1
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Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science 2023; 379:eabj7412. [PMID: 36656933 PMCID: PMC10515739 DOI: 10.1126/science.abj7412] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/12/2022] [Indexed: 01/21/2023]
Abstract
Multicellular life requires altruistic cooperation between cells. The adaptive immune system is a notable exception, wherein germinal center B cells compete vigorously for limiting positive selection signals. Studying primary human lymphomas and developing new mouse models, we found that mutations affecting BTG1 disrupt a critical immune gatekeeper mechanism that strictly limits B cell fitness during antibody affinity maturation. This mechanism converted germinal center B cells into supercompetitors that rapidly outstrip their normal counterparts. This effect was conferred by a small shift in MYC protein induction kinetics but resulted in aggressive invasive lymphomas, which in humans are linked to dire clinical outcomes. Our findings reveal a delicate evolutionary trade-off between natural selection of B cells to provide immunity and potentially dangerous features that recall the more competitive nature of unicellular organisms.
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Affiliation(s)
- Coraline Mlynarczyk
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Matt Teater
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Juhee Pae
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Christopher R. Chin
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biomedicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ling Wang
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Theinmozhi Arulraj
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Darko Barisic
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Antonin Papin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Ekaterina Kots
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonatan Ersching
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Arnab Bandyopadhyay
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ersilia Barin
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hui Xian Poh
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Chiara M. Evans
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Hao Shen
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hannah M. Isles
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Benedikt Pelzer
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ioanna Tsialta
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S. Doane
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Muhammad Hassan Rehman
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Medicine–Qatar, Doha, Qatar
| | - Jonah Melnick
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Wyatt Morgan
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Diu T. T. Nguyen
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samie R. Jaffrey
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - George Khelashvili
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gabriel D. Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Ari Melnick
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
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2
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Ascher DB, Kaminskas LM, Myung Y, Pires DEV. Using Graph-Based Signatures to Guide Rational Antibody Engineering. Methods Mol Biol 2023; 2552:375-397. [PMID: 36346604 DOI: 10.1007/978-1-0716-2609-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antibodies are essential experimental and diagnostic tools and as biotherapeutics have significantly advanced our ability to treat a range of diseases. With recent innovations in computational tools to guide protein engineering, we can now rationally design better antibodies with improved efficacy, stability, and pharmacokinetics. Here, we describe the use of the mCSM web-based in silico suite, which uses graph-based signatures to rapidly identify the structural and functional consequences of mutations, to guide rational antibody engineering to improve stability, affinity, and specificity.
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Affiliation(s)
- David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry, Cambridge University, Cambridge, UK
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Lisa M Kaminskas
- School of Biological Sciences, University of Queensland, St Lucia, QLD, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC, Australia.
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3
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Lee JH, Sutton HJ, Cottrell CA, Phung I, Ozorowski G, Sewall LM, Nedellec R, Nakao C, Silva M, Richey ST, Torres JL, Lee WH, Georgeson E, Kubitz M, Hodges S, Mullen TM, Adachi Y, Cirelli KM, Kaur A, Allers C, Fahlberg M, Grasperge BF, Dufour JP, Schiro F, Aye PP, Kalyuzhniy O, Liguori A, Carnathan DG, Silvestri G, Shen X, Montefiori DC, Veazey RS, Ward AB, Hangartner L, Burton DR, Irvine DJ, Schief WR, Crotty S. Long-primed germinal centres with enduring affinity maturation and clonal migration. Nature 2022; 609:998-1004. [PMID: 36131022 PMCID: PMC9491273 DOI: 10.1038/s41586-022-05216-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/09/2022] [Indexed: 02/06/2023]
Abstract
Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B (BGC) cells that last for at least 6 months. A 186-fold increase in BGC cells was present by week 10 compared with conventional immunization. Single-cell transcriptional profiling showed that both light- and dark-zone germinal centre states were sustained. Antibody somatic hypermutation of BGC cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding BGC cells were still 49-fold above baseline at 29 weeks, which suggests that they could remain active for even longer periods of time. High titres of HIV-neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing considerable immunodominance challenges for B cells1,2. Memory B cells generated under these long priming conditions had higher levels of antibody somatic hypermutation, and both memory B cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning more than the 6-month germinal centre period were identified, demonstrating continuous germinal centre activity and selection for at least 191 days with no further antigen exposure. A long-prime, slow-delivery (12 days) immunization approach holds promise for difficult vaccine targets and suggests that patience can have great value for tuning of germinal centres to maximize antibody responses.
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Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry J Sutton
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ivy Phung
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catherine Nakao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Murillo Silva
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sam Hodges
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tina-Marie Mullen
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kimberly M Cirelli
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Carolina Allers
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Marissa Fahlberg
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Brooke F Grasperge
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Jason P Dufour
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Faith Schiro
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Pyone P Aye
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Oleksandr Kalyuzhniy
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alessia Liguori
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Diane G Carnathan
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Guido Silvestri
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Xiaoying Shen
- Department of Surgery, Laboratory for AIDS Vaccine Research & Development, Duke University Medical Center, Duke University, Durham, NC, USA
| | - David C Montefiori
- Department of Surgery, Laboratory for AIDS Vaccine Research & Development, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Andrew B Ward
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lars Hangartner
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Darrell J Irvine
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA.
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Valenzuela Nieto G, Jara R, Watterson D, Modhiran N, Amarilla AA, Himelreichs J, Khromykh AA, Salinas-Rebolledo C, Pinto T, Cheuquemilla Y, Margolles Y, López González Del Rey N, Miranda-Chacon Z, Cuevas A, Berking A, Deride C, González-Moraga S, Mancilla H, Maturana D, Langer A, Toledo JP, Müller A, Uberti B, Krall P, Ehrenfeld P, Blesa J, Chana-Cuevas P, Rehren G, Schwefel D, Fernandez LÁ, Rojas-Fernandez A. Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. Sci Rep 2021; 11:3318. [PMID: 33558635 PMCID: PMC7870875 DOI: 10.1038/s41598-021-82833-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Despite unprecedented global efforts to rapidly develop SARS-CoV-2 treatments, in order to reduce the burden placed on health systems, the situation remains critical. Effective diagnosis, treatment, and prophylactic measures are urgently required to meet global demand: recombinant antibodies fulfill these requirements and have marked clinical potential. Here, we describe the fast-tracked development of an alpaca Nanobody specific for the receptor-binding-domain (RBD) of the SARS-CoV-2 Spike protein with potential therapeutic applicability. We present a rapid method for nanobody isolation that includes an optimized immunization regimen coupled with VHH library E. coli surface display, which allows single-step selection of Nanobodies using a simple density gradient centrifugation of the bacterial library. The selected single and monomeric Nanobody, W25, binds to the SARS-CoV-2 S RBD with sub-nanomolar affinity and efficiently competes with ACE-2 receptor binding. Furthermore, W25 potently neutralizes SARS-CoV-2 wild type and the D614G variant with IC50 values in the nanomolar range, demonstrating its potential as antiviral agent.
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Affiliation(s)
| | - Ronald Jara
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel Watterson
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Johanna Himelreichs
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Alexander A Khromykh
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | | | - Teresa Pinto
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Yorka Cheuquemilla
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Berking Biotechnology, Valdivia, Chile
| | - Yago Margolles
- Department of Microbial Biotechnology, National Biotechnology Center, Superior Council of Scientific Research, Madrid, Spain
| | | | - Zaray Miranda-Chacon
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Alexei Cuevas
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | | | - Camila Deride
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Institute of Veterinary Clinical Sciences, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile
| | | | - Héctor Mancilla
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel Maturana
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Munich, Germany
| | - Andreas Langer
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Munich, Germany
| | - Juan Pablo Toledo
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Ananda Müller
- Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
- Institute of Veterinary Clinical Sciences, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Benjamín Uberti
- Institute of Veterinary Clinical Sciences, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Paola Krall
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Department of Pediatrics and Children's Surgery Oriente, Universidad de Chile, Valdivia, Chile
| | - Pamela Ehrenfeld
- Institute of Anatomy, Histology, and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
- Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile
| | - Javier Blesa
- HM CINAC, Hospital Universitario HM Puerta del Sur, Mostoles, 28938, Madrid, Spain
| | - Pedro Chana-Cuevas
- CETRAM & Faculty of Medical Science, Universidad de Santiago de Chile, Santiago, Chile
| | - German Rehren
- Technology Transfer and Licensing Office, Universidad Austral de Chile, Valdivia, Chile
| | - David Schwefel
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Luis Ángel Fernandez
- Department of Microbial Biotechnology, National Biotechnology Center, Superior Council of Scientific Research, Madrid, Spain
| | - Alejandro Rojas-Fernandez
- Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.
- Berking Biotechnology, Valdivia, Chile.
- Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile, Valdivia, Chile.
- Institute of Philosophy and Complexity Sciences, Santiago, Chile.
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5
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Myung Y, Pires DEV, Ascher DB. mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Res 2020; 48:W125-W131. [PMID: 32432715 PMCID: PMC7319589 DOI: 10.1093/nar/gkaa389] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/18/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022] Open
Abstract
While antibodies are becoming an increasingly important therapeutic class, especially in personalized medicine, their development and optimization has been largely through experimental exploration. While there have been many efforts to develop computational tools to guide rational antibody engineering, most approaches are of limited accuracy when applied to antibody design, and have largely been limited to analysing a single point mutation at a time. To overcome this gap, we have curated a dataset of 242 experimentally determined changes in binding affinity upon multiple point mutations in antibody-target complexes (89 increasing and 153 decreasing binding affinity). Here, we have shown that by using our graph-based signatures and atomic interaction information, we can accurately analyse the consequence of multi-point mutations on antigen binding affinity. Our approach outperformed other available tools across cross-validation and two independent blind tests, achieving Pearson's correlations of up to 0.95. We have implemented our new approach, mmCSM-AB, as a web-server that can help guide the process of affinity maturation in antibody design. mmCSM-AB is freely available at http://biosig.unimelb.edu.au/mmcsm_ab/.
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Affiliation(s)
- Yoochan Myung
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, VIC 3004, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, VIC 3004, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC 3052, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, VIC 3004, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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6
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Chen H, Zhang Y, Ye AY, Du Z, Xu M, Lee CS, Hwang JK, Kyritsis N, Ba Z, Neuberg D, Littman DR, Alt FW. BCR selection and affinity maturation in Peyer's patch germinal centres. Nature 2020; 582:421-425. [PMID: 32499646 PMCID: PMC7478071 DOI: 10.1038/s41586-020-2262-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 02/28/2020] [Indexed: 12/23/2022]
Abstract
The antigen-binding variable regions of the B cell receptor (BCR) and of antibodies are encoded by exons that are assembled in developing B cells by V(D)J recombination1. The BCR repertoires of primary B cells are vast owing to mechanisms that create diversity at the junctions of V(D)J gene segments that contribute to complementarity-determining region 3 (CDR3), the region that binds antigen1. Primary B cells undergo antigen-driven BCR affinity maturation through somatic hypermutation and cellular selection in germinal centres (GCs)2,3. Although most GCs are transient3, those in intestinal Peyer's patches (PPs)-which depend on the gut microbiota-are chronic4, and little is known about their BCR repertoires or patterns of somatic hypermutation. Here, using a high-throughput assay that analyses both V(D)J segment usage and somatic hypermutation profiles, we elucidate physiological BCR repertoires in mouse PP GCs. PP GCs from different mice expand public BCR clonotypes (clonotypes that are shared between many mice) that often have canonical CDR3s in the immunoglobulin heavy chain that, owing to junctional biases during V(D)J recombination, appear much more frequently than predicted in naive B cell repertoires. Some public clonotypes are dependent on the gut microbiota and encode antibodies that are reactive to bacterial glycans, whereas others are independent of gut bacteria. Transfer of faeces from specific-pathogen-free mice to germ-free mice restored germ-dependent clonotypes, directly implicating BCR selection. We identified somatic hypermutations that were recurrently selected in such public clonotypes, indicating that affinity maturation occurs in mouse PP GCs under homeostatic conditions. Thus, persistent gut antigens select recurrent BCR clonotypes to seed chronic PP GC responses.
