of human CMV, where germline-encoded amino acids make key contacts with the gB protein. We constructed IgGs encoded by the germline IGVK3-11 and IGVH3-30 V-genes together with DNA encoding the respective CDR3 regions of the L chain and H chain found in a hypermutated anti-23F Ab. These IgGs encoded by germline V-genes bound specifically to 23F pneumococcal capsular polysaccharides with no reactivity to other serotypes of pneumococcal capsular polysaccharides or arrayed glycans and recognized L-rhamnose, a component of the 23F repeating subunit. IgGs encoded by this pair of germline V-genes mediated complement-dependent phagocytosis of encapsulated 23F S. pneumoniae by human neutrophils. Mutations in CDRL3 and CDRH3 had significant effects on binding. Thus, IGKV3-11 and IGHV3-30, depending on with which distinct DNA sequences encoding CDR3 they are recombined, can encode binding sites for protective Abs against chemically distinct Ags and thus, may encode innate immunological memory against human CMV and S. pneumoniae.
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Affiliation(s)
- Christy A Thomson
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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47
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Capturing the natural diversity of the human antibody response against vaccinia virus. J Virol 2010; 85:1820-33. [PMID: 21147924 DOI: 10.1128/jvi.02127-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The eradication of smallpox (variola) and the subsequent cessation of routine vaccination have left modern society vulnerable to bioterrorism employing this devastating contagious disease. The existing, licensed vaccines based on live vaccinia virus (VACV) are contraindicated for a substantial number of people, and prophylactic vaccination of large populations is not reasonable when there is little risk of exposure. Consequently, there is an emerging need to develop efficient and safe therapeutics to be used shortly before or after exposure, either alone or in combination with vaccination. We have characterized the human antibody response to smallpox vaccine (VACV Lister) in immunized volunteers and isolated a large number of VACV-specific antibodies that recognize a variety of different VACV antigens. Using this broad antibody panel, we have generated a fully human, recombinant analogue to plasma-derived vaccinia immunoglobulin (VIG), which mirrors the diversity and specificity of the human antibody immune response and offers the advantage of unlimited supply and reproducible specificity and activity. The recombinant VIG was found to display a high specific binding activity toward VACV antigens, potent in vitro VACV neutralizing activity, and a highly protective efficacy against VACV challenge in the mouse tail lesion model when given either prophylactically or therapeutically. Altogether, the results suggest that this compound has the potential to be used as an effective postexposure prophylaxis or treatment of disease caused by orthopoxviruses.
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48
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Kuan CT, Wakiya K, Keir ST, Li J, Herndon JE, Pastan I, Bigner DD. Affinity-matured anti-glycoprotein NMB recombinant immunotoxins targeting malignant gliomas and melanomas. Int J Cancer 2010; 129:111-21. [PMID: 20824708 DOI: 10.1002/ijc.25645] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 08/18/2010] [Indexed: 11/08/2022]
Abstract
Glycoprotein NMB (GPNMB), a transmembrane glycoprotein highly expressed in high-grade gliomas (HGGs), is an attractive target in cancer immunotherapy. We isolated a GPNMB-specific scFv clone, G49, from a human synthetic phage-display library. To obtain mutant single-chain variable-fragment antibodies (scFvs) with improved affinity and immunotoxins with increased activity, we subjected G49 to in vitro affinity maturation by a complementarity-determining-region (CDR) random-mutagenesis technique. Using light-chain CDR3 mutagenesis, cell-based panning by phage display, subsequent heavy-chain CDR1 mutagenesis, and flow-cytometric selection by yeast-surface display, we generated the mutant scFv clone 902V, with an overall 11-fold increase in affinity for GPNMB. Clone 902V was further randomized throughout the whole scFv by error-prone PCR, and one mutant, F6V, was selected by yeast-surface display. F6V scFv, differing from 902V by one amino-acid change in the light-chain CDR2, exhibited an affinity for GPNMB of 0.30 nM. The F6V mutant scFv clone was fused with a truncated form of Pseudomonas exotoxin A to form the immunotoxin F6V-PE38. F6V-PE38 demonstrated significant protein-synthesis-inhibition activity on GPNMB-expressing glioma and malignant melanoma cells (IC(50) = 0.5 ng/ml [8 pM]), a 60-fold improvement over G49 activity, but no cytotoxicity on GPNMB-negative cells. Furthermore, F6V-PE38 exhibited significant antitumor activity against subcutaneous malignant glioma xenografts in two nude-mouse models and a melanoma neoplastic meningitis model in athymic rats. These GPNMB-specific scFv antibodies and immunotoxins hold promise as reagents in targeted therapy for HGGs and other GPNMB-expressing malignancies.
