1
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Broketa M, Bruhns P. Single-Cell Technologies for the Study of Antibody-Secreting Cells. Front Immunol 2022; 12:821729. [PMID: 35173713 PMCID: PMC8841722 DOI: 10.3389/fimmu.2021.821729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Antibody-secreting cells (ASC), plasmablasts and plasma cells, are terminally differentiated B cells responsible for large-scale production and secretion of antibodies. ASC are derived from activated B cells, which may differentiate extrafollicularly or form germinal center (GC) reactions within secondary lymphoid organs. ASC therefore consist of short-lived, poorly matured plasmablasts that generally secrete lower-affinity antibodies, or long-lived, highly matured plasma cells that generally secrete higher-affinity antibodies. The ASC population is responsible for producing an immediate humoral B cell response, the polyclonal antibody repertoire, as well as in parallel building effective humoral memory and immunity, or potentially driving pathology in the case of autoimmunity. ASC are phenotypically and transcriptionally distinct from other B cells and further distinguishable by morphology, varied lifespans, and anatomical localization. Single cell analyses are required to interrogate the functional and transcriptional diversity of ASC and their secreted antibody repertoire and understand the contribution of individual ASC responses to the polyclonal humoral response. Here we summarize the current and emerging functional and molecular techniques for high-throughput characterization of ASC with single cell resolution, including flow and mass cytometry, spot-based and microfluidic-based assays, focusing on functional approaches of the secreted antibodies: specificity, affinity, and secretion rate.
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Affiliation(s)
- Matteo Broketa
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
- *Correspondence: Matteo Broketa, ; Pierre Bruhns,
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- *Correspondence: Matteo Broketa, ; Pierre Bruhns,
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2
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Van Lent J, Breukers J, Ven K, Ampofo L, Horta S, Pollet F, Imbrechts M, Geukens N, Vanhoorelbeke K, Declerck P, Lammertyn J. Miniaturized single-cell technologies for monoclonal antibody discovery. LAB ON A CHIP 2021; 21:3627-3654. [PMID: 34505611 DOI: 10.1039/d1lc00243k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.
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Affiliation(s)
- Julie Van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Louanne Ampofo
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Maya Imbrechts
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Paul Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
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3
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Horta S, Neumann F, Yeh SH, Langseth CM, Kangro K, Breukers J, Madaboosi N, Geukens N, Vanhoorelbeke K, Nilsson M, Lammertyn J. Evaluation of Immuno-Rolling Circle Amplification for Multiplex Detection and Profiling of Antigen-Specific Antibody Isotypes. Anal Chem 2021; 93:6169-6177. [PMID: 33823582 DOI: 10.1021/acs.analchem.1c00172] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antibody characterization is essential for understanding the immune system and development of diagnostics and therapeutics. Current technologies are mainly focusing on the detection of antigen-specific immunoglobulin G (IgG) using bulk singleplex measurements, which lack information on other isotypes and specificity of individual antibodies. Digital immunoassays based on nucleic acid amplification have demonstrated superior performance by allowing the detection of single molecules in a multiplex and sensitive manner. In this study, we demonstrate for the first time an immuno-rolling circle amplification (immuno-RCA) assay for the multiplex detection of three antigen-specific antibody isotypes (IgG, IgA, and IgM) and its integration with microengraving. To validate this approach, we used the autoimmune disease immune-mediated thrombotic thrombocytopenic purpura (iTTP) as the model disease with anti-ADAMTS13 autoantibodies as the diagnostic target molecules. To identify the anti-ADAMTS13 autoantibody isotypes, we designed a pool of three unique antibody-oligonucleotide conjugates for identification and subsequent amplification and visualization via RCA. To validate this approach, we first confirmed an assay specificity of >88% and a low limit of detection of 0.3 ng/mL in the spiked buffer. Subsequently, we performed a dilution series of an iTTP plasma sample for the multiplex detection of the three isotypes with higher sensitivity compared to an enzyme-linked immunosorbent assay. Finally, we demonstrated single-cell analysis of human B cells and hybridoma cells for the detection of secreted antibodies using microengraving and achieved a detection of 23.3 pg/mL secreted antibodies per hour. This approach could help to improve the understanding of antibody isotype distributions and their roles in various diseases.
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Affiliation(s)
- Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium.,Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Heverlee B-3001, Belgium
| | - Felix Neumann
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23B, Solna 171 65, Sweden
| | - Shu-Hao Yeh
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Heverlee B-3001, Belgium
| | - Christoffer Mattsson Langseth
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23B, Solna 171 65, Sweden
| | - Kadri Kangro
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium.,Icosagen Cell Factory OÜ, Kambja vald, Tartumaa 61713, Estonia
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Heverlee B-3001, Belgium
| | - Narayanan Madaboosi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23B, Solna 171 65, Sweden
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Tomtebodavägen 23B, Solna 171 65, Sweden
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Heverlee B-3001, Belgium
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4
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Bucheli OTM, Sigvaldadóttir I, Eyer K. Measuring single-cell protein secretion in immunology: Technologies, advances, and applications. Eur J Immunol 2021; 51:1334-1347. [PMID: 33734428 PMCID: PMC8252417 DOI: 10.1002/eji.202048976] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022]
Abstract
The dynamics, nature, strength, and ultimately protective capabilities of an active immune response are determined by the extracellular constitution and concentration of various soluble factors. Generated effector cells secrete such mediators, including antibodies, chemo‐ and cytokines to achieve functionality. These secreted factors organize the individual immune cells into functional tissues, initiate, orchestrate, and regulate the immune response. Therefore, a single‐cell resolved analysis of protein secretion is a valuable tool for studying the heterogeneity and functionality of immune cells. This review aims to provide a comparative overview of various methods to characterize immune reactions by measuring single‐cell protein secretion. Spot‐based and cytometry‐based assays, such as ELISpot and flow cytometry, respectively, are well‐established methods applied in basic research and clinical settings. Emerging novel technologies, such as microfluidic platforms, offer new ways to measure and exploit protein secretion in immune reactions. Further technological advances will allow the deciphering of protein secretion in immunological responses with unprecedented detail, linking secretion to functionality. Here, we summarize the development and recent advances of tools that allow the analysis of protein secretion at the single‐cell level, and discuss and contrast their applications within immunology.