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Affiliation(s)
- Huan Chen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Yuxiang Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Adam Yongxin Ye
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Zhou Du
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Mo Xu
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
- The Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Cheng-Sheng Lee
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Joyce K Hwang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Nia Kyritsis
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Zhaoqing Ba
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Donna Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dan R Littman
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
- The Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- The Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
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7
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Oyama H, Kiguchi Y, Morita I, Yamamoto C, Higashi Y, Taguchi M, Tagawa T, Enami Y, Takamine Y, Hasegawa H, Takeuchi A, Kobayashi N. Seeking high-priority mutations enabling successful antibody-breeding: systematic analysis of a mutant that gained over 100-fold enhanced affinity. Sci Rep 2020; 10:4807. [PMID: 32179767 PMCID: PMC7075871 DOI: 10.1038/s41598-020-61529-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/27/2020] [Indexed: 01/05/2023] Open
Abstract
"Antibody-breeding" has provided therapeutic/diagnostic antibody mutants with greater performance than native antibodies. Typically, random point mutations are introduced into the VH and VL domains of parent antibodies to generate diverse libraries of single-chain Fv fragments (scFvs), from which evolved mutants are selected. We produced an scFv against estradiol-17β with 11 amino acid substitutions and a >100-fold improved affinity constant (Ka = 1.19 × 1010 M-1) over the parent scFv, enabling immunoassays with >30-fold higher sensitivity. We systematically analyzed contributions of these substitutions to the affinity enhancement. Comparing various partial scFv revertants based on their Kas indicated that a revertant with four substitutions (VH-L100gQ, VL-I29V, -L36M, -S77G) exhibited somewhat higher affinity (Ka = 1.46 × 1010 M-1). Finally, the VH-L100gQ substitution, occurring in VH complementarity-determining region (CDR) 3, was found to be the highest-priority for improving the affinity, and VL-I29V and/or VL-L36M cooperated significantly. These findings encouraged us to reconsider the potential of VH-CDR3-targeting mutagenesis, which has been frequently attempted. The substitution(s) wherein might enable a "high rate of return" in terms of selecting mutants with dramatically enhanced affinities. The "high risk" of generating a tremendous excess of "junk mutants" can be overcome with the efficient selection systems that we developed.
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Affiliation(s)
- Hiroyuki Oyama
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yuki Kiguchi
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Izumi Morita
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Chika Yamamoto
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yuka Higashi
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Miku Taguchi
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Tatsuya Tagawa
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yuri Enami
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yuriko Takamine
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Hanako Hasegawa
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Atsuko Takeuchi
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Norihiro Kobayashi
- Kobe Pharmaceutical University, 4-19-1, Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan.
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8
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Saunders KO, Wiehe K, Tian M, Acharya P, Bradley T, Alam SM, Go EP, Scearce R, Sutherland L, Henderson R, Hsu AL, Borgnia MJ, Chen H, Lu X, Wu NR, Watts B, Jiang C, Easterhoff D, Cheng HL, McGovern K, Waddicor P, Chapdelaine-Williams A, Eaton A, Zhang J, Rountree W, Verkoczy L, Tomai M, Lewis MG, Desaire HR, Edwards RJ, Cain DW, Bonsignori M, Montefiori D, Alt FW, Haynes BF. Targeted selection of HIV-specific antibody mutations by engineering B cell maturation. Science 2019; 366:eaay7199. [PMID: 31806786 PMCID: PMC7168753 DOI: 10.1126/science.aay7199] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/05/2019] [Indexed: 12/16/2022]
Abstract
INTRODUCTION A major goal of HIV-1 vaccine development is the design of immunogens that induce broadly neutralizing antibodies (bnAbs). However, vaccination of humans has not resulted in the induction of affinity-matured and potent HIV-1 bnAbs. To devise effective vaccine strategies, we previously determined the maturation pathway of select HIV-1 bnAbs from acute infection through neutralizing antibody development. During their evolution, bnAbs acquire an abundance of improbable amino acid substitutions as a result of nucleotide mutations at variable region sequences rarely targeted by activation-induced cytidine deaminase, the enzyme responsible for antibody mutation. A subset of improbable mutations is essential for broad neutralization activity, and their acquisition represents a key roadblock to bnAb development. RATIONALE Current bnAb lineage-based vaccine strategies can initiate bnAb lineage development in animal models but have not specifically elicited the improbable mutations required for neutralization breadth. Induction of bnAbs requires vaccine strategies that specifically engage bnAb precursors and subsequently select for improbable mutations required for broadly neutralizing activity. We hypothesized that vaccination with immunogens that bind with moderate to high affinity to bnAb B cell precursors, and with higher affinity to precursors that have acquired improbable mutations, could initiate bnAb B cell lineages and select for key improbable mutations required for bnAb development. RESULTS We elicited serum neutralizing HIV-1 antibodies in human bnAb precursor knock-in mice and wild-type macaques vaccinated with immunogens designed to select for improbable mutations. We designed two HIV-1 envelope immunogens that bound precursor B cells of either a CD4 binding site or V3-glycan bnAb lineage. In vitro, these immunogens bound more strongly to bnAb precursors once the precursor acquired the desired improbable mutations. Vaccination of macaques with the CD4 binding site–targeting immunogen induced CD4 binding site serum neutralizing antibodies. Antibody sequences elicited in human bnAb precursor knock-in mice encoded functional improbable mutations critical for bnAb development. In bnAb precursor knock-in mice, we isolated a vaccine-elicited monoclonal antibody bearing functional improbable mutations that was capable of neutralizing multiple HIV-1 global isolates. Structures of a bnAb precursor, a bnAb, and the vaccine-elicited antibody revealed the precise roles that acquired improbable mutations played in recognizing the HIV-1 envelope. Thus, our immunogens elicited antibody responses in macaques and knock-in mice that exhibited the mutational patterns, structural characteristics, or neutralization profiles of nascent broadly neutralizing antibodies. CONCLUSION Our study represents a proof of concept for targeted selection of improbable mutations to guide antibody affinity maturation. Moreover, this study demonstrates a rational strategy for sequential immunogen design to circumvent the difficult roadblocks in HIV-1 bnAb induction by vaccination. We show that immunogens should exhibit differences in affinity across antibody maturation stages where improbable mutations are necessary for the desired antibody function. This strategy of selection of specific antibody nucleotides by immunogen design can be applied to B cell lineages targeting other pathogens where guided affinity maturation is needed for a protective antibody response.
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Affiliation(s)
- Kevin O Saunders
- Human Vaccine Institute and Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Priyamvada Acharya
- Human Vaccine Institute and Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Todd Bradley
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - S Munir Alam
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, KS 66049, USA
| | - Richard Scearce
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura Sutherland
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rory Henderson
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Haiyan Chen
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nelson R Wu
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Brian Watts
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chuancang Jiang
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David Easterhoff
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hwei-Ling Cheng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kelly McGovern
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peyton Waddicor
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aimee Chapdelaine-Williams
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Eaton
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinsong Zhang
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wes Rountree
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laurent Verkoczy
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark Tomai
- Corporate Research Materials Lab, 3M Company, St. Paul, MN 55144, USA
| | | | - Heather R Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66049, USA
| | - Robert J Edwards
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Derek W Cain
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David Montefiori
- Human Vaccine Institute and Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Barton F Haynes
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
- Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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9
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Warszawski S, Borenstein Katz A, Lipsh R, Khmelnitsky L, Ben Nissan G, Javitt G, Dym O, Unger T, Knop O, Albeck S, Diskin R, Fass D, Sharon M, Fleishman SJ. Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. PLoS Comput Biol 2019; 15:e1007207. [PMID: 31442220 PMCID: PMC6728052 DOI: 10.1371/journal.pcbi.1007207] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 09/05/2019] [Accepted: 06/21/2019] [Indexed: 11/18/2022] Open
Abstract
Antibodies developed for research and clinical applications may exhibit suboptimal stability, expressibility, or affinity. Existing optimization strategies focus on surface mutations, whereas natural affinity maturation also introduces mutations in the antibody core, simultaneously improving stability and affinity. To systematically map the mutational tolerance of an antibody variable fragment (Fv), we performed yeast display and applied deep mutational scanning to an anti-lysozyme antibody and found that many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface, within the antibody core. Rosetta design combined enhancing mutations, yielding a variant with tenfold higher affinity and substantially improved stability. To make this approach broadly accessible, we developed AbLIFT, an automated web server that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains (http://AbLIFT.weizmann.ac.il). We applied AbLIFT to two unrelated antibodies targeting the human antigens VEGF and QSOX1. Strikingly, the designs improved stability, affinity, and expression yields. The results provide proof-of-principle for bypassing laborious cycles of antibody engineering through automated computational affinity and stability design. Antibodies are highly important in research, biotechnology, and medical applications. Despite their great utility, however, many antibodies exhibit suboptimal stability and affinity, raising production costs and limiting their practical usefulness. To tackle this general limitation, we used deep mutational scanning to characterize the effects of mutations in an antibody variable fragment on its antigen-binding affinity. Surprisingly, many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface. We, therefore, developed an automated method, called AbLIFT (http://AbLIFT.weizmann.ac.il) to optimize this interface through design. Two unrelated antibodies were tested and showed improvements in expression levels, stability, and antigen-binding affinity. Since AbLIFT requires testing of only a few dozen specific designs, it may dramatically accelerate the development of promising antibodies into useful research and clinical tools.
