1
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Shilts J, Severin Y, Galaway F, Müller-Sienerth N, Chong ZS, Pritchard S, Teichmann S, Vento-Tormo R, Snijder B, Wright GJ. A physical wiring diagram for the human immune system. Nature 2022; 608:397-404. [PMID: 35922511 PMCID: PMC9365698 DOI: 10.1038/s41586-022-05028-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/28/2022] [Indexed: 12/14/2022]
Abstract
The human immune system is composed of a distributed network of cells circulating throughout the body, which must dynamically form physical associations and communicate using interactions between their cell-surface proteomes1. Despite their therapeutic potential2, our map of these surface interactions remains incomplete3,4. Here, using a high-throughput surface receptor screening method, we systematically mapped the direct protein interactions across a recombinant library that encompasses most of the surface proteins that are detectable on human leukocytes. We independently validated and determined the biophysical parameters of each novel interaction, resulting in a high-confidence and quantitative view of the receptor wiring that connects human immune cells. By integrating our interactome with expression data, we identified trends in the dynamics of immune interactions and constructed a reductionist mathematical model that predicts cellular connectivity from basic principles. We also developed an interactive multi-tissue single-cell atlas that infers immune interactions throughout the body, revealing potential functional contexts for new interactions and hubs in multicellular networks. Finally, we combined targeted protein stimulation of human leukocytes with multiplex high-content microscopy to link our receptor interactions to functional roles, in terms of both modulating immune responses and maintaining normal patterns of intercellular associations. Together, our work provides a systematic perspective on the intercellular wiring of the human immune system that extends from systems-level principles of immune cell connectivity down to mechanistic characterization of individual receptors, which could offer opportunities for therapeutic intervention. Systematic measurements of the interactions between proteins found on the surfaces of human leukocytes provides a global view of the way that immune cells are dynamically connected by receptors.
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Affiliation(s)
- Jarrod Shilts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
| | - Yannik Severin
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | | | - Zheng-Shan Chong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | - Sophie Pritchard
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Sarah Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Roser Vento-Tormo
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK. .,Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, UK.
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2
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Sun H, Hu N, Wang J. Application of Microfluidic Technology in Antibody Screening. Biotechnol J 2022; 17:e2100623. [PMID: 35481726 DOI: 10.1002/biot.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
Specific antibodies are widely used in the biomedical field. Current screening methods for specific antibodies mainly involve hybridoma technology and antibody engineering techniques. However, these technologies suffer from tedious screening processes, long preparation periods, high costs, low efficiency, and a degree of automation, which have become a bottleneck for the screening of specific antibodies. To overcome these difficulties, microfluidics has been developed as a promising technology for high-throughput screening and high purity of antibody. In this review, we provide an overview of the recent advances in microfluidic applications for specific antibody screening. In particular, hybridoma technology and four antibody engineering techniques (including phage display, single B cell antibody screening, antibody expression, and cell-free protein synthesis) based on microfluidics have been introduced, challenges, and the future outlook of these technologies are also discussed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
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3
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Zhang W, Li Q, Jia F, Hu Z, Wei Z. A Microfluidic Chip for Screening and Sequencing of Monoclonal Antibody at a Single-Cell Level. Anal Chem 2021; 93:10099-10105. [PMID: 34264632 DOI: 10.1021/acs.analchem.1c00918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pairing of heavy and light chains of an antibody decides the specificity of monoclonal antibodies (mAbs). Acquisition of the genes encoding variable regions of paired heavy and light chains (VH:VL) is crucial, but it is a labor- and cost-intensive process in traditional methods. The emerging microfluidic chips have brought us to a portal of directly acquiring natively paired VH:VL genes by sequencing single target cells. This study presents a novel method in which all processing steps for acquiring natively paired VH:VL genes from single cells are finished in a single microfluidic chip, not multiple discrete devices. The microfluidic chip performs single-cell trapping/in situ fluorescence examination of antibody specificity/cell lysis/gene amplification all at a single-cell level. By a proof-of-concept validation of efficiently acquiring paired VH:VL genes of anti-CD45 mAbs from single hybridoma cells, the microfluidic chip has been proved capable of trapping/screening/lysing single antibody-secreting cells and performing an on-chip reverse transcription-polymerase chain reaction. The presented method has realized remarkably improved cell loss/human labor/time cost, and more importantly, determinacy of native VH:VL gene pairing, which is one of the most decisive factors of effectiveness for antibody discovery.
