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Sokolov P, Evsegneeva I, Karaulov A, Sukhanova A, Nabiev I. Allergen Microarrays and New Physical Approaches to More Sensitive and Specific Detection of Allergen-Specific Antibodies. BIOSENSORS 2024; 14:353. [PMID: 39056629 PMCID: PMC11275078 DOI: 10.3390/bios14070353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
The prevalence of allergic diseases has increased tremendously in recent decades, which can be attributed to growing exposure to environmental triggers, changes in dietary habits, comorbidity, and the increased use of medications. In this context, the multiplexed diagnosis of sensitization to various allergens and the monitoring of the effectiveness of treatments for allergic diseases become particularly urgent issues. The detection of allergen-specific antibodies, in particular, sIgE and sIgG, is a modern alternative to skin tests due to the safety and efficiency of this method. The use of allergen microarrays to detect tens to hundreds of allergen-specific antibodies in less than 0.1 mL of blood serum enables the transition to a deeply personalized approach in the diagnosis of these diseases while reducing the invasiveness and increasing the informativeness of analysis. This review discusses the technological approaches underlying the development of allergen microarrays and other protein microarrays, including the methods of selection of the microarray substrates and matrices for protein molecule immobilization, the obtainment of allergens, and the use of different types of optical labels for increasing the sensitivity and specificity of the detection of allergen-specific antibodies.
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Affiliation(s)
- Pavel Sokolov
- Life Improvement by Future Technologies (LIFT) Center, 143025 Moscow, Russia
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
| | - Irina Evsegneeva
- Department of Clinical Immunology and Allergology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia; (I.E.); (A.K.)
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia; (I.E.); (A.K.)
| | - Alyona Sukhanova
- Laboratoire BioSpecT, Université de Reims Champagne-Ardenne, 51100 Reims, France;
| | - Igor Nabiev
- Life Improvement by Future Technologies (LIFT) Center, 143025 Moscow, Russia
- Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
- Department of Clinical Immunology and Allergology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia; (I.E.); (A.K.)
- Laboratoire BioSpecT, Université de Reims Champagne-Ardenne, 51100 Reims, France;
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Thornton EL, Paterson SM, Gidden Z, Horrocks MH, Laohakunakorn N, Regan L. Self-Assembling Protein Surfaces for In Situ Capture of Cell-Free-Synthesized Proteins. Front Bioeng Biotechnol 2022; 10:915035. [PMID: 35875503 PMCID: PMC9300835 DOI: 10.3389/fbioe.2022.915035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
We present a new method for the surface capture of proteins in cell-free protein synthesis (CFPS). We demonstrate the spontaneous self-assembly of the protein BslA into functionalizable surfaces on the surface of a CFPS reaction chamber. We show that proteins can be covalently captured by such surfaces, using “Catcher/Tag” technology. Importantly, proteins of interest can be captured either when synthesised in situ by CFPS above the BslA surfaces, or when added as pure protein. The simplicity and cost efficiency of this method suggest that it will find many applications in cell-free-based methods.
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Affiliation(s)
- Ella Lucille Thornton
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah Maria Paterson
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Zoe Gidden
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Nadanai Laohakunakorn
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Nadanai Laohakunakorn, ; Lynne Regan,
| | - Lynne Regan
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Nadanai Laohakunakorn, ; Lynne Regan,
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Kelwick RJR, Webb AJ, Freemont PS. Biological Materials: The Next Frontier for Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:399. [PMID: 32478045 PMCID: PMC7235315 DOI: 10.3389/fbioe.2020.00399] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Advancements in cell-free synthetic biology are enabling innovations in sustainable biomanufacturing, that may ultimately shift the global manufacturing paradigm toward localized and ecologically harmonized production processes. Cell-free synthetic biology strategies have been developed for the bioproduction of fine chemicals, biofuels and biological materials. Cell-free workflows typically utilize combinations of purified enzymes, cell extracts for biotransformation or cell-free protein synthesis reactions, to assemble and characterize biosynthetic pathways. Importantly, cell-free reactions can combine the advantages of chemical engineering with metabolic engineering, through the direct addition of co-factors, substrates and chemicals -including those that are cytotoxic. Cell-free synthetic biology is also amenable to automatable design cycles through which an array of biological materials and their underpinning biosynthetic pathways can be tested and optimized in parallel. Whilst challenges still remain, recent convergences between the materials sciences and these advancements in cell-free synthetic biology enable new frontiers for materials research.