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Affiliation(s)
- Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rosalie Lipsh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gabriel Javitt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Orli Knop
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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10
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Hussain K, Hargreaves CE, Rowley TF, Sopp JM, Latham KV, Bhatta P, Sherington J, Cutler RM, Humphreys DP, Glennie MJ, Strefford JC, Cragg MS. Impact of Human FcγR Gene Polymorphisms on IgG-Triggered Cytokine Release: Critical Importance of Cell Assay Format. Front Immunol 2019; 10:390. [PMID: 30899264 PMCID: PMC6417454 DOI: 10.3389/fimmu.2019.00390] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/14/2019] [Indexed: 12/17/2022] Open
Abstract
Monoclonal antibody (mAb) immunotherapy has transformed the treatment of allergy, autoimmunity, and cancer. The interaction of mAb with Fc gamma receptors (FcγR) is often critical for efficacy. The genes encoding the low-affinity FcγR have single nucleotide polymorphisms (SNPs) and copy number variation that can impact IgG Fc:FcγR interactions. Leukocyte-based in vitro assays remain one of the industry standards for determining mAb efficacy and predicting adverse responses in patients. Here we addressed the impact of FcγR genetics on immune cell responses in these assays and investigated the importance of assay format. FcγR genotyping of 271 healthy donors was performed using a Multiplex Ligation-Dependent Probe Amplification assay. Freeze-thawed/pre-cultured peripheral blood mononuclear cells (PBMCs) and whole blood samples from donors were stimulated with reagents spanning different mAb functional classes to evaluate the association of FcγR genotypes with T-cell proliferation and cytokine release. Using freeze-thawed/pre-cultured PBMCs, agonistic T-cell-targeting mAb induced T-cell proliferation and the highest levels of cytokine release, with lower but measurable responses from mAb which directly require FcγR-mediated cellular effects for function. Effects were consistent for individual donors over time, however, no significant associations with FcγR genotypes were observed using this assay format. In contrast, significantly elevated IFN-γ release was associated with the FCGR2A-131H/H genotype compared to FCGR2A-131R/R in whole blood stimulated with Campath (p ≤ 0.01) and IgG1 Fc hexamer (p ≤ 0.05). Donors homozygous for both the high affinity FCGR2A-131H and FCGR3A-158V alleles mounted stronger IFN-γ responses to Campath (p ≤ 0.05) and IgG1 Fc Hexamer (p ≤ 0.05) compared to donors homozygous for the low affinity alleles. Analysis revealed significant reductions in the proportion of CD14hi monocytes, CD56dim NK cells (p ≤ 0.05) and FcγRIIIa expression (p ≤ 0.05), in donor-matched freeze-thawed PBMC compared to whole blood samples, likely explaining the difference in association between FcγR genotype and mAb-mediated cytokine release in the different assay formats. These findings highlight the significant impact of FCGR2A and FCGR3A SNPs on mAb function and the importance of using fresh whole blood assays when evaluating their association with mAb-mediated cytokine release in vitro. This knowledge can better inform on the utility of in vitro assays for the prediction of mAb therapy outcome in patients.
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Affiliation(s)
- Khiyam Hussain
- Antibody and Vaccine Group, Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Chantal E. Hargreaves
- Antibody and Vaccine Group, Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Cancer Genomics Group, Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Joshua M. Sopp
- Antibody and Vaccine Group, Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kate V. Latham
- Cancer Genomics Group, Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | | | | | | | - Martin J. Glennie
- Antibody and Vaccine Group, Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan C. Strefford
- Cancer Genomics Group, Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Mark S. Cragg
- Antibody and Vaccine Group, Centre for Cancer Immunology, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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11
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Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Nucleic Acids Res 2018; 46:7436-7449. [PMID: 29931269 PMCID: PMC6101513 DOI: 10.1093/nar/gky550] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.
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Affiliation(s)
- Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich 8057, Switzerland
| | - Simon M Meng
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - William J Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
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12
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Burnett DL, Langley DB, Schofield P, Hermes JR, Chan TD, Jackson J, Bourne K, Reed JH, Patterson K, Porebski BT, Brink R, Christ D, Goodnow CC. Germinal center antibody mutation trajectories are determined by rapid self/foreign discrimination. Science 2018; 360:223-226. [PMID: 29650674 PMCID: PMC5922412 DOI: 10.1126/science.aao3859] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/02/2017] [Accepted: 02/20/2018] [Indexed: 01/01/2023]
Abstract
Antibodies have the specificity to differentiate foreign antigens that mimic self antigens, but it remains unclear how such specificity is acquired. In a mouse model, we generated B cells displaying an antibody that cross-reacts with two related protein antigens expressed on self versus foreign cells. B cell anergy was imposed by self antigen but reversed upon challenge with high-density foreign antigen, leading to germinal center recruitment and antibody gene hypermutation. Single-cell analysis detected rapid selection for mutations that decrease self affinity and slower selection for epistatic mutations that specifically increase foreign affinity. Crystal structures revealed that these mutations exploited subtle topological differences to achieve 5000-fold preferential binding to foreign over self epitopes. Resolution of antigenic mimicry drove the optimal affinity maturation trajectory, highlighting the value of retaining self-reactive clones as substrates for protective antibody responses.
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Affiliation(s)
- Deborah L Burnett
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
- St. Vincent's Clinical School, University of New South Wales Sydney, Sydney, Australia
| | - David B Langley
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
- St. Vincent's Clinical School, University of New South Wales Sydney, Sydney, Australia
| | - Jana R Hermes
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
| | - Tyani D Chan
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
- St. Vincent's Clinical School, University of New South Wales Sydney, Sydney, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
| | - Katherine Bourne
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
| | - Joanne H Reed
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
| | - Kate Patterson
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
| | - Benjamin T Porebski
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 OQH, UK
| | - Robert Brink
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia
- St. Vincent's Clinical School, University of New South Wales Sydney, Sydney, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia.
- St. Vincent's Clinical School, University of New South Wales Sydney, Sydney, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia.
- St. Vincent's Clinical School, University of New South Wales Sydney, Sydney, Australia
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13
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Abstract
Antibodies are the fastest growing class of pharmaceutical proteins and essential tools for research and diagnostics. Often antibodies do show a desirable specificity profile but lack sufficient affinity for the desired application. Here, we describe a method to increase the affinity of recombinant antibody fragments based on the construction of mutagenized phage display libraries.After the construction of a mutated antibody gene library by error-prone PCR, selection of high-affinity variants is either performed by panning in solution or on immobilized antigen with washing conditions optimized for off-rate-dependent selection. An additional screening protocol to identify antibodies with improved thermal stability is described.
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Affiliation(s)
- Tobias Unkauf
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - André Frenzel
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany.
- YUMAB GmbH, Braunschweig, Germany.
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14
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Abstract
Affinity maturation is a Darwinian process in which B lymphocytes evolve potent antibodies to encountered antigens and generate immune memory. Highly mutable complex pathogens present an immense antigenic diversity that continues to challenge natural immunity and vaccine design. Induction of broadly neutralizing antibodies (bnAbs) against this diversity by vaccination likely requires multiple exposures to distinct but related antigen variants, and yet how affinity maturation advances under such complex stimulation remains poorly understood. To fill the gap, we present an in silico model of affinity maturation to examine two realistic new aspects pertinent to vaccine development: loss in B cell diversity across successive immunization periods against different variants, and the presence of distracting epitopes that entropically disfavor the evolution of bnAbs. We find these new factors, which introduce additional selection pressures and constraints, significantly influence antibody breadth development, in a way that depends crucially on the temporal pattern of immunization (or selection forces). Curiously, a less diverse B cell seed may even favor the expansion and dominance of cross-reactive clones, but only when conflicting selection forces are presented in series rather than in a mixture. Moreover, the level of frustration due to evolutionary conflict dictates the degree of distraction. We further describe how antigenic histories select evolutionary paths of B cell lineages and determine the predominant mode of antibody responses. Sequential immunization with mutationally distant variants is shown to robustly induce bnAbs that focus on conserved elements of the target epitope, by thwarting strain-specific and distracted lineages. An optimal range of antigen dose underlies a fine balance between efficient adaptation and persistent reaction. These findings provide mechanistic guides to aid in design of vaccine strategies against fast mutating pathogens.
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Affiliation(s)
- Shenshen Wang
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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15
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Yang G, Guo H, Liu X, He G, Tian W, Cai K, Wang P, Wang W. [Construction and panning of scFv phage display library against recombinant interleukin 4 receptor]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2016; 32:829-833. [PMID: 27371853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Objective To construct the recombinant human interleukin 4 receptor (rhIL-4R) single-chain Fv (scFv) antibody library by phage display technique to obtain the anti-IL-4R scFv clones selected from the library. Methods Total RNA was extracted from splenocytes of the BALB/c mice immunized with rhIL-4R. Complementary DNA fragments of variable heavy (VH) and variable light (VL) chains of the antibodies were prepared by reverse transcription PCR and assembled into scFv by splice overlap extension PCR (SOE-PCR). Both scFv and the pCANTAB5E vector were respectively double-digested with restriction endonuclease Sfi I and Not I, connected with T4 ligase, and then transformed into the competent cells E.coli TG1; it was cultured in medium to obtain the phage scFv antibody library; after three rounds of enrichment and panning, the specific antigen scFv with high affinity was selected for the sequencing. Results After three rounds of panning, we obtained a diversity of approximately 2×10(8) anti-rhIL-4R scFv antibody library. Sequencing analysis of one positive clone showed that the anti-rhIL-4R scFv was 741 bp and coded 247 amino acids. The analysis of VBASE2 database indicated that VH and VL gene sequences of anti-rhIL-4R protein all had three complementarity determining regions and four backbone areas.Conclusion The anti-rhIL-4R scFv was obtained from the scFv antibody library.
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Affiliation(s)
- Guangyong Yang
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China
| | - Haitao Guo
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China
| | - Ximing Liu
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China
| | - Guangzhi He
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China. *Corresponding author, E-mail: heguangzhi7711@ sina.com
| | - Weiyi Tian
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China
| | - Kun Cai
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China
| | - Ping Wang
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China
| | - Wenjia Wang
- Guiyang College of Traditional Chinese Medicine, Guiyang 550002, China
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16
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Sheng Z, Schramm CA, Connors M, Morris L, Mascola JR, Kwong PD, Shapiro L. Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection. PLoS Comput Biol 2016; 12:e1004940. [PMID: 27191167 PMCID: PMC4871536 DOI: 10.1371/journal.pcbi.1004940] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/24/2016] [Indexed: 01/09/2023] Open
Abstract
Accumulation of somatic mutations in antibody variable regions is critical for antibody affinity maturation, with HIV-1 broadly neutralizing antibodies (bnAbs) generally requiring years to develop. We recently found that the rate at which mutations accumulate decreases over time, but the mechanism governing this slowing is unclear. In this study, we investigated whether natural selection and/or mutability of the antibody variable region contributed significantly to observed decrease in rate. We used longitudinally sampled sequences of immunoglobulin transcripts of single lineages from each of 3 donors, as determined by next generation sequencing. We estimated the evolutionary rates of the complementarity determining regions (CDRs), which are most significant for functional selection, and found they evolved about 1.5- to 2- fold faster than the framework regions. We also analyzed the presence of AID hotspots and coldspots at different points in lineage development and observed an average decrease in mutability of less than 10 percent over time. Altogether, the correlation between Darwinian selection strength and evolutionary rate trended toward significance, especially for CDRs, but cannot fully explain the observed changes in evolutionary rate. The mutability modulated by AID hotspots and coldspots changes correlated only weakly with evolutionary rates. The combined effects of Darwinian selection and mutability contribute substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineages. In an infected individual, the HIV-1 Env gene evolves at a rate of about 0.015 substitutions per site per year. Changes in viral epitopes in turn stimulate the co-evolution of recognizing antibody lineages. We previously showed that young antibody lineages can evolve at a rate ~10-fold faster than observed for HIV-1 and the rate of antibody evolution decreases over time. Here we investigate two factors, Darwinian selection and genetic mutability, which have been shown to influence evolutionary rates in other settings. We quantified both of these factors for three broadly HIV-1-neutralizing antibody lineages, and analyzed the association of these factors with changes in evolutionary rate. We found that Darwinian selection is a major factor in the slowing of evolutionary rate, while genetic mutability modulates antibody evolutionary rate weakly. Moreover, the combined effects of the two factors are unlikely to fully account for the slowing of antibody evolutionary rate.