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Affiliation(s)
- Weikai Zhang
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Qin Li
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Fei Jia
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zhiyuan Hu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.,School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.,Center for Neuroscience Research, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108 Fujian Province, China.,School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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4
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Szabó G, Antal-Szalmás P, Kerényi A, Pénzes K, Bécsi B, Kappelmayer J. Laboratory Approaches to Test the Function of Antiphospholipid Antibodies. Semin Thromb Hemost 2021; 48:132-144. [PMID: 34261151 DOI: 10.1055/s-0041-1730357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Antiphospholipid syndrome (APS) is a systemic autoimmune disorder caused by the presence of aPLs (antiphospholipid antibodies, i.e., anti-β2-glycoprotein I and anti-cardiolipin). Everyday practice in terms of laboratory diagnostics of APS includes determination of aPLs and well-known functional assays assessing for lupus anticoagulant (LA), in turn using various tests. According to recent guidelines, the recommended method for LA identification or exclusion is based on the Russell Viper Venom test and a sensitive activated partial thromboplastin time assay. Despite the fact that LA can be quantified in laboratory practice in this way, LA is still used as a binary parameter that is just one of the risk factors of thrombosis in APS. As of today, there are no other functional assays to routinely assess the risk of thrombosis in APS. It is well-known that APS patients display a wide range of clinical outcomes although they may express very similar laboratory findings. One way to solve this dilemma, could be if antibodies could be further delineated using more advanced functional tests. Therefore, we review the diagnostic approaches to test the function of aPLs. We further discuss how thrombin generation assays, and rotational thromboelastometry tests can be influenced by LA, and how experimental methods, such as flow cytometric platelet activation, surface plasmon resonance, or nano differential scanning fluorimetry can bring us closer to the puzzling interaction of aPLs with platelets as well as with their soluble protein ligand. These novel approaches may eventually enable better characterization of aPL, and also provide a better linkage to APS pathophysiology.
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Affiliation(s)
- Gábor Szabó
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Thrombosis, Haemostasis and Vascular Biology Programme, Kálmán Laki Doctoral School, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Antal-Szalmás
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Adrienne Kerényi
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Krisztina Pénzes
- Division of Medical Laboratory Sciences, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Bálint Bécsi
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Kappelmayer
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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5
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Autheman D, Crosnier C, Clare S, Goulding DA, Brandt C, Harcourt K, Tolley C, Galaway F, Khushu M, Ong H, Romero-Ramirez A, Duffy CW, Jackson AP, Wright GJ. An invariant Trypanosoma vivax vaccine antigen induces protective immunity. Nature 2021; 595:96-100. [PMID: 34040257 DOI: 10.1038/s41586-021-03597-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023]
Abstract
Trypanosomes are protozoan parasites that cause infectious diseases, including African trypanosomiasis (sleeping sickness) in humans and nagana in economically important livestock1,2. An effective vaccine against trypanosomes would be an important control tool, but the parasite has evolved sophisticated immunoprotective mechanisms-including antigenic variation3-that present an apparently insurmountable barrier to vaccination. Here we show, using a systematic genome-led vaccinology approach and a mouse model of Trypanosoma vivax infection4, that protective invariant subunit vaccine antigens can be identified. Vaccination with a single recombinant protein comprising the extracellular region of a conserved cell-surface protein that is localized to the flagellum membrane (which we term 'invariant flagellum antigen from T. vivax') induced long-lasting protection. Immunity was passively transferred with immune serum, and recombinant monoclonal antibodies to this protein could induce sterile protection and revealed several mechanisms of antibody-mediated immunity, including a major role for complement. Our discovery identifies a vaccine candidate for an important parasitic disease that has constrained socioeconomic development in countries in sub-Saharan Africa5, and provides evidence that highly protective vaccines against trypanosome infections can be achieved.