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Affiliation(s)
- Olivia T M Bucheli
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Ingibjörg Sigvaldadóttir
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
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5
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Belanger M, Ball AG, Catterton MA, Kinman AW, Anbaei P, Groff BD, Melchor SJ, Lukens JR, Ross AE, Pompano RR. Acute Lymph Node Slices Are a Functional Model System to Study Immunity Ex Vivo. ACS Pharmacol Transl Sci 2021; 4:128-142. [PMID: 33615167 PMCID: PMC7887751 DOI: 10.1021/acsptsci.0c00143] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Indexed: 02/07/2023]
Abstract
The lymph node is a highly organized and dynamic structure that is critical for facilitating the intercellular interactions that constitute adaptive immunity. Most ex vivo studies of the lymph node begin by reducing it to a cell suspension, thus losing the spatial organization, or fixing it, thus losing the ability to make repeated measurements. Live murine lymph node tissue slices offer the potential to retain spatial complexity and dynamic accessibility, but their viability, level of immune activation, and retention of antigen-specific functions have not been validated. Here we systematically characterized live murine lymph node slices as a platform to study immunity. Live lymph node slices maintained the expected spatial organization and cell populations while reflecting the 3D spatial complexity of the organ. Slices collected under optimized conditions were comparable to cell suspensions in terms of both 24-h viability and inflammation. Slices responded to T cell receptor cross-linking with increased surface marker expression and cytokine secretion, in some cases more strongly than matched lymphocyte cultures. Furthermore, slices processed protein antigens, and slices from vaccinated animals responded to ex vivo challenge with antigen-specific cytokine secretion. In summary, lymph node slices provide a versatile platform to investigate immune functions in spatially organized tissue, enabling well-defined stimulation, time-course analysis, and parallel read-outs.
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Affiliation(s)
- Maura
C. Belanger
- Department
of Chemistry, University of Virginia College
of Arts and Sciences, Charlottesville, Virginia 22904, United States
- Carter
Immunology Center, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Alexander G. Ball
- Carter
Immunology Center, University of Virginia, Charlottesville, Virginia 22904, United States
- Department
of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22904, United States
| | - Megan A. Catterton
- Department
of Chemistry, University of Virginia College
of Arts and Sciences, Charlottesville, Virginia 22904, United States
| | - Andrew W.L. Kinman
- Department
of Chemistry, University of Virginia College
of Arts and Sciences, Charlottesville, Virginia 22904, United States
| | - Parastoo Anbaei
- Department
of Chemistry, University of Virginia College
of Arts and Sciences, Charlottesville, Virginia 22904, United States
| | - Benjamin D. Groff
- Department
of Chemistry, University of Virginia College
of Arts and Sciences, Charlottesville, Virginia 22904, United States
| | - Stephanie J. Melchor
- Carter
Immunology Center, University of Virginia, Charlottesville, Virginia 22904, United States
- Department
of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia 22904, United States
| | - John R. Lukens
- Carter
Immunology Center, University of Virginia, Charlottesville, Virginia 22904, United States
- Department
of Neuroscience and Center for Brain Immunology and Glia (BIG), University of Virginia School of Medicine, Charlottesville, Virginia 22904, United States
| | - Ashley E. Ross
- Department
of Chemistry, University of Cincinnati, Cincinnati, Ohio 45220, United States
| | - Rebecca R. Pompano
- Department
of Chemistry, University of Virginia College
of Arts and Sciences, Charlottesville, Virginia 22904, United States
- Carter
Immunology Center, University of Virginia, Charlottesville, Virginia 22904, United States
- Department
of Biomedical Engineering, University of
Virginia School of Engineering and Applied Sciences, Charlottesville, Virginia 22904, United States
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6
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Pedreño-Lopez N, Ricciardi MJ, Rosen BC, Song G, Andrabi R, Burton DR, Rakasz EG, Watkins DI. An Automated Fluorescence-Based Method to Isolate Bone Marrow-Derived Plasma Cells from Rhesus Macaques Using SIVmac239 SOSIP.664. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:781-790. [PMID: 32953929 PMCID: PMC7476808 DOI: 10.1016/j.omtm.2020.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/31/2020] [Indexed: 11/20/2022]
Abstract
Simian immunodeficiency virus (SIV) infection of Indian rhesus macaques (RMs) is one of the best-characterized animal models for human immunodeficiency virus (HIV) infection. Monoclonal antibodies (mAbs) have shown promise for prevention and treatment of HIV infection. However, it has been difficult to isolate mAbs that potently neutralize the highly pathogenic SIVmac239 strain. This has been largely due to the low frequency of circulating B cells encoding neutralizing Abs. Here we describe a novel technique to isolate mAbs directly from bone marrow-derived, Ab-secreting plasma cells. We employed an automated micromanipulator to isolate single SIVmac239 SOSIP.664-specific plasma cells from the bone marrow of a SIVmac239-infected RM with serum neutralization titers against SIVmac239. After picking plasma cells, we obtained 44 paired Ab sequences. Ten of these mAbs were SIV specific. Although none of these mAbs neutralized SIVmac239, three mAbs completely neutralized the related SIVmac316 strain. The majority of these mAbs bound to primary rhesus CD4+ T cells infected with SIVmac239 and induced Ab-dependent cellular cytotoxicity. This method is a first step in successful isolation of antigen-specific bone marrow-derived plasma cells from RMs.