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Affiliation(s)
- Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Chaim A. Schramm
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Center for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, South Africa
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, New York, United States of America
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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17
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Asti L, Uguzzoni G, Marcatili P, Pagnani A. Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. PLoS Comput Biol 2016; 12:e1004870. [PMID: 27074145 PMCID: PMC4830580 DOI: 10.1371/journal.pcbi.1004870] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 11/18/2022] Open
Abstract
The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high-frequency mutation rate in the genome region that codes for the antibody active site. Eventually, cells that produce antibodies with higher affinity for their cognate antigen are selected and clonally expanded. Here, we propose a new statistical approach based on maximum entropy modeling in which a scoring function related to the binding affinity of antibodies against a specific antigen is inferred from a sample of sequences of the immune repertoire of an individual. We use our inference strategy to infer a statistical model on a data set obtained by sequencing a fairly large portion of the immune repertoire of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10-6), outperforming other sequence- and structure-based models.
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Affiliation(s)
- Lorenzo Asti
- Dipartimento di Scienze di Base e Applicate per l’Ingegneria, Sapienza University of Roma, Roma, Italy
- Human Genetics Foundation, Molecular Biotechnology Center, Torino, Italy
| | - Guido Uguzzoni
- Human Genetics Foundation, Molecular Biotechnology Center, Torino, Italy
- Sorbonne Universités, UPMC, UMR 7238, Computational and Quantitative Biology, 15, rue de l’Ecole de Médecine - BC 1540 - 75006 Paris, France
- Dipartimento di Fisica, Universià di Parma, Parma, Italy
| | - Paolo Marcatili
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Andrea Pagnani
- Human Genetics Foundation, Molecular Biotechnology Center, Torino, Italy
- Department of Applied Science and Technologies (DISAT), Politecnico di Torino, Torino, Italy
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18
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Rodríguez-Cortez VC, Del Pino-Molina L, Rodríguez-Ubreva J, López-Granados E, Ballestar E. Dissecting Epigenetic Dysregulation of Primary Antibody Deficiencies. J Clin Immunol 2016; 36 Suppl 1:48-56. [PMID: 26984849 DOI: 10.1007/s10875-016-0267-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 01/04/2023]
Abstract
Primary antibody deficiencies (PADs), the most prevalent inherited primary immunodeficiencies (PIDs), are associated with a wide range of genetic alterations (both monogenic or polygenic) in B cell-specific genes. However, correlations between the genotype and clinical manifestations are not evident in all cases indicating that genetic interactions, environmental and epigenetic factors may have a role in PAD pathogenesis. The recent identification of key defects in DNA methylation in common variable immunodeficiency as well as the multiple evidences on the role of epigenetic control during B cell differentiation, activation and during antibody formation highlight the importance of investing research efforts in dissecting the participation of epigenetic defects in this group of diseases. This review focuses on the role of epigenetic control in B cell biology which can provide clues for the study of potential novel pathogenic defects involved in PADs.
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Affiliation(s)
- Virginia C Rodríguez-Cortez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lucia Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain.
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19
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Wu YCB, James LK, Vander Heiden JA, Uduman M, Durham SR, Kleinstein SH, Kipling D, Gould HJ. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. J Allergy Clin Immunol 2015; 134:604-12. [PMID: 25171866 PMCID: PMC4151999 DOI: 10.1016/j.jaci.2014.07.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/11/2014] [Accepted: 04/25/2014] [Indexed: 11/18/2022]
Abstract
Background Previous studies of immunoglobulin gene sequences in patients with allergic diseases using low-throughput Sanger sequencing have limited the analytic depth for characterization of IgE repertoires. Objectives We used a high-throughput, next-generation sequencing approach to characterize immunoglobulin heavy-chain gene (IGH) repertoires in patients with seasonal allergic rhinitis (AR) with the aim of better understanding the underlying disease mechanisms. Methods IGH sequences in matched peripheral blood and nasal biopsy specimens from nonallergic healthy control subjects (n = 3) and patients with grass pollen–related AR taken in season (n = 3) or out of season (n = 4) were amplified and pyrosequenced on the 454 GS FLX+ System. Results A total of 97,610 IGH (including 8,135 IgE) sequences were analyzed. Use of immunoglobulin heavy-chain variable region gene families 1 (IGHV1) and 5 (IGHV5) was higher in IgE clonotypic repertoires compared with other antibody classes independent of atopic status. IgE repertoires measured inside the grass pollen season were more diverse and more mutated (particularly in the biopsy specimens) and had more evidence of antigen-driven selection compared with those taken outside of the pollen season or from healthy control subjects. Clonal relatedness was observed for IgE between the blood and nasal biopsy specimens. Furthermore in patients with AR, but not healthy control subjects, we found clonal relatedness between IgE and IgG classes. Conclusion This is the first report that exploits next-generation sequencing to determine local and peripheral blood IGH repertoires in patients with respiratory allergic disease. We demonstrate that natural pollen exposure was associated with changes in IgE repertoires that were suggestive of ongoing germinal center reactions. Furthermore, these changes were more often apparent in nasal biopsy specimens compared with peripheral blood and in patients with AR compared with healthy control subjects.
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Affiliation(s)
- Yu-Chang B Wu
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom; Medical Research Council and Asthma UK Centre, Allergic Mechanisms in Asthma, London, United Kingdom.
| | - Louisa K James
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom; Medical Research Council and Asthma UK Centre, Allergic Mechanisms in Asthma, London, United Kingdom
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Conn
| | - Mohamed Uduman
- Department of Pathology, Yale School of Medicine, New Haven, Conn
| | - Stephen R Durham
- Medical Research Council and Asthma UK Centre, Allergic Mechanisms in Asthma, London, United Kingdom; Allergy and Clinical Immunology, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Conn; Department of Pathology, Yale School of Medicine, New Haven, Conn
| | - David Kipling
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Hannah J Gould
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom; Medical Research Council and Asthma UK Centre, Allergic Mechanisms in Asthma, London, United Kingdom
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20
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Abstract
The Escherichia coli bacteriophage, Qβ (Coliphage Qβ), offers a favorable alternative to M13 for in vitro evolution of displayed peptides and proteins due to high mutagenesis rates in Qβ RNA replication that better simulate the affinity maturation processes of the immune response. We describe a benchtop in vitro evolution system using Qβ display of the VP1 G-H loop peptide of foot-and-mouth disease virus (FMDV). DNA encoding the G-H loop was fused to the A1 minor coat protein of Qβ resulting in a replication-competent hybrid phage that efficiently displayed the FMDV peptide. The surface-localized FMDV VP1 G-H loop cross-reacted with the anti-FMDV monoclonal antibody (mAb) SD6 and was found to decorate the corners of the Qβ icosahedral shell by electron microscopy. Evolution of Qβ-displayed peptides, starting from fully degenerate coding sequences corresponding to the immunodominant region of VP1, allowed rapid in vitro affinity maturation to SD6 mAb. Qβ selected under evolutionary pressure revealed a non-canonical, but essential epitope for mAb SD6 recognition consisting of an Arg-Gly tandem pair. Finally, the selected hybrid phages induced polyclonal antibodies in guinea pigs with good affinity to both FMDV and hybrid Qβ-G-H loop, validating the requirement of the tandem pair epitope. Qβ-display emerges as a novel framework for rapid in vitro evolution with affinity-maturation to molecular targets.
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Affiliation(s)
- Claudia Skamel
- Campus Technologies Freiburg (CTF) GmbH, Agency for Technology Transfer at the University and University Medical Center Freiburg, Freiburg, Germany
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology and Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Alain Bopda Waffo
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama, United States of America
- * E-mail:
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21
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Derer S, Glorius P, Schlaeth M, Lohse S, Klausz K, Muchhal U, Desjarlais JR, Humpe A, Valerius T, Peipp M. Increasing FcγRIIa affinity of an FcγRIII-optimized anti-EGFR antibody restores neutrophil-mediated cytotoxicity. MAbs 2014; 6:409-21. [PMID: 24492248 PMCID: PMC3984330 DOI: 10.4161/mabs.27457] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/07/2013] [Accepted: 12/07/2013] [Indexed: 01/27/2023] Open
Abstract
Antibody-dependent cell-mediated cytotoxicity (ADCC) has been suggested as an essential mechanism for the in vivo activity of cetuximab, an epidermal growth factor receptor (EGFR)-targeting therapeutic antibody. Thus, enhancing the affinity of human IgG1 antibodies to natural killer (NK) cell-expressed FcγRIIIa by glyco- or protein-engineering of their Fc portion has been demonstrated to improve NK cell-mediated ADCC and to represent a promising strategy to improve antibody therapy. However, human polymorphonuclear (PMN) effector cells express the highly homologous FcγRIIIb isoform, which is described to be ineffective in triggering ADCC. Here, non-fucosylated or protein-engineered anti-EGFR antibodies with optimized FcγRIIIa affinities demonstrated the expected benefit in NK cell-mediated ADCC, but did not mediate ADCC by PMN, which could be restored by FcγRIIIb blockade. Furthermore, eosinophils and PMN from paroxysmal nocturnal hemoglobinuria patients that expressed no or low levels of FcγRIIIb mediated effective ADCC with FcγRIII-optimized anti-EGFR antibody. Additional experiments with double FcγRIIa/FcγRIII-optimized constructs demonstrated enhanced PMN-mediated ADCC compared with single FcγRIII-optimized antibody. In conclusion, our data demonstrate that FcγRIIIb engagement impairs PMN-mediated ADCC activity of FcγRIII-optimized anti-EGFR antibodies, while further optimization of FcγRIIa binding significantly restores PMN recruitment.
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MESH Headings
- Antibodies, Monoclonal, Humanized/genetics
- Antibodies, Monoclonal, Humanized/metabolism
- Antibody Affinity/genetics
- Antibody-Dependent Cell Cytotoxicity/genetics
- Cells, Cultured
- Cetuximab
- Cytotoxicity, Immunologic/genetics
- Eosinophils/immunology
- ErbB Receptors/immunology
- Glycosylation
- Hemoglobinuria, Paroxysmal/immunology
- Hemoglobinuria, Paroxysmal/therapy
- Humans
- Immunoglobulin Fc Fragments/genetics
- Immunoglobulin G/genetics
- Immunoglobulin G/metabolism
- Immunotherapy/methods
- Immunotherapy/trends
- Neutrophils/immunology
- Polymorphism, Genetic
- Protein Engineering
- Receptors, IgG/genetics
- Receptors, IgG/immunology
- Receptors, IgG/metabolism
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Affiliation(s)
- Stefanie Derer
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
| | - Pia Glorius
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
| | - Martin Schlaeth
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
| | - Stefan Lohse
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
| | - Katja Klausz
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
| | | | | | - Andreas Humpe
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
| | - Thomas Valerius
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
| | - Matthias Peipp
- Division of Stem Cell Transplantation and Immunotherapy; 2nd Department of Medicine; University Hospital Schleswig-Holstein and Christian-Albrechts-University; Kiel, Germany
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22
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Abstract
High-affinity antibodies are crucial for development of monoclonal antibody (MAb)-based therapeutics for human diseases. Many new detailed methods for affinity maturation have been developed to improve MAb qualities by site-directed mutagenesis, chain shuffling, and error-prone PCR. Site-directed mutagenesis on hotspots in variable heavy (VH) complementary-determining region (CDR) 3 is a commonly used method for improving therapeutic potency and efficacy of targeted MAbs. Strategies for affinity maturation via multi-site-directed mutagenesis in VH-CDR3 described here are for valuable technical tool in the armamentarium of immunologists for development of fast-performance MAbs. Our strategy includes (1) selection of targeted MAb, (2) replacement of certain amino acid residues (e.g., negative or neutral charge to positive amino acids) in VH-CDR3, and (3) determination of binding activity to a target antigen.