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Affiliation(s)
- Richard J. R. Kelwick
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Alexander J. Webb
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- The London Biofoundry, Imperial College Translation & Innovation Hub, London, United Kingdom
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, United Kingdom
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Kilb N, Herz T, Burger J, Woehrle J, Meyer PA, Roth G. Protein Microarray Copying: Easy on-Demand Protein Microarray Generation Compatible with Fluorescence and Label-Free Real-Time Analysis. Chembiochem 2019; 20:1554-1562. [PMID: 30730095 DOI: 10.1002/cbic.201800699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/07/2019] [Indexed: 01/19/2023]
Abstract
Protein microarrays are essential to understand complex protein interaction networks. Their production, however, is a challenge and renders this technology unattractive for many laboratories. Recent developments in cell-free protein microarray generation offer new opportunities, but are still expensive and cumbersome in practice. Herein, we describe a cost-effective and user-friendly method for the cell-free production of protein microarrays. From a polydimethylsiloxane (PDMS) flow cell containing an expressible DNA microarray, proteins of interest are synthesised by cell-free expression and then immobilised on a capture surface. The resulting protein microarray can be regarded as a "copy" of the DNA microarray. 2 His6 - and Halo-tagged fluorescent reference proteins were used to demonstrate the functionality of nickel nitrilotriacetic acid (Ni-NTA) and Halo-bind surfaces in this copy system. The described process can be repeated several times on the same DNA microarray. The identity and functionality of the proteins were proven during the copy process by their fluorescence and on the surface through a fluorescent immune assay. Also, single-colour reflectometry (SCORE) was applied to show that, on such copied arrays, real-time binding kinetic measurements were possible.
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Affiliation(s)
- Normann Kilb
- AG Roth-Lab for Microarray Copying, ZBSA-Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.,Faculty of Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Tobias Herz
- AG Roth-Lab for Microarray Copying, ZBSA-Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.,Faculty of Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Jürgen Burger
- AG Roth-Lab for Microarray Copying, ZBSA-Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.,IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79104, Freiburg, Germany
| | - Johannes Woehrle
- AG Roth-Lab for Microarray Copying, ZBSA-Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.,IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79104, Freiburg, Germany
| | - Philipp A Meyer
- AG Roth-Lab for Microarray Copying, ZBSA-Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.,IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79104, Freiburg, Germany
| | - Günter Roth
- AG Roth-Lab for Microarray Copying, ZBSA-Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.,Faculty of Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.,BIOSS-Centre for Biological Signal Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
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Ueno S, Shioya M, Ichiki T. Fluorometric Measurement of Adenosine 5'-Triphosphate Using Exonuclease V Activity. J PHOTOPOLYM SCI TEC 2018. [DOI: 10.2494/photopolymer.31.699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shingo Ueno
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion
- Department of Materials Engineering, School of Engineering, The University of Tokyo
| | - Mika Shioya
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion
| | - Takanori Ichiki
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion
- Department of Materials Engineering, School of Engineering, The University of Tokyo
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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Bender J, Bognar S, Camagna M, Donauer JAM, Eble JW, Emig R, Fischer S, Jesser R, Keilholz L, Kokotek DMU, Neumann J, Nicklaus S, Oude Weernink RRQPT, Stühn LG, Wössner N, Krämer SD, Schwenk P, Gensch N, Roth G, Ulbrich MH. Multiplexed antibody detection from blood sera by immobilization of in vitro expressed antigens and label-free readout via imaging reflectometric interferometry (iRIf). Biosens Bioelectron 2018; 115:97-103. [PMID: 29803867 DOI: 10.1016/j.bios.2018.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/18/2018] [Accepted: 05/10/2018] [Indexed: 11/30/2022]
Abstract
The detection of antibodies from blood sera is crucial for diagnostic purposes. Miniaturized protein assays in combination with microfluidic setups hold great potential by enabling automated handling and multiplexed analyses. Yet, the separate expression, purification, and storage of many individual proteins are time consuming and limit applicability. In vitro cell-free expression has been proposed as an alternative procedure for the generation of protein assays. We report the successful in vitro expression of different model proteins from DNA templates with an optimized expression mix. His10-tagged proteins were specifically captured and immobilized on a Ni-NTA coated sensor surface directly from the in vitro expression mix. Finally, the specific binding of antibodies from rabbit-derived blood sera to the immobilized proteins was monitored by imaging reflectometric interferometry (iRIf). Antibodies in the blood sera could be identified by binding to the respective epitopes with minimal cross reactivity. The results show the potential of in vitro expression and label-free detection for binding assays in general and diagnostic purposes in specific.
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Affiliation(s)
- Julian Bender
- Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Sabine Bognar
- Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Maurizio Camagna
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Julia A M Donauer
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Julian W Eble
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Ramona Emig
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Sabrina Fischer
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Rabea Jesser
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Luisa Keilholz
- Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel M U Kokotek
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Julika Neumann
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Simon Nicklaus
- Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Ricardo R Q P T Oude Weernink
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Lara G Stühn
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Nathalie Wössner
- Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Stefan D Krämer
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; ZBSA - Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
| | - Philipp Schwenk
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Nicole Gensch
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Günter Roth
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; ZBSA - Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany.
| | - Maximilian H Ulbrich
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; Renal Division, Freiburg University Medical Center, 79106 Freiburg, Germany.
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Schinn SM, Broadbent A, Bradley WT, Bundy BC. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA. N Biotechnol 2016; 33:480-7. [PMID: 27085957 DOI: 10.1016/j.nbt.2016.04.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022]
Abstract
A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems.
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Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - William T Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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