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Affiliation(s)
- Nuria Pedreño-Lopez
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA
- Corresponding author: Nuria Pedreño-Lopez, Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA.
| | - Michael J. Ricciardi
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA
| | - Brandon C. Rosen
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA
- Medical Scientist Training Program, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Eva G. Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - David I. Watkins
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA
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7
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Liu L, Chen D, Wang J, Chen J. Advances of Single-Cell Protein Analysis. Cells 2020; 9:E1271. [PMID: 32443882 PMCID: PMC7290353 DOI: 10.3390/cells9051271] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Proteins play a significant role in the key activities of cells. Single-cell protein analysis provides crucial insights in studying cellular heterogeneities. However, the low abundance and enormous complexity of the proteome posit challenges in analyzing protein expressions at the single-cell level. This review summarizes recent advances of various approaches to single-cell protein analysis. We begin by discussing conventional characterization approaches, including fluorescence flow cytometry, mass cytometry, enzyme-linked immunospot assay, and capillary electrophoresis. We then detail the landmark advances of microfluidic approaches for analyzing single-cell protein expressions, including microfluidic fluorescent flow cytometry, droplet-based microfluidics, microwell-based assay (microengraving), microchamber-based assay (barcoding microchips), and single-cell Western blotting, among which the advantages and limitations are compared. Looking forward, we discuss future research opportunities and challenges for multiplexity, analyte, throughput, and sensitivity of the microfluidic approaches, which we believe will prompt the research of single-cell proteins such as the molecular mechanism of cell biology, as well as the clinical applications for tumor treatment and drug development.
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Affiliation(s)
- Lixing Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Sannier G, Dubé M, Kaufmann DE. Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity. Front Microbiol 2020; 11:297. [PMID: 32194526 PMCID: PMC7064469 DOI: 10.3389/fmicb.2020.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
The need for definitive answers probably explains our natural tendency to seek simplicity. The reductionist “bulk” approach, in which a mean behavior is attributed to a heterogeneous cell population, fulfills this need by considerably helping the conceptualization of complex biological processes. However, the limits of this methodology are becoming increasingly clear as models seek to explain biological events occurring in vivo, where heterogeneity is the rule. Research in the HIV-1 field is no exception: the challenges encountered in the development of preventive and curative anti-HIV-1 strategies may well originate in part from inadequate assumptions built on bulk technologies, highlighting the need for new perspectives. The emergence of diverse single-cell technologies set the stage for potential breakthrough discoveries, as heterogeneous processes can now be investigated with an unprecedented depth in topics as diverse as HIV-1 tropism, dynamics of the replication cycle, latency, viral reservoirs and immune control. In this review, we summarize recent advances in the HIV-1 field made possible by single-cell technologies, and contextualize their importance.
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Affiliation(s)
- Gérémy Sannier
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Consortium for HIV/AIDS Vaccine Development (Scripps CHAVD), La Jolla, CA, United States
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9
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Abstract
The existence of cellular heterogeneity and its central relevance to biological phenomena provides a strong rationale for a need for analytical methods that enable analysis at the single-cell level. Analysis of the genome and transcriptome is possible at the single-cell level, but the comprehensive interrogation of the proteome with this level of resolution remains challenging. Single-cell protein analysis tools are advancing rapidly, however, and providing insights into collections of proteins with great relevance to cell and disease biology. Here, we review single-cell protein analysis technologies and assess their advantages and limitations. The emerging technologies presented have the potential to reveal new insights into tumour heterogeneity and therapeutic resistance, elucidate mechanisms of immune response and immunotherapy, and accelerate drug discovery.
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10
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Chen Z, Chen JJ, Fan R. Single-Cell Protein Secretion Detection and Profiling. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:431-449. [PMID: 30978293 DOI: 10.1146/annurev-anchem-061318-115055] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Secreted proteins play important roles in mediating various biological processes such as cell-cell communication, differentiation, migration, and homeostasis at the population or tissue level. Here, we review bioanalytical technologies and devices for detecting protein secretions from single cells. We begin by discussing conventional approaches followed by detailing the latest advances in microengineered systems for detecting single-cell protein secretions with an emphasis on multiplex measurement. These platforms include droplet microfluidics, micro-/nanowell-based assays, and microchamber-based assays, among which the advantages and limitations are compared. Microscale systems also enable the tracking of protein secretion dynamics in single cells, further empowering the study of the cell-cell communication network. Looking forward, we discuss the remaining challenges and future opportunities that will transform basic research of cellular secretion functions at the systems level and the clinical applications for immune monitoring and cancer treatment.