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Affiliation(s)
- Delphine Autheman
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Cécile Crosnier
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Simon Clare
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, UK
| | - David A Goulding
- Electron and Advanced Light Microscopy, Wellcome Sanger Institute, Hinxton, UK
| | - Cordelia Brandt
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Malhar Khushu
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Han Ong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | | | - Craig W Duffy
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Andrew P Jackson
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK.
- Department of Biology, University of York, York, UK.
- Hull York Medical School, University of York, York, UK.
- York Biomedical Research Institute, University of York, York, UK.
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6
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Himananto O, Yoohat K, Danwisetkanjana K, Kumpoosiri M, Rukpratanporn S, Theppawong Y, Phuengwas S, Makornwattana M, Charlermroj R, Karoonuthaisiri N, Thummabenjapone P, Kositcharoenkul N, Gajanandana O. Double antibody pairs sandwich-ELISA (DAPS-ELISA) detects Acidovorax citrulli serotypes with broad coverage. PLoS One 2020; 15:e0237940. [PMID: 32853255 PMCID: PMC7451559 DOI: 10.1371/journal.pone.0237940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/05/2020] [Indexed: 11/18/2022] Open
Abstract
Acidovorax citrulli, a seedborne bacterium and quarantine pest, causes the devastating bacterial fruit blotch disease in cucurbit plants. Immunological assays such as ELISA are widely used in routine field inspections for this bacterium. However, to the best of our knowledge, none of the currently available monoclonal antibodies (MAbs) can detect all common A. citrulli strains. We therefore aimed to produce a panel of MAbs and to develop an ELISA-based method capable of detecting all A. citrulli strains. We used a high-throughput bead array technique to screen and characterize A. citrulli-specific MAbs produced from hybridoma clones. The hybridoma library was simultaneously screened against five A. citrulli strains (PSA, KK9, SQA, SQB and P) and the closely related bacterium, Delftia acidovorans. Three MAbs exhibiting different binding patterns to A. citrulli were used to develop an ELISA-based method called “double antibody pairs sandwich ELISA” (DAPS-ELISA). DAPS-ELISA employing mixtures of MAbs was able to specifically detect all 16 A. citrulli strains tested without cross-reactivity with other bacteria. By contrast, our previously developed MAb capture-sandwich ELISA (MC-sELISA) and a commercial test kit detected only 15 and 14 of 16 strains, respectively. The sensitivity of the DAPS-ELISA ranged from 5×105 to 1×106 CFU/mL, while those of the MC-sELISA and the commercial test kit ranged from 5×104 to 1×107 CFU/mL and 5×104 to 5×105 CFU/mL, respectively. DAPS-ELISA thus represents an alternative method enabling rapid, accurate, and inexpensive detection of all A. citrulli strains. The method can be applied to seed testing prior to planting as well as to routine field inspections.