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Affiliation(s)
- Hyung-Yong Kim
- Diagnostics and Translational Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Gaithersburg, MD, USA
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23
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Mandrup OA, Friis NA, Lykkemark S, Just J, Kristensen P. A novel heavy domain antibody library with functionally optimized complementarity determining regions. PLoS One 2013; 8:e76834. [PMID: 24116173 PMCID: PMC3792991 DOI: 10.1371/journal.pone.0076834] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 08/30/2013] [Indexed: 11/29/2022] Open
Abstract
Today a number of synthetic antibody libraries of different formats have been created and used for the selection of a large number of recombinant antibodies. One of the determining factors for successful isolation of recombinant antibodies from libraries lies in the quality of the libraries i.e. the number of correctly folded, functional antibodies contained in the library. Here, we describe the construction of a novel, high quality, synthetic single domain antibody library dubbed Predator. The library is based on the HEL4 domain antibody with the addition of recently reported mutations concerning the amino acid composition at positions critical for the folding characteristics and aggregation propensities of domain antibodies. As a unique feature, the CDR3 of the library was designed to mimic the natural human immune response by designating amino acids known to be prevalent in functional antibodies to the diversity in CDR3. CDR randomizations were performed using trinucleotide synthesis to avoid the presence of stop codons. Furthermore a novel cycle free elongation method was used for the conversion of the synthesized single stranded DNA containing the randomized CDRs into double stranded DNA of the library. In addition a modular approach has been adopted for the scaffold in which each CDR region is flanked by unique restrictions sites, allowing easy affinity maturation of selected clones by CDR shuffling. To validate the quality of the library, one round phage display selections were performed on purified antigens and highly complex antigen mixtures such as cultured eukaryotic cells resulting in several specific binders. The further characterization of some of the selected clones, however, indicates a reduction in thermodynamic stability caused by the inclusion the additional mutations to the HEL4 scaffold.
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Affiliation(s)
| | - Niels Anton Friis
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simon Lykkemark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Sino-Danish Centre for Education and Research, Aarhus, Denmark
| | - Jesper Just
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter Kristensen
- Department of Engineering, Aarhus University, Aarhus, Denmark
- * E-mail:
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24
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Shaheen HH, Prinz B, Chen MT, Pavoor T, Lin S, Houston-Cummings NR, Moore R, Stadheim TA, Zha D. A dual-mode surface display system for the maturation and production of monoclonal antibodies in glyco-engineered Pichia pastoris. PLoS One 2013; 8:e70190. [PMID: 23875020 PMCID: PMC3707868 DOI: 10.1371/journal.pone.0070190] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/14/2013] [Indexed: 11/22/2022] Open
Abstract
State-of-the-art monoclonal antibody (mAb) discovery methods that utilize surface display techniques in prokaryotic and eukaryotic cells require multiple steps of reformatting and switching of hosts to transition from display to expression. This results in a separation between antibody affinity maturation and full-length mAb production platforms. Here, we report for the first time, a method in Glyco-engineered Pichiapastoris that enables simultaneous surface display and secretion of full-length mAb molecules with human-like N-glycans using the same yeast cell. This paradigm takes advantage of homo-dimerization of the Fc portion of an IgG molecule to a surface-anchored "bait" Fc, which results in targeting functional “half” IgGs to the cell wall of Pichiapastoris without interfering with the secretion of full length mAb. We show the utility of this method in isolating high affinity, well-expressed anti-PCSK9 leads from a designed library that was created by mating yeasts containing either light chain or heavy chain IgG libraries. Coupled with Glyco-engineered Pichiapastoris, this method provides a powerful tool for the discovery and production of therapeutic human mAbs in the same host thus improving drug developability and potentially shortening the discovery time cycle.
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Affiliation(s)
- Hussam H. Shaheen
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
- * E-mail: (HS); (DZ)
| | - Bianka Prinz
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
| | - Ming-Tang Chen
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
| | - Tej Pavoor
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
| | - Song Lin
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
| | - Nga Rewa Houston-Cummings
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
| | - Renee Moore
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
| | - Terrance A. Stadheim
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
| | - Dongxing Zha
- GlycoFi, Biologics Discovery, Merck Research Laboratories, Merck & Co., Inc., Lebanon, New Hampshire, United States of America
- * E-mail: (HS); (DZ)
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25
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González-Muñoz A, Bokma E, O’Shea D, Minton K, Strain M, Vousden K, Rossant C, Jermutus L, Minter R. Tailored amino acid diversity for the evolution of antibody affinity. MAbs 2012; 4:664-72. [PMID: 22926024 PMCID: PMC3502233 DOI: 10.4161/mabs.21728] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Antibodies are a unique class of proteins with the ability to adapt their binding sites for high affinity and high specificity to a multitude of antigens. Many analyses have been performed on antibody sequences and structures to elucidate which amino acids have a predominant role in antibody interactions with antigens. These studies have generally not distinguished between amino acids selected for broad antigen specificity in the primary immune response and those selected for high affinity in the secondary immune response. By studying a large data set of affinity matured antibodies derived from in vitro directed evolution experiments, we were able to specifically highlight a subset of amino acids associated with affinity improvements. In a comparison of affinity maturations using either tailored or full amino acid diversification, the tailored approach was found to be at least as effective at improving affinity while requiring fewer mutagenesis libraries than the traditional method. The resulting sequence data also highlight the potential for further reducing amino acid diversity for high affinity binding interactions.
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26
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Karauzum H, Chen G, Abaandou L, Mahmoudieh M, Boroun AR, Shulenin S, Devi VS, Stavale E, Warfield KL, Zeitlin L, Roy CJ, Sidhu SS, Aman MJ. Synthetic human monoclonal antibodies toward staphylococcal enterotoxin B (SEB) protective against toxic shock syndrome. J Biol Chem 2012; 287:25203-15. [PMID: 22645125 PMCID: PMC3408135 DOI: 10.1074/jbc.m112.364075] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/04/2012] [Indexed: 01/25/2023] Open
Abstract
Staphylococcal enterotoxin B (SEB) is a potent toxin that can cause toxic shock syndrome and act as a lethal and incapacitating agent when used as a bioweapon. There are currently no vaccines or immunotherapeutics available against this toxin. Using phage display technology, human antigen-binding fragments (Fabs) were selected against SEB, and proteins were produced in Escherichia coli cells and characterized for their binding affinity and their toxin neutralizing activity in vitro and in vivo. Highly protective Fabs were converted into full-length IgGs and produced in mammalian cells. Additionally, the production of anti-SEB antibodies was explored in the Nicotiana benthamiana plant expression system. Affinity maturation was performed to produce optimized lead anti-SEB antibody candidates with subnanomolar affinities. IgGs produced in N. benthamiana showed characteristics comparable with those of counterparts produced in mammalian cells. IgGs were tested for their therapeutic efficacy in the mouse toxic shock model using different challenge doses of SEB and a treatment with 200 μg of IgGs 1 h after SEB challenge. The lead candidates displayed full protection from lethal challenge over a wide range of SEB challenge doses. Furthermore, mice that were treated with anti-SEB IgG had significantly lower IFNγ and IL-2 levels in serum compared with mock-treated mice. In summary, these anti-SEB monoclonal antibodies represent excellent therapeutic candidates for further preclinical and clinical development.
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Affiliation(s)
- Hatice Karauzum
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Gang Chen
- the Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Laura Abaandou
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Mahta Mahmoudieh
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Atefeh R. Boroun
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Sergey Shulenin
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - V. Sathya Devi
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Eric Stavale
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | | | - Larry Zeitlin
- Mapp Biopharmaceutical, San Diego, California 92121, and
| | - Chad J. Roy
- the Tulane National Primate Research Center, Tulane School of Medicine, Covington, Louisiana 70433
| | - Sachdev S. Sidhu
- the Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - M. Javad Aman
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
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27
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Tian H, Bai FL, Xu LM, Wang WF, Niu ZS, Ren GP, Li DS. [Affinity optimization of an anti-hIL17A single-chain Fv antibody through error-prone PCR technique]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2012; 28:722-732. [PMID: 22768863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
AIM To optimize antibody affinity of a humanized anti-hIL17A single-chain Fv (scFV) antibody through error-prone polymerase chain reaction (PCR) so as to develop a therapeutic humanized antibody for the treatment of rheumatoid arthritis (RA). METHODS Variable regions of heavy chain and light chain were subjected to random mutation by error-prone PCR and a scFv library was constructed by overlapping PCR. The library was screened for improved mutants by the bacterial inner membrane display technique and flow cytometry (FCM). Real-time PCR was used to detect neutralization effects of the purified scFv antibody mutants on mRNA expressions of IL-6 and IL-8 in HeLa cells stimulated by hIL17A. RESULTS We obtained five mutants with improved affinity. FCM revealed that the affinity of three clones was greatly enhanced as compared with the parent clone. All mutants retained binding specificity to hIL17A. Real-time PCR results showed that all five mutants could block hIL17A stimulation of HeLa cells to express IL-6 and IL-8, and the neutralization effects were positively related to mutant affinity. CONCLUSION Error-prone PCR technique is a feasible method for antibody affinity optimization in vitro, which is able to improve the affinity and neutralization capacity of antibody on the basis of its unchanged antigen binding specificity. This study provides potential drug candidates aimed for the treatment of rheumatoid arthritis and an alternative method of optimizing antibody affinity in vitro.
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Affiliation(s)
- Hui Tian
- Department of Biopharmaceutics, College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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28
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Hayes CJ, Leonard P, O'Kennedy R. Overcoming antibody expression and screening limitations by smart design: applications to PSA immunoassay development. Protein Expr Purif 2012; 83:84-91. [PMID: 22433448 DOI: 10.1016/j.pep.2012.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 11/19/2022]
Abstract
Improving the functional and structural properties of target proteins can often be a challenge for researchers. This paper highlights the importance of antibody construct on screening performance, and ultimately, the clone that is selected. We report the reformatting of phage-selected single chain antibody variable region fragments (scFvs) into single chain antibody fragments (scAbs) for improved screening and binding studies. The generation of a scAb, which had a fused human kappa light chain constant domain (C(k)), was shown to significantly improve expression levels in Escherichia coli. Antibody expression levels were compared between the two antibody constructs (scFv and scAb) by ELISA and a 100-fold improvement was observed. The C(k) domain in the expressed scAb also facilitated high throughput analysis by a Biacore capture assay approach. Individual functional scAbs were ranked on the basis of their remaining binding percentage after 5 min dissociation. Selected antibodies were further characterised by kinetic analysis and a sandwich-based immunoassay developed. The scAb construct enhanced expression levels significantly, facilitating antibody screening and immunoassay development for prostate-specific antigen (PSA), a marker for prostate cancer.