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Affiliation(s)
- Zhuo Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
| | - Jonathan J Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
- Yale Cancer Center, Yale Stem Cell Center, Human and Translational Immunology Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
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11
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Kirpach J, Colone A, Bürckert JP, Faison WJ, Dubois ARSX, Sinner R, Reye AL, Muller CP. Detection of a Low Level and Heterogeneous B Cell Immune Response in Peripheral Blood of Acute Borreliosis Patients With High Throughput Sequencing. Front Immunol 2019; 10:1105. [PMID: 31156648 PMCID: PMC6532064 DOI: 10.3389/fimmu.2019.01105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 04/30/2019] [Indexed: 01/08/2023] Open
Abstract
The molecular diagnosis of acute Borreliosis is complicated and better strategies to improve the diagnostic processes are warranted. High Throughput Sequencing (HTS) of human B cell repertoires after e.g., Dengue virus infection or influenza vaccination revealed antigen-associated “CDR3 signatures” which may have the potential to support diagnosis in infectious diseases. The human B cell immune response to Borrelia burgdorferi sensu lato—the causative agent of Borreliosis—has mainly been studied at the antibody level, while less attention has been given to the cellular part of the humoral immune response. There are indications that Borrelia actively influence the B cell immune response and that it is therefore not directly comparable to responses induced by other infections. The main goal of this study was to identify B cell features that could be used to support diagnosis of Borreliosis. Therefore, we characterized the B cell immune response in these patients by combining multicolor flow cytometry, single Borrelia-reactive B cell receptor (BCR) sequencing, and B cell repertoire deep sequencing. Our phenotyping experiments showed, that there is no significant difference between B cell subpopulations of acute Borreliosis patients and controls. BCR sequences from individual epitope-reactive B cells had little in common between each other. HTS showed, however, a higher complementarity determining region 3 (CDR3) amino acid (aa) sequence overlap between samples from different timepoints in patients as compared to controls. This indicates, that HTS is sensitive enough to detect ongoing B cell immune responses in these patients. Although each individual's repertoire was dominated by rather unique clones, clustering of bulk BCR repertoire sequences revealed a higher overlap of IgG BCR repertoire sequences between acute patients than controls. Even if we have identified a few Borrelia-associated CDR3aa sequences, they seem to be rather unique for each patient and therefore not suitable as biomarkers.
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Affiliation(s)
- Josiane Kirpach
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Alessia Colone
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Jean-Philippe Bürckert
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - William J Faison
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Axel R S X Dubois
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Regina Sinner
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Anna L Reye
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Claude P Muller
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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12
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Therapeutic Antibody Discovery in Infectious Diseases Using Single-Cell Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:89-102. [PMID: 29943298 DOI: 10.1007/978-981-13-0502-3_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Since the discovery of mouse hybridoma technology by Kohler and Milstein in 1975, significant progress has been made in monoclonal antibody production. Advances in B cell immortalization and phage display technologies have generated a myriad of valuable monoclonal antibodies for diagnosis and treatment. Technological breakthroughs in various fields of 'omics have shed crucial insights into cellular heterogeneity of a biological system in which the functional individuality of a single cell must be considered. Based on this important concept, remarkable discoveries in single-cell analysis have made in identifying and isolating functional B cells that produce beneficial therapeutic monoclonal antibodies. In this review, we will discuss three traditional methods of antibody discovery. Recent technological platforms for single-cell antibody discovery will be reviewed. We will discuss the application of the single-cell analysis in finding therapeutic antibodies for human immunodeficiency virus and emerging Zika arbovirus.
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13
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Abstract
Staphylococcus aureus causes severe disease in humans for which no licensed vaccine exists. A novel vaccine is in development that targets multiple elements of the bacteria since single-component vaccines have not shown efficacy to date. How these multiple components alter the immune response raised by the vaccine is not well studied. We found that the addition of two protein components did not alter substantially the antibody responses raised with respect to function or mobilization of B cells. There was also not a substantial change in the activity of T cells, another part of the adaptive response. This study showed that protection by this vaccine may be mediated primarily by antibody protection. Staphylococcus aureus causes severe disease in humans for which no licensed vaccine exists. A novel S. aureus vaccine (SA4Ag) is in development, targeting the capsular polysaccharides (CPs) and two virulence-associated surface proteins. Vaccine-elicited antibody responses to CPs are efficacious against serious infection by other encapsulated bacteria. Studies of natural S. aureus infection have also shown a role for TH17 and/or TH1 responses in protection. Single-antigen vaccines, including CPs, have not been effective against S. aureus; a multiantigen vaccine approach is likely required. However, the impact of addition of protein antigens on the immune response to CPs has not been studied. Here, the immune response induced by a bivalent CP conjugate vaccine (to model the established mechanism of action of vaccine-induced protection against Gram-positive pathogens) was compared to the response induced by SA4Ag, which contains both CP conjugates and protein antigens, in cynomolgus macaques. Microengraving, flow cytometry, opsonophagocytic assays, and Luminex technology were used to analyze the B-cell, T-cell, functional antibody, and innate immune responses. Both the bivalent CP vaccine and SA4Ag induced cytokine production from naive cells and antigen-specific memory B-cell and functional antibody responses. Increases in levels of circulating, activated T cells were not apparent following vaccination, nor was a TH17 or TH1 response evident. However, our data are consistent with a vaccine-induced recruitment of T follicular helper (TFH) cells to lymph nodes. Collectively, these data suggest that the response to SA4Ag is primarily mediated by B cells and antibodies that abrogate important S. aureus virulence mechanisms. IMPORTANCEStaphylococcus aureus causes severe disease in humans for which no licensed vaccine exists. A novel vaccine is in development that targets multiple elements of the bacteria since single-component vaccines have not shown efficacy to date. How these multiple components alter the immune response raised by the vaccine is not well studied. We found that the addition of two protein components did not alter substantially the antibody responses raised with respect to function or mobilization of B cells. There was also not a substantial change in the activity of T cells, another part of the adaptive response. This study showed that protection by this vaccine may be mediated primarily by antibody protection.