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Affiliation(s)
- Orawan Himananto
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
- * E-mail:
| | - Kirana Yoohat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Kannawat Danwisetkanjana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Mallika Kumpoosiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sombat Rukpratanporn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Yada Theppawong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sudtida Phuengwas
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Manlika Makornwattana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Ratthaphol Charlermroj
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Petcharat Thummabenjapone
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | | | - Oraprapai Gajanandana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
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7
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Paul M, Weller MG. Antibody Screening by Microarray Technology-Direct Identification of Selective High-Affinity Clones. Antibodies (Basel) 2020; 9:E1. [PMID: 31906477 PMCID: PMC7175374 DOI: 10.3390/antib9010001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 01/27/2023] Open
Abstract
The primary screening of hybridoma cells is a time-critical and laborious step during the development of monoclonal antibodies. Often, critical errors occur in this phase, which supports the notion that the generation of monoclonal antibodies with hybridoma technology is difficult to control and hence, a risky venture. We think that it is crucial to improve the screening process to eliminate most of the critical deficits of the conventional approach. With this new microarray-based procedure, several advances could be achieved: Selectivity for excellent binders, high-throughput, reproducible signals, avoidance of misleading avidity (multivalency) effects, and performance of simultaneous competition experiments. The latter can also be used to select clones of desired cross-reactivity properties. In this paper, a model system with two excellent clones against carbamazepine, two weak clones, and blank supernatant containing fetal bovine serum was designed to examine the effectiveness of the new system. The excellent clones could be detected largely independent of the immunoglobulin G (IgG) concentration, which is usually unknown during the clone screening since the determination and subsequent adjustment of the antibody concentration are not feasible in most cases. Furthermore, in this approach, the enrichment, isolation, and purification of IgG for characterization is not necessary. Raw cell culture supernatant can be used directly, even when fetal calf serum (FCS) or other complex media is used. In addition, an improved method for the oriented antibody-immobilization on epoxy-silanized slides is presented. Based on the results of this model system with simulated hybridoma supernatants, we conclude that this approach should be preferable to most other protocols leading to many false positives, causing expensive and lengthy elimination steps to weed out the poor clones.
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Affiliation(s)
| | - Michael G. Weller
- Federal Institute for Materials Research and Testing (BAM), Division 1.5 Protein Analysis, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany;
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8
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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9
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Shembekar N, Hu H, Eustace D, Merten CA. Single-Cell Droplet Microfluidic Screening for Antibodies Specifically Binding to Target Cells. Cell Rep 2019; 22:2206-2215. [PMID: 29466744 PMCID: PMC5842027 DOI: 10.1016/j.celrep.2018.01.071] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/18/2017] [Accepted: 01/24/2018] [Indexed: 11/18/2022] Open
Abstract
Monoclonal antibodies are a main player in modern drug discovery. Many antibody screening formats exist, each with specific advantages and limitations. Nonetheless, it remains challenging to screen antibodies for the binding of cell-surface receptors (the most important class of all drug targets) or for the binding to target cells rather than purified proteins. Here, we present a high-throughput droplet microfluidics approach employing dual-color normalized fluorescence readout to detect antibody binding. This enables us to obtain quantitative data on target cell recognition, using as little as 33 fg of IgG per assay. Starting with an excess of hybridoma cells releasing unspecific antibodies, individual clones secreting specific binders (of target cells co-encapsulated into droplets) could be enriched 220-fold after sorting 80,000 clones in a single experiment. This opens the way for therapeutic antibody discovery, especially since the single-cell approach is in principle also applicable to primary human plasma cells. Binding assay with co-encapsulation of hybridoma and target cell in droplets Signal normalization allows quantitative detection of Ab binding without focusing Droplet sorting for antibody binding shows enrichment of specific hybridoma cells 33 fg of antibody can be detected and up to 80,000 clones can be screened
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Affiliation(s)
- Nachiket Shembekar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, Germany
| | - Hongxing Hu
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, Germany
| | - David Eustace
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, Germany
| | - Christoph A Merten
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, Germany.
