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Kylilis N, Riangrungroj P, Lai HE, Salema V, Fernández LÁ, Stan GBV, Freemont PS, Polizzi KM. Whole-Cell Biosensor with Tunable Limit of Detection Enables Low-Cost Agglutination Assays for Medical Diagnostic Applications. ACS Sens 2019; 4:370-378. [PMID: 30623662 DOI: 10.1021/acssensors.8b01163] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Whole-cell biosensors can form the basis of affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing, but to date the detection of analytes such as proteins that cannot easily diffuse across the cell membrane has been challenging. Here we developed a novel biosensing platform based on cell agglutination using an E. coli whole-cell biosensor surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design to detect a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations using straightforward design rules and a mathematical model. Finally, we re-engineer our whole-cell biosensor for the detection of a medically relevant biomarker by the display of two different nanobodies against human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for field-testing in the developing world, emergency or disaster relief sites, as well as routine medical testing and personalized medicine.
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Affiliation(s)
- Nicolas Kylilis
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pinpunya Riangrungroj
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hung-En Lai
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Valencio Salema
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Cantoblanco UAM, 28049 Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Cantoblanco UAM, 28049 Madrid, Spain
| | - Guy-Bart V. Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Paul S. Freemont
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Karen M. Polizzi
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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Salema V, Fernández LÁ. Escherichia coli surface display for the selection of nanobodies. Microb Biotechnol 2017; 10:1468-1484. [PMID: 28772027 PMCID: PMC5658595 DOI: 10.1111/1751-7915.12819] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022] Open
Abstract
Nanobodies (Nbs) are the smallest functional antibody fragments known in nature and have multiple applications in biomedicine or environmental monitoring. Nbs are derived from the variable segment of camelid heavy chain‐only antibodies, known as VHH. For selection, libraries of VHH gene segments from naïve, immunized animals or of synthetic origin have been traditionally cloned in E. coli phage display or yeast display systems, and clones binding the target antigen recovered, usually from plastic surfaces with the immobilized antigen (phage display) or using fluorescence‐activated cell sorting (FACS; yeast display). This review briefly describes these conventional approaches and focuses on the distinct properties of an E. coli display system developed in our laboratory, which combines the benefits of both phage display and yeast display systems. We demonstrate that E. coli display using an N‐terminal domain of intimin is an effective platform for the surface display of VHH libraries enabling selection of high‐affinity Nbs by magnetic cell sorting and direct selection on live mammalian cells displaying the target antigen on their surface. Flow cytometry analysis of E. coli bacteria displaying the Nbs on their surface allows monitoring of the selection process, facilitates screening, characterization of antigen‐binding clones, specificity, ligand competition and estimation of the equilibrium dissociation constant (KD).
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Affiliation(s)
- Valencio Salema
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Salema V, Mañas C, Cerdán L, Piñero-Lambea C, Marín E, Roovers RC, Van Bergen En Henegouwen PMP, Fernández LÁ. High affinity nanobodies against human epidermal growth factor receptor selected on cells by E. coli display. MAbs 2016; 8:1286-1301. [PMID: 27472381 PMCID: PMC5058628 DOI: 10.1080/19420862.2016.1216742] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Most therapeutic antibodies (Abs) target cell surface proteins on tumor and immune cells. Cloning of Ab gene libraries in E. coli and their display on bacteriophages is commonly used to select novel therapeutic Abs binding target antigens, either purified or expressed on cells. However, the sticky nature of bacteriophages renders phage display selections on cells challenging. We previously reported an E. coli display system for expression of VHHs (i.e., nanobodies, Nbs) on the surface of bacteria and selection of high-affinity clones by magnetic cell sorting (MACS). Here, we demonstrate that E. coli display is also an attractive method for isolation of Nbs against cell surface antigens, such as the epidermal growth factor receptor (EGFR), upon direct selection and screening of Ab libraries on live cells. We employ a whole cell-based strategy using a VHH library obtained by immunization with human tumor cells over-expressing EGFR (i.e., A431), and selection of bacterial clones bound to murine fibroblast NIH-3T3 cells transfected with human EGFR, after depletion of non-specific clones on untransfected cells. This strategy resulted in the isolation of high-affinity Nbs binding distinct epitopes of EGFR, including Nbs competing with the ligand, EGF, as characterized by flow cytometry of bacteria displaying the Nbs and binding assays with purified Nbs using surface plasmon resonance. Hence, our study demonstrates that E. coli display of VHH libraries and selection on cells enables efficient isolation and characterization of high-affinity Nbs against cell surface antigens.