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14
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Patil SU, Shreffler WG. Novel vaccines: Technology and development. J Allergy Clin Immunol 2018; 143:844-851. [PMID: 29970235 DOI: 10.1016/j.jaci.2018.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 05/04/2018] [Accepted: 05/25/2018] [Indexed: 11/17/2022]
Abstract
The development and widespread use of vaccines, which are defined by the World Health Organization as "biological preparations that improve immunity to a particular disease," represents one of the most significant strides in medicine. Vaccination was first applied to reduce mortality and morbidity from infectious diseases. The World Health Organization estimates that vaccines prevent 2 to 3 million human deaths annually, and these numbers would increase by at least 6 million if all children received the recommended vaccination schedule. However, the origins of allergen immunotherapy share the same intellectual paradigm, and subsequent innovations in vaccine technology have been applied beyond the prevention of infection, including in the treatment of cancer and allergic diseases. This review will focus on how new and more rational approaches to vaccine development use novel biotechnology, target new mechanisms, and shape the immune system response, with an emphasis on discoveries that have direct translational relevance to the treatment of allergic diseases.
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Affiliation(s)
- Sarita U Patil
- Department of Pediatrics, Division of Allergy and Immunology, Massachusetts General Hospital, Boston, Mass; Department of Medicine, Division of Rheumatology, Allergy, and Immunology, Center for Inflammatory and Immunological Diseases, Harvard Medical School, Boston, Mass.
| | - Wayne G Shreffler
- Department of Pediatrics, Division of Allergy and Immunology, Massachusetts General Hospital, Boston, Mass; Department of Medicine, Division of Rheumatology, Allergy, and Immunology, Center for Inflammatory and Immunological Diseases, Harvard Medical School, Boston, Mass
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15
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Correa I, Ilieva KM, Crescioli S, Lombardi S, Figini M, Cheung A, Spicer JF, Tutt ANJ, Nestle FO, Karagiannis P, Lacy KE, Karagiannis SN. Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells. Front Immunol 2018; 9:493. [PMID: 29628923 PMCID: PMC5876289 DOI: 10.3389/fimmu.2018.00493] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/26/2018] [Indexed: 11/30/2022] Open
Abstract
Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.
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Affiliation(s)
- Isabel Correa
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom
| | - Kristina M Ilieva
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom
| | - Silvia Crescioli
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom
| | - Sara Lombardi
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Mariangela Figini
- Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Anthony Cheung
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom
| | - James F Spicer
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Andrew N J Tutt
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom.,Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Frank O Nestle
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Immunology and Inflammation Therapeutic Research Area, Sanofi US, Cambridge, MA, United States
| | - Panagiotis Karagiannis
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Department of Oncology, Haematology and Stem Cell Transplantation, University Hospital of Hamburg Eppendorf, Hamburg, Germany
| | - Katie E Lacy
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Sophia N Karagiannis
- St. John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, King's College London, London, United Kingdom.,Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, London, United Kingdom
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16
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Park H, Kim H, Doh J. Multifunctional Microwell Arrays for Single Cell Level Functional Analysis of Lymphocytes. Bioconjug Chem 2017; 29:672-679. [DOI: 10.1021/acs.bioconjchem.7b00620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Jia B, McNeil LK, Dupont CD, Tsioris K, Barry RM, Scully IL, Ogunniyi AO, Gonzalez C, Pride MW, Gierahn TM, Liberator PA, Jansen KU, Love JC. Longitudinal multiparameter single-cell analysis of macaques immunized with pneumococcal protein-conjugated or unconjugated polysaccharide vaccines reveals distinct antigen specific memory B cell repertoires. PLoS One 2017; 12:e0183738. [PMID: 28910279 PMCID: PMC5598952 DOI: 10.1371/journal.pone.0183738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 08/10/2017] [Indexed: 12/24/2022] Open
Abstract
Background The efficacy of protein-conjugated pneumococcal polysaccharide vaccines has been well characterized for children. The level of protection conferred by unconjugated polysaccharide vaccines remains less clear, particularly for elderly individuals who have had prior antigenic experience through immunization with unconjugated polysaccharide vaccines or natural exposure to Streptococcus pneumoniae. Methods We compared the magnitude, diversity and genetic biases of antigen-specific memory B cells in two groups of adult cynomolgus macaques that were immunized with a 7-valent conjugated vaccine and boosted after five years with either a 13-valent pneumococcal polysaccharide conjugate vaccine (13vPnC) or a 23-valent unconjugated pneumococcal polysaccharide vaccine (23vPS) using microengraving (a single-cell analysis method) and single-cell RT-PCR. Results Seven days after boosting, the mean frequency of antigen-specific memory B cells was significantly increased in macaques vaccinated with 13vPnC compared to those receiving 23vPS. The 13vPnC-vaccinated macaques also exhibited a more even distribution of antibody specificities to four polysaccharides in the vaccine (PS4, 6B, 14, 23F) that were examined. However, single-cell analysis of the antibody variable region sequences from antigen-specific B cells elicited by unconjugated and conjugated vaccines indicated that both the germline gene segments forming the heavy chains and the average lengths of the Complementary Determining Region 3 (CDR3) were similar. Conclusions Our results confirm that distinctive differences can manifest between antigen-specific memory B cell repertoires in nonhuman primates immunized with conjugated and unconjugated pneumococcal polysaccharide vaccines. The study also supports the notion that the conjugated vaccines have a favorable profile in terms of both the frequency and breadth of the anamnestic response among antigen-specific memory B cells.