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10
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Loreck K, Mitrenga S, Meemken D, Heinze R, Reissig A, Mueller E, Ehricht R, Engemann C, Greiner M. Development of a miniaturized protein microarray as a new serological IgG screening test for zoonotic agents and production diseases in pigs. PLoS One 2019; 14:e0217290. [PMID: 31116794 PMCID: PMC6530865 DOI: 10.1371/journal.pone.0217290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022] Open
Abstract
In order to monitor the occurrence of zoonotic agents in pig herds as well as to improve herd health management, the development of new cost-effective diagnostic methods for pigs is necessary. In this study, a protein microarray-based assay for the simultaneous detection of immunoglobulin G (IgG) antibodies against different zoonotic agents and pathogens causing production diseases in pigs was developed. Therefore, antigens of ten different important swine pathogens (Toxoplasma gondii, Yersinia enterocolitica, Salmonella spp., Trichinella spp., Mycobacterium avium, Hepatitis E virus, Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, the porcine reproductive and respiratory syndrome virus, Influenza A virus) were spotted and covalently immobilized as 'antigen-spots' on microarray chips in order to test pig serum for the occurrence of antibodies. Pig serum was sampled at three German abattoirs and ELISA tests for the different pathogens were conducted with the purpose of creating a panel of reference samples for microarray analysis. To evaluate the accuracy of the antigens on the microarray, receiver operating characteristic (ROC) curve analysis using the ELISA test results as reference was performed for the different antigens. High area under curve values were achieved for the antigens of two zoonotic agents: Toxoplasma gondii (0.91), Yersinia enterocolitica (0.97) and for three production diseases: Actinobacillus pleuropneumoniae (0.77), Mycoplasma hyopneumoniae (0.94) and the porcine reproductive and respiratory syndrome virus (0.87). With the help of the newly developed microarray assay, collecting data on the occurrence of antibodies against zoonotic agents and production diseases in pig herds could be minimized to one measurement, resulting in an efficient screening test.
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Affiliation(s)
- Katharina Loreck
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sylvia Mitrenga
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Diana Meemken
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
| | | | - Annett Reissig
- Leibniz-Institute of Photonic Technology (IPHT), Department for Optical Molecular Diagnostics and Systems Technology, Jena, Germany
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
| | - Elke Mueller
- Leibniz-Institute of Photonic Technology (IPHT), Department for Optical Molecular Diagnostics and Systems Technology, Jena, Germany
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
| | - Ralf Ehricht
- Leibniz-Institute of Photonic Technology (IPHT), Department for Optical Molecular Diagnostics and Systems Technology, Jena, Germany
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
| | | | - Matthias Greiner
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Exposure, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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11
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Segaliny AI, Li G, Kong L, Ren C, Chen X, Wang JK, Baltimore D, Wu G, Zhao W. Functional TCR T cell screening using single-cell droplet microfluidics. LAB ON A CHIP 2018; 18:3733-3749. [PMID: 30397689 PMCID: PMC6279597 DOI: 10.1039/c8lc00818c] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Adoptive T cell transfer, in particular TCR T cell therapy, holds great promise for cancer immunotherapy with encouraging clinical results. However, finding the right TCR T cell clone is a tedious, time-consuming, and costly process. Thus, there is a critical need for single cell technologies to conduct fast and multiplexed functional analyses followed by recovery of the clone of interest. Here, we use droplet microfluidics for functional screening and real-time monitoring of single TCR T cell activation upon recognition of target tumor cells. Notably, our platform includes a tracking system for each clone as well as a sorting procedure with 100% specificity validated by downstream single cell reverse-transcription PCR and sequencing of TCR chains. Our TCR screening prototype will facilitate immunotherapeutic screening and development of T cell therapies.