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Affiliation(s)
- Chien-Tsun Kuan
- Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, NC 27710, USA.
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49
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Luo J, Obmolova G, Huang A, Strake B, Teplyakov A, Malia T, Muzammil S, Zhao Y, Gilliland GL, Feng Y. Coevolution of antibody stability and Vκ CDR-L3 canonical structure. J Mol Biol 2010; 402:708-19. [PMID: 20727359 DOI: 10.1016/j.jmb.2010.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/29/2010] [Accepted: 08/05/2010] [Indexed: 12/16/2022]
Abstract
Antibodies recognize antigens through six hypervariable loops, five of which have a limited set of conformations known as canonical structures. For κ light chains, the majority of CDR-L3 [the third hypervariable loop of the light chain variable domain (V(L))] adopts the type 1 canonical structure (CS1), with a cis-proline at position 95. Here, we present the design and structural studies of the monoclonal antibody mAb15 and related mutants that contained a series of progressively germline mutations only in the heavy chain variable domain (V(H)) that ultimately led to an increase of more than 11°C in the melting temperature (T(m)) of the antigen-binding fragment (Fab). The all-trans CDR-L3 structure in the wild type is significantly different from any known CDR-L3 canonical structures. In the thermally stable mutants, the L94(L)-S95(L) peptide bond adopts an energetically unfavorable non-X-proline cis conformation, but the overall CDR-L3 loop converted to CS1. The stabilized V(H) appears to function as a specific molecular chaperone that facilitated the trans-cis isomerization of S95(L). Thus, it is plausible that proline is the evolutionary choice to maintain overall structure and stability for V(L). These results provide new insights into the evolution of CS1 and suggest a potential molecular switch mechanism at position 95 that links CDR-L3 structural diversity and antibody stability and will have implications for antibody engineering.
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Affiliation(s)
- Jinquan Luo
- Centocor Research and Development, Inc., Radnor, PA 19087, USA.
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50
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Zhou T, Georgiev I, Wu X, Yang ZY, Dai K, Finzi A, Kwon YD, Scheid J, Shi W, Xu L, Yang Y, Zhu J, Nussenzweig MC, Sodroski J, Shapiro L, Nabel GJ, Mascola JR, Kwong PD. Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science 2010; 329:811-7. [PMID: 20616231 PMCID: PMC2981354 DOI: 10.1126/science.1192819] [Citation(s) in RCA: 938] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
During HIV-1 infection, antibodies are generated against the region of the viral gp120 envelope glycoprotein that binds CD4, the primary receptor for HIV-1. Among these antibodies, VRC01 achieves broad neutralization of diverse viral strains. We determined the crystal structure of VRC01 in complex with a human immunodeficiency virus HIV-1 gp120 core. VRC01 partially mimics CD4 interaction with gp120. A shift from the CD4-defined orientation, however, focuses VRC01 onto the vulnerable site of initial CD4 attachment, allowing it to overcome the glycan and conformational masking that diminishes the neutralization potency of most CD4-binding-site antibodies. To achieve this recognition, VRC01 contacts gp120 mainly through immunoglobulin V-gene regions substantially altered from their genomic precursors. Partial receptor mimicry and extensive affinity maturation thus facilitate neutralization of HIV-1 by natural human antibodies.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivelin Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhi-Yong Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kaifan Dai
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrés Finzi
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, MA 02115, USA
| | - Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Johannes Scheid
- Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065 USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ling Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiang Zhu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065 USA
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Gary J. Nabel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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