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Affiliation(s)
- Bin Jia
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lisa K. McNeil
- Pfizer Vaccine Research and Early Development, Pearl River, New York, United States of America
| | - Christopher D. Dupont
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Konstantinos Tsioris
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rachel M. Barry
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ingrid L. Scully
- Pfizer Vaccine Research and Early Development, Pearl River, New York, United States of America
| | - Adebola O. Ogunniyi
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Christopher Gonzalez
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Michael W. Pride
- Pfizer Vaccine Research and Early Development, Pearl River, New York, United States of America
| | - Todd M. Gierahn
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul A. Liberator
- Pfizer Vaccine Research and Early Development, Pearl River, New York, United States of America
| | - Kathrin U. Jansen
- Pfizer Vaccine Research and Early Development, Pearl River, New York, United States of America
| | - J. Christopher Love
- Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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18
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Carbonetti S, Oliver BG, Vigdorovich V, Dambrauskas N, Sack B, Bergl E, Kappe SHI, Sather DN. A method for the isolation and characterization of functional murine monoclonal antibodies by single B cell cloning. J Immunol Methods 2017; 448:66-73. [PMID: 28554543 DOI: 10.1016/j.jim.2017.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/25/2017] [Accepted: 05/25/2017] [Indexed: 01/21/2023]
Abstract
Monoclonal antibody technologies have enabled dramatic advances in immunology, the study of infectious disease, and modern medicine over the past 40years. However, many monoclonal antibody discovery procedures are labor- and time-intensive, low efficiency, and expensive. Here we describe an optimized mAb discovery platform for the rapid and efficient isolation, cloning and characterization of monoclonal antibodies in murine systems. In this platform, antigen-binding splenic B cells from immunized mice are isolated by FACS and cocultured with CD40L positive cells to induce proliferation and mAb production. After 12days of coculture, cell culture supernatants are screened for antigen, and IgG positivity and RNA is isolated for reverse-transcription. Positive-well cDNA is then amplified by PCR and the resulting amplicons can be cloned into ligation-independent expression vectors, which are then used directly to transfect HEK293 cells for recombinant antibody production. After 4days of growth, conditioned medium can be screened using biolayer interferometry for antigen binding and affinity measurements. Using this method, we were able to isolate six unique, functional monoclonal antibodies against an antigen of the human malaria parasite Plasmodium falciparum. Importantly, this method incorporates several important advances that circumvent the need for single-cell PCR, restriction cloning, and large scale protein production, and can be applied to a wide array of protein antigens.
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Affiliation(s)
- Sara Carbonetti
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA
| | - Brian G Oliver
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA
| | - Vladimir Vigdorovich
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA
| | - Nicholas Dambrauskas
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA
| | - Brandon Sack
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA
| | - Emilee Bergl
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA
| | - Stefan H I Kappe
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA
| | - D Noah Sather
- Center for Infectious Disease Research (formerly Seattle BioMed), Seattle, WA, USA.
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19
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Ross AE, Belanger MC, Woodroof JF, Pompano RR. Spatially resolved microfluidic stimulation of lymphoid tissue ex vivo. Analyst 2017; 142:649-659. [PMID: 27900374 PMCID: PMC7863610 DOI: 10.1039/c6an02042a] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The lymph node is a structurally complex organ of the immune system, whose dynamic cellular arrangements are thought to control much of human health. Currently, no methods exist to precisely stimulate substructures within the lymph node or analyze local stimulus-response behaviors, making it difficult to rationally design therapies for inflammatory disease. Here we describe a novel integration of live lymph node slices with a microfluidic system for local stimulation. Slices maintained the cellular organization of the lymph node while making its core experimentally accessible. The 3-layer polydimethylsiloxane device consisted of a perfusion chamber stacked atop stimulation ports fed by underlying microfluidic channels. Fluorescent dextrans similar in size to common proteins, 40 and 70 kDa, were delivered to live lymph node slices with 284 ± 9 μm and 202 ± 15 μm spatial resolution, respectively, after 5 s, which is sufficient to target functional zones of the lymph node. The spread and quantity of stimulation were controlled by varying the flow rates of delivery; these were predictable using a computational model of isotropic diffusion and convection through the tissue. Delivery to two separate regions simultaneously was demonstrated, to mimic complex intercellular signaling. Delivery of a model therapeutic, glucose-conjugated albumin, to specific regions of the lymph node indicated that retention of the drug was greater in the B-cell zone than in the T-cell zone. Together, this work provides a novel platform, the lymph node slice-on-a-chip, to target and study local events in the lymph node and to inform the development of new immunotherapeutics.
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Affiliation(s)
- Ashley E Ross
- University of Virginia, Dept. of Chemistry, PO Box 400319, McCormick Rd, Charlottesville, VA 22904, USA.