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MESH Headings
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/metabolism
- Cell Line, Tumor
- Equipment Design
- Humans
- Immunotherapy, Adoptive
- Microfluidic Analytical Techniques/instrumentation
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/analysis
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/metabolism
- Single-Cell Analysis/instrumentation
- Single-Cell Analysis/methods
- T-Lymphocytes/chemistry
- T-Lymphocytes/cytology
- T-Lymphocytes/metabolism
- T-Lymphocytes/transplantation
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Affiliation(s)
- Aude I. Segaliny
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Guideng Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Lingshun Kong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Ci Ren
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Xiaoming Chen
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
| | - Jessica K. Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A
| | - Guikai Wu
- Amberstone Biosciences LLC, Irvine, CA 92617, U.S.A
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, U.S.A
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, U.S.A
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, U.S.A
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, U.S.A
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12
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Verma V, Kaur C, Grover P, Gupta A, Chaudhary VK. Biotin-tagged proteins: Reagents for efficient ELISA-based serodiagnosis and phage display-based affinity selection. PLoS One 2018; 13:e0191315. [PMID: 29360877 PMCID: PMC5779676 DOI: 10.1371/journal.pone.0191315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 01/03/2018] [Indexed: 02/06/2023] Open
Abstract
The high-affinity interaction between biotin and streptavidin has opened avenues for using recombinant proteins with site-specific biotinylation to achieve efficient and directional immobilization. The site-specific biotinylation of proteins carrying a 15 amino acid long Biotin Acceptor Peptide tag (BAP; also known as AviTag) is effected on a specific lysine either by co-expressing the E. coli BirA enzyme in vivo or by using purified recombinant E. coli BirA enzyme in the presence of ATP and biotin in vitro. In this paper, we have designed a T7 promoter-lac operator-based expression vector for rapid and efficient cloning, and high-level cytosolic expression of proteins carrying a C-terminal BAP tag in E. coli with TEV protease cleavable N-terminal deca-histidine tag, useful for initial purification. Furthermore, a robust three-step purification pipeline integrated with well-optimized protocols for TEV protease-based H10 tag removal, and recombinant BirA enzyme-based site-specific in vitro biotinylation is described to obtain highly pure biotinylated proteins. Most importantly, the paper demonstrates superior sensitivities in indirect ELISA with directional and efficient immobilization of biotin-tagged proteins on streptavidin-coated surfaces in comparison to passive immobilization. The use of biotin-tagged proteins through specific immobilization also allows more efficient selection of binders from a phage-displayed naïve antibody library. In addition, for both these applications, specific immobilization requires much less amount of protein as compared to passive immobilization and can be easily multiplexed. The simplified strategy described here for the production of highly pure biotin-tagged proteins will find use in numerous applications, including those, which may require immobilization of multiple proteins simultaneously on a solid surface.
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Affiliation(s)
- Vaishali Verma
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Charanpreet Kaur
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Payal Grover
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Amita Gupta
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail: (VKC); (AG)
| | - Vijay K. Chaudhary
- Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail: (VKC); (AG)
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13
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Haisch C. Raman-based microarray readout: a review. Anal Bioanal Chem 2016; 408:4535-45. [PMID: 26973235 DOI: 10.1007/s00216-016-9444-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/16/2016] [Accepted: 02/23/2016] [Indexed: 11/26/2022]
Abstract
For a quarter of a century, microarrays have been part of the routine analytical toolbox. Label-based fluorescence detection is still the commonest optical readout strategy. Since the 1990s, a continuously increasing number of label-based as well as label-free experiments on Raman-based microarray readout concepts have been reported. This review summarizes the possible concepts and methods and their advantages and challenges. A common label-based strategy is based on the binding of selective receptors as well as Raman reporter molecules to plasmonic nanoparticles in a sandwich immunoassay, which results in surface-enhanced Raman scattering signals of the reporter molecule. Alternatively, capture of the analytes can be performed by receptors on a microarray surface. Addition of plasmonic nanoparticles again leads to a surface-enhanced Raman scattering signal, not of a label but directly of the analyte. This approach is mostly proposed for bacteria and cell detection. However, although many promising readout strategies have been discussed in numerous publications, rarely have any of them made the step from proof of concept to a practical application, let alone routine use. Graphical Abstract Possible realization of a SERS (Surface-Enhanced Raman Scattering) system for microarray readout.
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Affiliation(s)
- Christoph Haisch
- Technische Universität München, Marchioninistrasse 17, 81377, Munich, Germany.