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Affiliation(s)
- C J Hayes
- Applied Biochemistry Group, School of Biotechnology, Dublin City University, Dublin 9, Ireland
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29
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Abstract
This protocol describes the generation of human antibody libraries in Fab format from 2.5 × 10(7) human peripheral blood or bone marrow mononuclear cells for their subsequent selection by phage display. Although it can be applied to the mining of both human naïve and immune antibody repertoires, the procedure is primarily intended for the generation of fully human monoclonal antibodies from patients with endogenous antibody responses of interest and limited availability of clinical specimens.
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Affiliation(s)
- Christoph Rader
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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30
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Ye J, Bromage E, Kaattari I, Kaattari S. Transduction of binding affinity by B lymphocytes: a new dimension in immunological regulation. Dev Comp Immunol 2011; 35:982-990. [PMID: 21300090 DOI: 10.1016/j.dci.2011.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 01/15/2011] [Accepted: 01/19/2011] [Indexed: 05/30/2023]
Abstract
To date, immunologists have operated with two primary paradigms governing the antibody response: (1) that affinity maturation is primarily dependent upon antigen-driven selection of both the germline and somatically amended repertoires, and (2) that antibody effector function is isotypically determined. The teleost model now suggests that these classical paradigms should be broadened to incorporate the ability of the B cell to transduce the strength of antigen recognition (affinity) into structural modifications of its antibody product, which, in turn, modulates the antibody's effector function. Although this relationship, thus far, has only been examined and demonstrated in the teleost, we find a number of the individual elements of this structural/functional relationship have been reported for mammalian IgM, which prompts future investigations into its universality. In sum, these findings suggest a heretofore unrecognized feature of B lymphocyte affinity discrimination, which transduces the affinity of antigen recognition into functionally modified antibodies.
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Affiliation(s)
- Jianmin Ye
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, United States
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31
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Mouquet H, Scheid JF, Zoller MJ, Krogsgaard M, Ott RG, Shukair S, Artyomov MN, Pietzsch J, Connors M, Pereyra F, Walker BD, Ho DD, Wilson PC, Seaman MS, Eisen HN, Chakraborty AK, Hope TJ, Ravetch JV, Wardemann H, Nussenzweig MC. Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature 2010; 467:591-5. [PMID: 20882016 PMCID: PMC3699875 DOI: 10.1038/nature09385] [Citation(s) in RCA: 328] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 07/30/2010] [Indexed: 11/08/2022]
Abstract
During immune responses, antibodies are selected for their ability to bind to foreign antigens with high affinity, in part by their ability to undergo homotypic bivalent binding. However, this type of binding is not always possible. For example, the small number of gp140 glycoprotein spikes displayed on the surface of the human immunodeficiency virus (HIV) disfavours homotypic bivalent antibody binding. Here we show that during the human antibody response to HIV, somatic mutations that increase antibody affinity also increase breadth and neutralizing potency. Surprisingly, the responding naive and memory B cells produce polyreactive antibodies, which are capable of bivalent heteroligation between one high-affinity anti-HIV-gp140 combining site and a second low-affinity site on another molecular structure on HIV. Although cross-reactivity to self-antigens or polyreactivity is strongly selected against during B-cell development, it is a common serologic feature of certain infections in humans, including HIV, Epstein-Barr virus and hepatitis C virus. Seventy-five per cent of the 134 monoclonal anti-HIV-gp140 antibodies cloned from six patients with high titres of neutralizing antibodies are polyreactive. Despite the low affinity of the polyreactive combining site, heteroligation demonstrably increases the apparent affinity of polyreactive antibodies to HIV.
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Affiliation(s)
- Hugo Mouquet
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
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32
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Li B, Zhao L, Wang C, Guo H, Wu L, Zhang X, Qian W, Wang H, Guo Y. The protein-protein interface evolution acts in a similar way to antibody affinity maturation. J Biol Chem 2010; 285:3865-3871. [PMID: 20007707 PMCID: PMC2823529 DOI: 10.1074/jbc.m109.076547] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Indexed: 12/22/2022] Open
Abstract
Understanding the evolutionary mechanism that acts at the interfaces of protein-protein complexes is a fundamental issue with high interest for delineating the macromolecular complexes and networks responsible for regulation and complexity in biological systems. To investigate whether the evolution of protein-protein interface acts in a similar way as antibody affinity maturation, we incorporated evolutionary information derived from antibody affinity maturation with common simulation techniques to evaluate prediction success rates of the computational method in affinity improvement in four different systems: antibody-receptor, antibody-peptide, receptor-membrane ligand, and receptor-soluble ligand. It was interesting to find that the same evolutionary information could improve the prediction success rates in all the four protein-protein complexes with an exceptional high accuracy (>57%). One of the most striking findings in our present study is that not only in the antibody-combining site but in other protein-protein interfaces almost all of the affinity-enhancing mutations are located at the germline hotspot sequences (RGYW or WA), indicating that DNA hot spot mechanisms may be widely used in the evolution of protein-protein interfaces. Our data suggest that the evolution of distinct protein-protein interfaces may use the same basic strategy under selection pressure to maintain interactions. Additionally, our data indicate that classical simulation techniques incorporating the evolutionary information derived from in vivo antibody affinity maturation can be utilized as a powerful tool to improve the binding affinity of protein-protein complex with a high accuracy.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal, Murine-Derived
- Antibody Affinity/genetics
- Antibody Affinity/immunology
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Base Sequence
- Binding Sites/genetics
- CTLA-4 Antigen
- Computer Simulation
- Crystallography, X-Ray
- Evolution, Molecular
- Interleukin-2 Receptor alpha Subunit/chemistry
- Interleukin-2 Receptor alpha Subunit/genetics
- Interleukin-2 Receptor alpha Subunit/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Protein Binding
- Protein Interaction Mapping/methods
- Protein Structure, Tertiary
- Proteins/chemistry
- Proteins/genetics
- Proteins/metabolism
- Rituximab
- Sequence Homology, Amino Acid
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Affiliation(s)
- Bohua Li
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and
| | - Lei Zhao
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433
| | - Chong Wang
- the School of Medicine and School of Pharmacy, The Center for Antibody Medicine of Ministry of Education, Shanghai Jiao Tong University, 227 South Chongqing Road, Shanghai 200025, China
| | - Huaizu Guo
- the School of Medicine and School of Pharmacy, The Center for Antibody Medicine of Ministry of Education, Shanghai Jiao Tong University, 227 South Chongqing Road, Shanghai 200025, China
| | - Lan Wu
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433
| | - Xunming Zhang
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433
| | - Weizhu Qian
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and
| | - Hao Wang
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and
| | - Yajun Guo
- From the International Joint Cancer Institute and 301 General Hospital Cancer Center, Second Military Medical University, Shanghai 200433; the National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering & Antibody, Shanghai 201203, and; the School of Medicine and School of Pharmacy, The Center for Antibody Medicine of Ministry of Education, Shanghai Jiao Tong University, 227 South Chongqing Road, Shanghai 200025, China.
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33
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Sharma D, Bastard K, Guethlein LA, Norman PJ, Yawata N, Yawata M, Pando M, Thananchai H, Dong T, Rowland-Jones S, Brodsky FM, Parham P. Dimorphic motifs in D0 and D1+D2 domains of killer cell Ig-like receptor 3DL1 combine to form receptors with high, moderate, and no avidity for the complex of a peptide derived from HIV and HLA-A*2402. J Immunol 2009; 183:4569-82. [PMID: 19752231 PMCID: PMC2827337 DOI: 10.4049/jimmunol.0901734] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Comparison of mutant killer cell Ig-like receptor (KIR) 3DL1*015 substituted at natural positions of variation showed that tryptophan/leucine dimorphism at position 283 uniquely changes receptor conformation and can strongly influence binding of the A24nef tetramer. Dimorphic motifs at positions 2, 47, and 54 in D0 and 182 and 283 in D1+D2 distinguish the two 3DL1 lineages, typified by 3DL1*005 and 3DL1*015. The interlineage recombinant, KIR3DL1*001, combines D0 of 3DL1*005 with D1+D2 of 3DL1*015 and binds A24nef more strongly than either parent. In contrast, the reciprocal recombinant with D0 from 3DL1*015 and D1+D2 from 3DL1*005 cannot bind A24nef. Thus, D0 polymorphism directly affects the avidity of the KIR3DL1 ligand binding site. From these observations, multiple sequence alignment, and homology modeling, we constructed structural models for KIR3DL1 and its complex with A24nef. In these models, D0, D1, and D2 come together to form a binding surface for A24nef, which is contacted by all three Ig-like domains. A central pocket binds arginine 83, the only Bw4 motif residue essential for KIR3DL1 interaction, similar to the binding of lysine 80 in HLA-C by KIR2DL1. Central to this interaction is a salt bridge between arginine 83 of Bw4 and glutamate 282 of 3DL1, which juxtaposes the functionally influential dimorphism at position 283. Further 3DL1 mutants were tested and shown to have A24nef-binding properties consistent with the models. A24nef was not bound by KIR3DS1, the activating counterpart of KIR3DL1. Moreover, introducing any one of three residues specific to KIR3DS1, serine 163, arginine 166, or leucine 199, into 3DL1*015, abrogated A24nef binding.
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MESH Headings
- Amino Acid Motifs/genetics
- Amino Acid Motifs/immunology
- Amino Acid Sequence
- Amino Acid Substitution/genetics
- Amino Acid Substitution/immunology
- Antibody Affinity/genetics
- Gene Products, nef/genetics
- Gene Products, nef/metabolism
- HLA-A Antigens/genetics
- HLA-A Antigens/metabolism
- HLA-A24 Antigen
- HLA-B Antigens/genetics
- HLA-B Antigens/metabolism
- Humans
- Jurkat Cells
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Killer Cells, Natural/virology
- Leucine/genetics
- Leucine/metabolism
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Polymorphism, Genetic/immunology
- Protein Binding/genetics
- Protein Binding/immunology
- Protein Structure, Tertiary/genetics
- Receptors, KIR3DL1/genetics
- Receptors, KIR3DL1/immunology
- Receptors, KIR3DL1/metabolism
- Tryptophan/genetics
- Tryptophan/metabolism
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Affiliation(s)
- Deepti Sharma
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karine Bastard
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- UMR CNRS 6204, Faculté des Sciences et des Techniques, Université de Nantes, France
| | - Lisbeth A. Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul J. Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nobuyo Yawata
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Makoto Yawata
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcelo Pando
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hathairat Thananchai
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
| | - Tao Dong
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
| | - Sarah Rowland-Jones
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
| | - Frances M. Brodsky
- Departments of Bioengineering and Therapeutic Sciences, and Microbiology and Immunology, University of California San Francisco, San Francisco, USA
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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34
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Xiao X, Chen W, Feng Y, Zhu Z, Prabakaran P, Wang Y, Zhang MY, Longo NS, Dimitrov DS. Germline-like predecessors of broadly neutralizing antibodies lack measurable binding to HIV-1 envelope glycoproteins: implications for evasion of immune responses and design of vaccine immunogens. Biochem Biophys Res Commun 2009; 390:404-9. [PMID: 19748484 PMCID: PMC2787893 DOI: 10.1016/j.bbrc.2009.09.029] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 09/08/2009] [Indexed: 01/02/2023]
Abstract
Several human monoclonal antibodies (hmAbs) including b12, 2G12, and 2F5 exhibit relatively potent and broad HIV-1-neutralizing activity. However, their elicitation in vivo by vaccine immunogens based on the HIV-1 envelope glycoprotein (Env) has not been successful. We have hypothesized that HIV-1 has evolved a strategy to reduce or eliminate the immunogenicity of the highly conserved epitopes of such antibodies by using “holes” (absence or very weak binding to these epitopes of germline antibodies that is not sufficient to initiate and/or maintain an efficient immune response) in the human germline B cell receptor (BCR) repertoire. To begin to test this hypothesis we have designed germline-like antibodies corresponding most closely to b12, 2G12, and 2F5 as well as to X5, m44, and m46 which are cross-reactive but with relatively modest neutralizing activity as natively occurring antibodies due to size and/or other effects. The germline-like X5, m44, and m46 bound with relatively high affinity to all tested Envs. In contrast, germline-like b12, 2G12, and 2F5 lacked measurable binding to Envs in an ELISA assay although the corresponding mature antibodies did. These results provide initial evidence that Env structures containing conserved vulnerable epitopes may not initiate humoral responses by binding to germline antibodies. Even if such responses are initiated by very weak binding undetectable in our assay it is likely that they will be outcompeted by responses to structures containing the epitopes of X5, m44, m46, and other antibodies that bind germline BCRs with much higher affinity/avidity. This hypothesis, if further supported by data, could contribute to our understanding of how HIV-1 evades immune responses and offer new concepts for design of effective vaccine immunogens.