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20
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Generation of Long-Lived Bone Marrow Plasma Cells Secreting Antibodies Specific for the HIV-1 gp41 Membrane-Proximal External Region in the Absence of Polyreactivity. J Virol 2016; 90:8875-90. [PMID: 27466419 PMCID: PMC5021391 DOI: 10.1128/jvi.01089-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED An effective preventive vaccine is highly sought after in order to stem the current HIV-1 pandemic. Both conservation of contiguous gp41 membrane-proximal external region (MPER) amino acid sequences across HIV-1 clades and the ability of anti-MPER broadly neutralizing antibodies (BNAbs) to block viral hemifusion/fusion establish the MPER as a prime vaccination target. In earlier studies, we described the development of an MPER vaccine formulation that takes advantage of liposomes to array the MPER on a lipid bilayer surface, paralleling its native configuration on the virus membrane while also incorporating molecular adjuvant and CD4 T cell epitope cargo. Here we demonstrate that several immunizations with MPER/liposomes induce high levels of bone marrow long-lived plasma cell (LLPC) antibody production. Single-cell immunoglobulin gene retrieval analysis shows that these plasma cells are derived from a germ line repertoire of B cells with a diverse representation of immunoglobulin genes, exhibiting antigen-driven positive selection. Characterization of LLPC recombinant monoclonal antibodies (rMAbs) indicates that antigen recognition is achieved through convergence on a common epitopic focus by utilizing various complementarity-determining region H3 (CDRH3) lengths. Importantly, the vast majority of rMAbs produced from these cells lack polyreactivity yet manifest antigen specificity in the context of lipids, shaping MPER-specific paratopes through selective pressure. Taken together, these findings demonstrate that the MPER is a vaccine target with minimal risk of generating off-target autoimmunity. IMPORTANCE A useful vaccine must generate desired long-term, antigen-specific antibody responses devoid of polyreactivity or autoreactivity. The common polyreactive features of some HIV-1 BNAbs have raised concern about elicitation of anti-MPER antibodies. Utilizing single-LLPC repertoire analysis and biophysical characterization of anti-MPER rMAbs, we show that their fine specificities require a structural fitness of the antibody combining site involving heavy and light chain variable domains shaped by somatic hypermutation and affinity maturation of B cells in the germinal center. Perhaps more importantly, our results demonstrate that the majority of MPER-specific antibodies are not inherently polyspecific and/or autoreactive, suggesting that polyreactivity of MPER-specific antibodies is separable from their antigen specificity.
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21
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Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JNH, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC. Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integr Biol (Camb) 2015; 7:1587-97. [PMID: 26481611 PMCID: PMC4754972 DOI: 10.1039/c5ib00169b] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
West Nile virus (WNV) infection is an emerging mosquito-borne disease that can lead to severe neurological illness and currently has no available treatment or vaccine. Using microengraving, an integrated single-cell analysis method, we analyzed a cohort of subjects infected with WNV - recently infected and post-convalescent subjects - and efficiently identified four novel WNV neutralizing antibodies. We also assessed the humoral response to WNV on a single-cell and repertoire level by integrating next generation sequencing (NGS) into our analysis. The results from single-cell analysis indicate persistence of WNV-specific memory B cells and antibody-secreting cells in post-convalescent subjects. These cells exhibited class-switched antibody isotypes. Furthermore, the results suggest that the antibody response itself does not predict the clinical severity of the disease (asymptomatic or symptomatic). Using the nucleotide coding sequences for WNV-specific antibodies derived from single cells, we revealed the ontogeny of expanded WNV-specific clones in the repertoires of recently infected subjects through NGS and bioinformatic analysis. This analysis also indicated that the humoral response to WNV did not depend on an anamnestic response, due to an unlikely previous exposure to the virus. The innovative and integrative approach presented here to analyze the evolution of neutralizing antibodies from natural infection on a single-cell and repertoire level can also be applied to vaccine studies, and could potentially aid the development of therapeutic antibodies and our basic understanding of other infectious diseases.
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Affiliation(s)
- Konstantinos Tsioris
- Department of Chemical Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Bldg. 76-253, Cambridge, MA 02139, USA.
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22
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Gallerano D, Cabauatan CR, Sibanda EN, Valenta R. HIV-Specific Antibody Responses in HIV-Infected Patients: From a Monoclonal to a Polyclonal View. Int Arch Allergy Immunol 2015; 167:223-41. [PMID: 26414324 DOI: 10.1159/000438484] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
HIV infections represent a major global health threat, affecting more than 35 million individuals worldwide. High infection rates and problems associated with lifelong antiretroviral treatment emphasize the need for the development of prophylactic and therapeutic immune intervention strategies. It is conceivable that insights for the design of new immunogens capable of eliciting protective immune responses may come from the analysis of HIV-specific antibody responses in infected patients. Using sophisticated technologies, several monoclonal neutralizing antibodies were isolated from HIV-infected individuals. However, the majority of polyclonal antibody responses found in infected patients are nonneutralizing. Comprehensive analyses of the molecular targets of HIV-specific antibody responses identified that during natural infection antibodies are mainly misdirected towards gp120 epitopes outside of the CD4-binding site and against regions and proteins that are not exposed on the surface of the virus. We therefore argue that vaccines aiming to induce protective responses should include engineered immunogens, which are capable of focusing the immune response towards protective epitopes.
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Affiliation(s)
- Daniela Gallerano
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
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23
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Ozkumur AY, Goods BA, Love JC. Development of a High-Throughput Functional Screen Using Nanowell-Assisted Cell Patterning. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4643-50. [PMID: 26121321 PMCID: PMC4754792 DOI: 10.1002/smll.201500674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/30/2015] [Indexed: 05/04/2023]
Abstract
Living-cell-based screens can facilitate lead discovery of functional therapeutics of interest. A versatile and scalable method is reported that uses dense arrays of nanowells for imparting defined patterns on monolayers of cells. It is shown that this approach can coordinate a multi-component biological assay by designing and implementing a high-throughput, functional nanoliter-scale neutralization assay to identify neutralizing antibodies against HIV.