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Affiliation(s)
- Valencio Salema
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Carmen Mañas
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Lidia Cerdán
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Carlos Piñero-Lambea
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Elvira Marín
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
| | - Rob C Roovers
- b Cell Biology, Department of Biology, Science Faculty, Utrecht University , Utrecht , The Netherlands
| | | | - Luis Ángel Fernández
- a Department of Microbial Biotechnology , Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco , Madrid , Spain
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Campuzano S, Salema V, Moreno-Guzmán M, Gamella M, Yáñez-Sedeño P, Fernández L, Pingarrón J. Disposable amperometric magnetoimmunosensors using nanobodies as biorecognition element. Determination of fibrinogen in plasma. Biosens Bioelectron 2014; 52:255-60. [DOI: 10.1016/j.bios.2013.08.055] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/24/2013] [Accepted: 08/28/2013] [Indexed: 01/10/2023]
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Salema V, Marín E, Martínez-Arteaga R, Ruano-Gallego D, Fraile S, Margolles Y, Teira X, Gutierrez C, Bodelón G, Fernández LÁ. Selection of single domain antibodies from immune libraries displayed on the surface of E. coli cells with two β-domains of opposite topologies. PLoS One 2013; 8:e75126. [PMID: 24086454 PMCID: PMC3781032 DOI: 10.1371/journal.pone.0075126] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/08/2013] [Indexed: 01/21/2023] Open
Abstract
Screening of antibody (Ab) libraries by direct display on the surface of E. coli cells is hampered by the presence of the outer membrane (OM). In this work we demonstrate that the native β-domains of EhaA autotransporter and intimin, two proteins from enterohemorrhagic E. coli O157:H7 (EHEC) with opposite topologies in the OM, are effective systems for the display of immune libraries of single domain Abs (sdAbs) from camelids (nanobodies or VHH) on the surface of E. coli K-12 cells and for the selection of high affinity sdAbs using magnetic cell sorting (MACS). We analyzed the capacity of EhaA and intimin β-domains to display individual sdAbs and sdAb libraries obtained after immunization with the extracellular domain of the translocated intimin receptor from EHEC (TirMEHEC). We demonstrated that both systems displayed functional sdAbs on the surface of E. coli cells with little proteolysis and cellular toxicity, although E. coli cells displaying sdAbs with the β-domain of intimin showed higher antigen-binding capacity. Both E. coli display libraries were screened for TirMEHEC binding clones by MACS. High affinity binders were selected by both display systems, although more efficiently with the intimin β-domain. The specificity of the selected clones against TirMEHEC was demonstrated by flow cytometry of E. coli cells, along with ELISA and surface plasmon resonance with purified sdAbs. Finally, we employed the E. coli cell display systems to provide an estimation of the affinity of the selected sdAb by flow cytometry analysis under equilibrium conditions.
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Affiliation(s)
- Valencio Salema
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Elvira Marín
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Rocio Martínez-Arteaga
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - David Ruano-Gallego
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Sofía Fraile
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Yago Margolles
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Xema Teira
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Carlos Gutierrez
- Department of Animal Medicine and Surgery, Veterinary Faculty, Universidad de Las Palmas de Gran Canaria (UPGC), Las Palmas, Canary Islands, Spain
| | - Gustavo Bodelón
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
- * E-mail:
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Salema V, Fernández LÁ. High yield purification of nanobodies from the periplasm of E. coli as fusions with the maltose binding protein. Protein Expr Purif 2013; 91:42-8. [DOI: 10.1016/j.pep.2013.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/02/2013] [Accepted: 07/05/2013] [Indexed: 01/31/2023]
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