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Affiliation(s)
- Xiaodong Xiao
- Protein Interactions Group, CCRNP, NCI-Frederick, NIH, Frederick, MD 21702, USA
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35
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Bie CQ, Yang DH, Liu L. [Construction, expression and characterization of humanized single-chain Fv dimers for hepatocellular carcinoma]. Zhonghua Gan Zang Bing Za Zhi 2009; 17:466-467. [PMID: 19567031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Cai-qun Bie
- Department of Gastroenterology, the First Affiliated Hospital of Jinan University, Guangzhou, China
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36
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Rohatgi S, Dutta D, Tahir S, Sehgal D. Molecular Dissection of Antibody Responses against Pneumococcal Surface Protein A: Evidence for Diverse DH-Less Heavy Chain Gene Usage and Avidity Maturation. J Immunol 2009; 182:5570-85. [PMID: 19380805 DOI: 10.4049/jimmunol.0803254] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Bacterial/biosynthesis
- Antibodies, Bacterial/genetics
- Antibodies, Bacterial/metabolism
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/metabolism
- Antibody Affinity/genetics
- Antibody Diversity/genetics
- Bacterial Proteins/immunology
- Base Sequence
- Epitopes, B-Lymphocyte/metabolism
- Female
- Gene Deletion
- Gene Rearrangement, B-Lymphocyte, Heavy Chain/genetics
- Hybridomas
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/metabolism
- Membrane Proteins/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred CBA
- Molecular Sequence Data
- Multigene Family/immunology
- Streptococcus pneumoniae/immunology
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Affiliation(s)
- Soma Rohatgi
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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Affiliation(s)
- Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America.
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Poulsen TR, Meijer PJ, Jensen A, Nielsen LS, Andersen PS. Kinetic, affinity, and diversity limits of human polyclonal antibody responses against tetanus toxoid. J Immunol 2007; 179:3841-50. [PMID: 17785821 DOI: 10.4049/jimmunol.179.6.3841] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Due to technical limitations, little knowledge exists on the composition of Ag-specific polyclonal Ab responses. Hence, we here present a molecular analysis of two representative human Ab repertoires isolated by using a novel single-cell cloning approach. The observed genetic diversity among tetanus toxoid-specific plasma cells indicate that human polyclonal repertoires are limited to the order of 100 B cell clones and hypermutated variants thereof. Affinity and kinetic binding constants are log-normally distributed, and median values are close to the proposed affinity ceilings for positive selection. Abs varied a million-fold in affinity but were restricted in their off-rates with an upper limit of 2 x 10(-3) s(-1). Identification of Abs of high affinity without hypermutations in combination with a modest effect of hypermutations on observed affinity increases indicate that Abs selected from the naive repertoire are not only of low affinity but cover a relatively large span in affinity, reaching into the subnanomolar range.
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MESH Headings
- Adult
- Amino Acid Sequence
- Antibodies, Bacterial/biosynthesis
- Antibodies, Bacterial/genetics
- Antibodies, Bacterial/isolation & purification
- Antibodies, Bacterial/metabolism
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/genetics
- Antibody Affinity/genetics
- Antibody Diversity/genetics
- Clostridium tetani/immunology
- Complementarity Determining Regions/biosynthesis
- Complementarity Determining Regions/genetics
- Female
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Humans
- Immunoglobulin Joining Region/biosynthesis
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Variable Region/biosynthesis
- Immunoglobulin Variable Region/genetics
- Kinetics
- Male
- Molecular Sequence Data
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Tetanus Toxoid/immunology
- Tetanus Toxoid/metabolism
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Trisler K, Looger LL, Sharma V, Baker M, Benson DE, Trauger S, Schultz PG, Smider VV. A Metalloantibody That Irreversibly Binds a Protein Antigen. J Biol Chem 2007; 282:26344-53. [PMID: 17617633 DOI: 10.1074/jbc.m704675200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibody affinity is critically important in therapeutic applications, as well as steady state diagnostic assays. Picomolar affinity antibodies, approaching the association limit of protein-protein interactions, have been discovered for highly potent antigens, but even such high-affinity binders have off-rates sufficient to negate therapeutic efficacy. To cross this affinity threshold, antibodies that tether their targets in a manner other than reversible non-covalent interaction will be required. Here we report the design and construction of an antibody that forms an irreversible complex with a protein antigen in a metal-dependent reaction. The complex resists thermal and chemical denaturation, as well as attempts to remove the coordinating metal ion. Such irreversibly binding antibodies could facilitate the development of next generation "reactive antibody" therapeutics and diagnostics.
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40
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Fischer SF, Bouillet P, O'Donnell K, Light A, Tarlinton DM, Strasser A. Proapoptotic BH3-only protein Bim is essential for developmentally programmed death of germinal center-derived memory B cells and antibody-forming cells. Blood 2007; 110:3978-84. [PMID: 17720882 PMCID: PMC2190612 DOI: 10.1182/blood-2007-05-091306] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
T cell-dependent B-cell immune responses induce germinal centers that are sites for expansion, diversification, and selection of antigen-specific B cells. During the immune response, antigen-specific B cells are removed in a process that favors the retention of cells with improved affinity for antigen, a cell death process inhibited by excess Bcl-2. In this study, we examined the role of the BH3-only protein Bim, an initiator of apoptosis in the Bcl-2-regulated pathway, in the programmed cell death accompanying an immune response. After immunization, Bim-deficient mice showed persistence of both memory B cells lacking affinity-enhancing mutations in their immunoglobulin genes and antibody-forming cells secreting low-affinity antibodies. This was accompanied by enhanced survival of both cell types in culture. We have identified for the first time the physiologic mechanisms for killing low-affinity antibody-expressing B cells in an immune response and have shown this to be dependent on the BH3-only protein Bim.
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Affiliation(s)
- Silke F Fischer
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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41
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Mølle I, Melsvik D, Østergaard M. Rapid single-step methods for detection of two immune defence gene polymorphisms: the myeloperoxidase (MPO) G-129A and the Fc gamma receptor 2A (FCGR2A) H/R131. J Immunol Methods 2007; 324:105-9. [PMID: 17582430 DOI: 10.1016/j.jim.2007.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 05/08/2007] [Accepted: 05/13/2007] [Indexed: 10/23/2022]
Abstract
Polymorphisms of immune defence genes may act as disease modifiers and are studied by many researchers. A conclusive analysis of the impact of genetic variations typically requires a large number of sample specimens, and in retrospective studies this may include samples of reduced quality, e.g. formalin-fixed paraffin-embedded tissue specimens. Here we describe two new single-step methods for rapid and sensitive analysis of: 1. The G-129A myeloperoxidase (MPO) promoter polymorphism, which affects the amount of myeloperoxidase in neutrophils. 2. The Fc gamma receptor 2A (FCGR2A)-H/R131 polymorphism, which is critical to the binding of IgG2 immune complexes to phagocytes.
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MESH Headings
- Alanine/genetics
- Amino Acid Substitution/genetics
- Antibody Affinity/genetics
- Antigens, CD/blood
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Arginine/genetics
- Cells, Cultured
- Glycine/genetics
- Histidine/genetics
- Humans
- Immunity, Innate/genetics
- Neutrophils/enzymology
- Peroxidase/blood
- Peroxidase/genetics
- Phagocytes/metabolism
- Polymorphism, Restriction Fragment Length
- Receptors, IgG/blood
- Receptors, IgG/genetics
- Receptors, IgG/metabolism
- Retrospective Studies
- Reverse Transcriptase Polymerase Chain Reaction
- Tumor Cells, Cultured
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Affiliation(s)
- Ingolf Mølle
- Department of Haematology, Aarhus University Hospital, DK-8000 C, Denmark.
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Pan N, Shi L, Huang LH, Zhou L, He DS, Zhang YG. [Production and property identification of monoclonal antibodies against DAF molecules by DNA immunization followed by a single boost with cell antigen]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2007; 23:652-6. [PMID: 17618592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
AIM To produce mAb against DAF by DNA immunization followed by a single boost with cell antigen and to characterize its property. METHODS Recombinant plasmid pcDNA3.1/DAF was constructed by molecular cloning technique and injected into mice quadriceps muscle of thigh. To boost the DAF immunized mice, HPB-All cell antigen were injected on day 3 before cell fusion. The affinity and property of mAb to natural membrane protein and denatured protein were identified by FCM, fluorescence microscope and Western blot. RESULTS Two mAb against DAF were obtained, namely 2B6B and 2B6E. The affinity constant of 2B6E was 1.81x10(-7) mol/L. The isotype of the two mAbs were IgG2a, and the epitope of them was different. FCM, fluorescence microscope and Western blot indicated that the obtained mAb had affinity to natural membrane protein and denatured protein with high specificity. CONCLUSION This study indicates that the DNA immunization and cell antigen boost method enables mice to produce mAb against DAF. The low frequency of nonspecific mAb is one of the advantages of this method compared to the conventional cell immunization method. Moreover the mAb generated by this method has satisfactory binding activity and specificity.
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Affiliation(s)
- Na Pan
- Department of Immunology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Tianjin 300020, China
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43
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Wang Z, Kim GB, Woo JH, Liu YY, Mathias A, Stavrou S, Neville DM. Improvement of a Recombinant Anti-Monkey Anti-CD3 Diphtheria Toxin Based Immunotoxin by Yeast Display Affinity Maturation of the scFv. Bioconjug Chem 2007; 18:947-55. [PMID: 17352456 DOI: 10.1021/bc0603438] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, a bivalent recombinant anti-human CD3 diphtheria toxin (DT) based immunotoxin derived from the scFv of UCHT1 antibody has been made that shows enhanced bioactivity and is free from the side effects of Fc receptor interaction. In this case, the diminution of CD3 binding due to the placement of the scFv domain at the C-terminus of the truncated DT in single scFv immunotoxins was compensated by adding an additional scFv domain. However, this strategy was less successful for constructing an anti-rhesus recombinant immunotoxin derived from the scFv of FN18 antibody due to poor binding of the anti-rhesus bivalent immunotoxin. We report here that, by increasing the FN18 scFv affinity through random mutagenesis and selection with a dye-labeled monkey CD3epsilongamma recombinant heterodimer, we greatly improved the bioactivity of FN18 derived immunotoxin. The best mutant, C207, contained nine mutations, two of which were located in CDRs that changed the charge from negative to positive. Binding affinity of the C207 scFv to the monkey T cell line HSC-F increased 9.8-fold. The potency of the C207 bivalent immunotoxin assayed by inhibition of protein synthesis increased by 238-fold.