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Affiliation(s)
- Ayca Yalcin Ozkumur
- Electrical and Electronics Engineering Department, Bahcesehir University, Istanbul, Turkey
| | - Brittany A. Goods
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts 02139, USA
| | - J. Christopher Love
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research at MIT Cambridge, Massachusetts 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, United States
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24
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Shah KA, Clark JJ, Goods BA, Politano TJ, Mozdzierz NJ, Zimnisky RM, Leeson RL, Love JC, Love KR. Automated pipeline for rapid production and screening of HIV-specific monoclonal antibodies using pichia pastoris. Biotechnol Bioeng 2015; 112:2624-9. [PMID: 26032261 DOI: 10.1002/bit.25663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 12/30/2022]
Abstract
Monoclonal antibodies (mAbs) that bind and neutralize human pathogens have great therapeutic potential. Advances in automated screening and liquid handling have resulted in the ability to discover antigen-specific antibodies either directly from human blood or from various combinatorial libraries (phage, bacteria, or yeast). There remain, however, bottlenecks in the cloning, expression and evaluation of such lead antibodies identified in primary screens that hinder high-throughput screening. As such, "hit-to-lead identification" remains both expensive and time-consuming. By combining the advantages of overlap extension PCR (OE-PCR) and a genetically stable yet easily manipulatable microbial expression host Pichia pastoris, we have developed an automated pipeline for the rapid production and screening of full-length antigen-specific mAbs. Here, we demonstrate the speed, feasibility and cost-effectiveness of our approach by generating several broadly neutralizing antibodies against human immunodeficiency virus (HIV).
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Affiliation(s)
- Kartik A Shah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts
| | - John J Clark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts
| | - Brittany A Goods
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts
| | - Timothy J Politano
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts
| | - Nicholas J Mozdzierz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts
| | - Ross M Zimnisky
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts
| | - Rachel L Leeson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts. .,MIT Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts.
| | - Kerry R Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts. .,MIT Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts.
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25
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Patil SU, Ogunniyi AO, Calatroni A, Tadigotla VR, Ruiter B, Ma A, Moon J, Love J, Shreffler WG. Peanut oral immunotherapy transiently expands circulating Ara h 2-specific B cells with a homologous repertoire in unrelated subjects. J Allergy Clin Immunol 2015; 136:125-134.e12. [PMID: 25985925 PMCID: PMC4494892 DOI: 10.1016/j.jaci.2015.03.026] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/16/2015] [Accepted: 03/12/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Peanut oral immunotherapy (PNOIT) induces persistent tolerance to peanut in a subset of patients and induces specific antibodies that might play a role in clinical protection. However, the contribution of induced antibody clones to clinical tolerance in PNOIT is unknown. OBJECTIVE We hypothesized that PNOIT induces a clonal, allergen-specific B-cell response that could serve as a surrogate for clinical outcomes. METHODS We used a fluorescent Ara h 2 multimer for affinity selection of Ara h 2-specific B cells and subsequent single-cell immunoglobulin amplification. The diversity of related clones was evaluated by means of next-generation sequencing of immunoglobulin heavy chains from circulating memory B cells with 2x250 paired-end sequencing on the Illumina MiSeq platform. RESULTS Expression of class-switched antibodies from Ara h 2-positive cells confirms enrichment for Ara h 2 specificity. PNOIT induces an early and transient expansion of circulating Ara h 2-specific memory B cells that peaks at week 7. Ara h 2-specific sequences from memory cells have rates of nonsilent mutations consistent with affinity maturation. The repertoire of Ara h 2-specific antibodies is oligoclonal. Next-generation sequencing-based repertoire analysis of circulating memory B cells reveals evidence for convergent selection of related sequences in 3 unrelated subjects, suggesting the presence of similar Ara h 2-specific B-cell clones. CONCLUSIONS Using a novel affinity selection approach to identify antigen-specific B cells, we demonstrate that the early PNOIT-induced Ara h 2-specific B-cell receptor repertoire is oligoclonal and somatically hypermutated and shares similar clonal groups among unrelated subjects consistent with convergent selection.
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Affiliation(s)
- Sarita U. Patil
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Food Allergy Center, Massachusetts General Hospital and MassGeneral Hospital for Children
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA
| | - Adebola O. Ogunniyi
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA
| | | | | | - Bert Ruiter
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Food Allergy Center, Massachusetts General Hospital and MassGeneral Hospital for Children
| | - Alex Ma
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - James Moon
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - J.Christopher Love
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard Medical School
| | - Wayne G. Shreffler
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Food Allergy Center, Massachusetts General Hospital and MassGeneral Hospital for Children
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26
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Chan CEZ, Lim APC, MacAry PA, Hanson BJ. The role of phage display in therapeutic antibody discovery. Int Immunol 2014; 26:649-57. [PMID: 25135889 PMCID: PMC7185696 DOI: 10.1093/intimm/dxu082] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phage display involves the expression of selected proteins on the surface of filamentous phage through fusion with phage coat protein, with the genetic sequence packaged within, linking phenotype to genotype selection. When combined with antibody libraries, phage display allows for rapid in vitro selection of antigen-specific antibodies and recovery of their corresponding coding sequence. Large non-immune and synthetic human libraries have been constructed as well as smaller immune libraries based on capturing a single individual’s immune repertoire. This completely in vitro process allows for isolation of antibodies against poorly immunogenic targets as well as those that cannot be obtained by animal immunization, thus further expanding the utility of the approach. Phage antibody display represents the first developed methodology for high throughput screening for human therapeutic antibody candidates. Recently, other methods have been developed for generation of fully human therapeutic antibodies, such as single B-cell screening, next-generation genome sequencing and transgenic mice with human germline B-cell genes. While each of these have their particular advantages, phage display has remained a key methodology for human antibody discovery due its in vitro process. Here, we review the continuing role of this technique alongside other developing technologies for therapeutic antibody discovery.
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Affiliation(s)
- Conrad E Z Chan
- Biological Defence Program, Defense Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Angeline P C Lim
- Biological Defence Program, Defense Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Paul A MacAry
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore Immunology Program, Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Brendon J Hanson
- Biological Defence Program, Defense Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
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