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14
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Szafran AT, Mancini MG, Nickerson JA, Edwards DP, Mancini MA. Use of HCA in subproteome-immunization and screening of hybridoma supernatants to define distinct antibody binding patterns. Methods 2015; 96:75-84. [PMID: 26521976 DOI: 10.1016/j.ymeth.2015.10.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/15/2022] Open
Abstract
Understanding the properties and functions of complex biological systems depends upon knowing the proteins present and the interactions between them. Recent advances in mass spectrometry have given us greater insights into the participating proteomes, however, monoclonal antibodies remain key to understanding the structures, functions, locations and macromolecular interactions of the involved proteins. The traditional single immunogen method to produce monoclonal antibodies using hybridoma technology are time, resource and cost intensive, limiting the number of reagents that are available. Using a high content analysis screening approach, we have developed a method in which a complex mixture of proteins (e.g., subproteome) is used to generate a panel of monoclonal antibodies specific to a subproteome located in a defined subcellular compartment such as the nucleus. The immunofluorescent images in the primary hybridoma screen are analyzed using an automated processing approach and classified using a recursive partitioning forest classification model derived from images obtained from the Human Protein Atlas. Using an ammonium sulfate purified nuclear matrix fraction as an example of reverse proteomics, we identified 866 hybridoma supernatants with a positive immunofluorescent signal. Of those, 402 produced a nuclear signal from which patterns similar to known nuclear matrix associated proteins were identified. Detailed here is our method, the analysis techniques, and a discussion of the application to further in vivo antibody production.
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Affiliation(s)
- Adam T Szafran
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Maureen G Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Jeffrey A Nickerson
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, United States
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States; Department of Immunology & Pathology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States.
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15
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Screening hybridomas for anabolic androgenic steroids by steroid analog antigen microarray. Bioanalysis 2015; 7:1201-9. [PMID: 25973986 DOI: 10.4155/bio.15.67] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Currently, dozens of anabolic androgenic steroids (AAS) are forbidden in the World Anti-Doping Agency Prohibited List, however, despite extensive investigation, there are still lots of AAS without corresponding monoclonal antibodies. RESULTS A steroid analog antigen microarray made up of ten AAS was fabricated to screen the hybridoma and it was found an original unsuccessful clone turned out to be a candidate anti-boldenone antibody, without any cross-reactions with endogenous AAS or 44 different AAS standard reference materials tested. CONCLUSION Our findings suggested that steroid analog antigen microarray could be a promising tool to screen and characterize new applications of antibodies for structure analogs, and this also exhibits the potential to fast identify effective epitopes of hybridomas in a single assay.
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16
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Staudt N, Müller-Sienerth N, Fane-Dremucheva A, Yusaf SP, Millrine D, Wright GJ. A panel of recombinant monoclonal antibodies against zebrafish neural receptors and secreted proteins suitable for wholemount immunostaining. Biochem Biophys Res Commun 2014; 456:527-33. [PMID: 25490391 DOI: 10.1016/j.bbrc.2014.11.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/27/2014] [Indexed: 12/18/2022]
Abstract
Cell surface receptors and secreted proteins play important roles in neural recognition processes, but because their site of action can be a long distance from neuron cell bodies, antibodies that label these proteins are valuable to understand their function. The zebrafish embryo is a popular vertebrate model for neurobiology, but suffers from a paucity of validated antibody reagents. Here, we use the entire ectodomain of neural zebrafish cell surface or secreted proteins expressed in mammalian cells to select monoclonal antibodies to ten different antigens. The antibodies were characterised by Western blotting and the sensitivity of their epitopes to formalin fixation was determined. The rearranged antigen binding regions of the antibodies were amplified and cloned which enabled expression in a recombinant form from a single plasmid. All ten antibodies gave specific staining patterns within formalin-treated embryonic zebrafish brains, demonstrating that this generalised approach is particularly efficient to elicit antibodies that stain native antigen in fixed wholemount tissue. Finally, we show that additional tags can be easily added to the recombinant antibodies for convenient multiplex staining. The antibodies and the approaches described here will help to address the lack of well-defined antibody reagents in zebrafish research.
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Affiliation(s)
- Nicole Staudt
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | | | | | - Shahnaz P Yusaf
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - David Millrine
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Gavin J Wright
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.
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17
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Stagljar I. Editorial for ''advances in OMICs-based disciplines". Biochem Biophys Res Commun 2014; 445:681-682. [PMID: 24691180 DOI: 10.1016/j.bbrc.2014.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Igor Stagljar
- Donnelly Centre, Department of Molecular Genetics, Department of Biochemistry, University of Toronto, 160 College Street, Room 1204, Toronto, Ontario M5S 3E1, Canada.
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