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Affiliation(s)
- Zhirui Wang
- Section on Biophysical Chemistry, Laboratory of Molecular Biology, National Institute of Mental Health, Building 10 Rm 3D46, 10 Center Drive, Bethesda, Maryland 20892-1216, USA
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44
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Gerber HP, Wu X, Yu L, Wiesmann C, Liang XH, Lee CV, Fuh G, Olsson C, Damico L, Xie D, Meng YG, Gutierrez J, Corpuz R, Li B, Hall L, Rangell L, Ferrando R, Lowman H, Peale F, Ferrara N. Mice expressing a humanized form of VEGF-A may provide insights into the safety and efficacy of anti-VEGF antibodies. Proc Natl Acad Sci U S A 2007; 104:3478-83. [PMID: 17360669 PMCID: PMC1805509 DOI: 10.1073/pnas.0611492104] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
VEGF-A is important in tumor angiogenesis, and a humanized anti-VEGF-A monoclonal antibody (bevacizumab) has been approved by the FDA as a treatment for metastatic colorectal and nonsquamous, non-small-cell lung cancer in combination with chemotherapy. However, contributions of both tumor- and stromal-cell derived VEGF-A to vascularization of human tumors grown in immunodeficient mice hindered direct comparison between the pharmacological effects of anti-VEGF antibodies with different abilities to block host VEGF. Therefore, by gene replacement technology, we engineered mice to express a humanized form of VEGF-A (hum-X VEGF) that is recognized by many anti-VEGF antibodies and has biochemical and biological properties comparable with WT mouse and human VEGF-A. The hum-X VEGF mouse model was then used to compare the activity and safety of a panel of VEGF Mabs with different affinities for VEGF-A. Although in vitro studies clearly showed a correlation between binding affinity and potency at blocking endothelial cell proliferation stimulated by VEGF, in vivo experiments failed to document any consistent correlation between antibody affinity and the ability to inhibit tumor growth and angiogenesis in most animal models. However, higher-affinity antibodies were more likely to result in glomerulosclerosis during long-term treatment.
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Affiliation(s)
| | - Xiumin Wu
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Lanlan Yu
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | | | | | | | - Germaine Fuh
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | | | - Lisa Damico
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - David Xie
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Y. Gloria Meng
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | | | - Racquel Corpuz
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Bing Li
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Linda Hall
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Linda Rangell
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Ron Ferrando
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Henry Lowman
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Franklin Peale
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
| | - Napoleone Ferrara
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080
- To whom correspondence should be addressed. E-mail:
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45
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Oh MY, Joo HY, Hur BU, Jeong YH, Cha SH. Enhancing phage display of antibody fragments using gIII-amber suppression. Gene 2007; 386:81-9. [PMID: 17088027 DOI: 10.1016/j.gene.2006.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 08/07/2006] [Accepted: 08/08/2006] [Indexed: 10/24/2022]
Abstract
The effect of utilizing Ex12 helper phage, a mutant M13K07 helper having two amber codons at the gIII (gIII-amber), in combination with Escherichia coli host strains belonging to the supE genotype on improving the phage display of antibody fragments was investigated. Because of an inefficient read-through of the UAG codons, Ex12 helper phage produced approximately 10% of the intracellular wt pIII in the supE host cells compared to M13K07. The phage progenies rescued from the supE XL-1 Blue MRF' strain carrying the recombinant phagemid, pCMTG-SP112, by Ex12 helper phage displayed both antibody-DeltapIII fusion and wt pIII at a ratio of 1:1.5, and achieved a 50-fold greater display of the antibody-DeltapIII compared to those obtained by a conventional phage rescue using M13K07. Additionally observed were a 100-fold increase in antigen-binding functionality and a drastic improvement on antigen-specific panning efficiency by the phage progenies. Our approach permits the display of at least one antibody fragment as well as more than one copy of wt pIII on the surface of recombinant phages, and this would make the phagemid-based phage display technology more practical and reliable.
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Affiliation(s)
- Mi-Young Oh
- IG Therapy Co., Rm. 112, Nong 3rd Building, Kangwon National University, Chuncheon, Gangwon-do 200-701, South Korea
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Abstract
Synthetic antibody libraries, whose repertoires are designed, have advanced in the last decade to rival natural repertoire-based libraries. Many types of diversity design have been shown to generate highly functional libraries. Defined template and defined diversity in synthetic antibody libraries improve the process of discovering and optimizing new antibodies. Synthetic libraries with different diversity design have targeted different epitopes on antigens, including epitopes that are unlikely to be targeted by immunization and hybridoma. Cross-species binding antibodies are prime examples of products generated by synthetic antibody libraries, and they are becoming the tools of choice to validate the selection of targeted molecules in therapeutic development. Synthetic antibody libraries complement the existing natural repertoire-based antibody libraries and hybridoma approach to maximize the potentials of antibodies as therapeutics.
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Affiliation(s)
- Germaine Fuh
- Genentech, Inc., Department of Protein Engineering, 1 DNA Way, South San Francisco, CA 94080, USA.
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47
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Kopsidas G, Roberts AS, Coia G, Streltsov VA, Nuttall SD. In vitro improvement of a shark IgNAR antibody by Qbeta replicase mutation and ribosome display mimics in vivo affinity maturation. Immunol Lett 2006; 107:163-8. [PMID: 17069896 DOI: 10.1016/j.imlet.2006.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 09/23/2006] [Accepted: 09/23/2006] [Indexed: 01/28/2023]
Abstract
We have employed a novel mutagenesis system, which utilizes an error-prone RNA dependent RNA polymerase from Qbeta bacteriophage, to create a diverse library of single domain antibody fragments based on the shark IgNAR antibody isotype. Coupling of these randomly mutated mRNA templates directly to the translating ribosome allowed in vitro selection of affinity matured variants showing enhanced binding to target, the apical membrane antigen 1 (AMA1) from Plasmodium falciparum. One mutation mapping to the IgNAR CDR1 loop was not readily additive to other changes, a result explained by structural analysis of aromatic interactions linking the CDR1, CDR3, and Ig framework regions. This combination appeared also to be counter-selected in experiments, suggesting that in vitro affinity maturation is additionally capable of discriminating against incorrectly produced protein variants. Interestingly, a further mutation was directed to a position in the IgNAR heavy loop 4 which is also specifically targeted during the in vivo shark response to antigen, providing a correlation between natural processes and laboratory-based affinity maturation systems.
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Affiliation(s)
- George Kopsidas
- EvoGenix Limited, 343 Royal Parade, Parkville, Vic. 3052, Australia
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Abstract
High affinity antibodies are crucial both for the discovery and validation of biomarkers for human health and disease and as clinical diagnostic and therapeutic reagents. This review describes some of the latest technologies for the design, mutation and selection of high affinity antibodies that provide a paradigm for molecular evolution of a far wider range of proteins including enzymes. Strategies include both in vivo and in vitro methods and embrace the latest concepts for antibody display and selection. Specifically, affinity enhancement can be tailored to the target-binding surface, typically the complementary determining region (CDR) loops in antibodies, whereas enhanced stability, expression or catalytic properties can be affected by selected changes to the core protein scaffold. Together, these technologies provide a rapid and powerful strategy to drive the next generation of protein-based reagents for numerous clinical, environmental and agribusiness applications.
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Affiliation(s)
- Kim L Wark
- CRC for Diagnostics at CSIRO Molecular and Health Technologies, 343 Royal Parade, Parkville 3052, Australia.
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49
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Groves M, Lane S, Douthwaite J, Lowne D, Rees DG, Edwards B, Jackson RH. Affinity maturation of phage display antibody populations using ribosome display. J Immunol Methods 2006; 313:129-39. [PMID: 16730741 DOI: 10.1016/j.jim.2006.04.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 03/29/2006] [Accepted: 04/07/2006] [Indexed: 10/24/2022]
Abstract
A comparison has been performed, using phage display or ribosome display, of stringent selections on antibody populations derived from three rounds of phage display selection. Stringent selections were performed by reducing concentrations of the antigen, bovine insulin, down to 1 nM. Higher affinity antibodies were isolated using ribosome display in a process that introduces random mutations across the clone population. Whereas the highest affinity antibody produced by phage display, D3, has a K(d) of 5.8 nM as a scFv fragment, ribosome display generated higher affinity variants of this antibody with K(d) values of 189 pM and 152 pM, without or with the use of error prone mutagenesis, respectively. The affinities were further increased for each antibody on conversion of the scFv fragments to whole IgG format, to a K(d) of less than 21 pM for the highest affinity variant of D3. Mutation of VH D101 of antibody D3 to glycine or valine, removing the salt bridge between K94 and D101 at the base of VHCDR3, was responsible for the enhanced affinity observed. In addition to the variants of D3, other unrelated antibodies of comparable or higher affinity for insulin, were isolated by ribosome display, but not phage display, indicating that ribosome display can enrich for different populations of antibodies. Affinity maturation of phage antibody populations using ribosome display is a valuable method of rapidly generating diverse, high affinity antibodies to antigen and should be readily applicable to the isolation of antibodies for the detection and assay of biomarkers.
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Affiliation(s)
- Maria Groves
- Cambridge Antibody Technology, Milstein Building, Granta Park, Cambridge CB1 6GH, UK
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50
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Harvey BR, Shanafelt AB, Baburina I, Hui R, Vitone S, Iverson BL, Georgiou G. Engineering of recombinant antibody fragments to methamphetamine by anchored periplasmic expression. J Immunol Methods 2006; 308:43-52. [PMID: 16337958 DOI: 10.1016/j.jim.2005.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 09/13/2005] [Accepted: 09/15/2005] [Indexed: 11/18/2022]
Abstract
The detection of methamphetamine and other chemically related illicit drugs relies extensively on immunoassays. Here we report the cloning and affinity maturation of an anti-methamphetamine antibody which is being employed in the current commercial assays. An anti-methamphetamine scFv was cloned from hybridoma cells, expressed in bacteria and its affinity towards methamphetamine and N-ethylamphetamine (ethamphetamine) was determined by Surface Plasmon Resonance (SPR). The anti-methamphetamine scFv gene was subjected to random mutagenesis by error prone PCR and variants with improved affinity were isolated from the resulting library by a novel screening methodology termed Anchored Periplasmic Expression (APEx) [Harvey, B.R., Georgiou, G., Hayhurst, A., Jeong, K.J., Iverson, B.L., Rogers, G.K. (2004). Anchored periplasmic expression, a versatile technology for the isolation of high-affinity antibodies from Escherichia coli-expressed libraries. Proc. Natl. Acad. Sci. U. S. A. 101, 9193.]. The isolated clones exhibited improved affinity to these illicit drugs, yet maintained low cross-reactivity to over-the-counter drugs. In addition, all clones displayed improved expression characteristics in Escherichia coli. The affinity improved scFv antibodies are thus likely to be useful in methamphetamine class immunodiagnostics.
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Affiliation(s)
- Barrett R Harvey
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, USA
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