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van Aalen EA, Lurvink JJJ, Vermeulen L, van Gerven B, Ni Y, Arts R, Merkx M. Turning Antibodies into Ratiometric Bioluminescent Sensors for Competition-Based Homogeneous Immunoassays. ACS Sens 2024; 9:1401-1409. [PMID: 38380622 DOI: 10.1021/acssensors.3c02478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Here we present LUCOS (Luminescent Competition Sensor), a modular and broadly applicable bioluminescent diagnostic platform enabling the detection of both small molecules and protein biomarkers. The construction of LUCOS sensors entails the covalent and site-specific coupling of a bioluminescent sensor component to an analyte-specific antibody via protein G-mediated photoconjugation. Target detection is accomplished through intramolecular competition with a tethered analyte competitor for antibody binding. We established two variants of LUCOS: an inherent ratiometric LUCOSR variant and an intensiometric LUCOSI version, which can be used for ratiometric detection upon the addition of a split calibrator luciferase. To demonstrate the versatility of the LUCOS platform, sensors were developed for the detection of the small molecule cortisol and the protein biomarker NT-proBNP. Sensors for both targets displayed analyte-dependent changes in the emission ratio and enabled detection in the micromolar concentration range (KD,app = 16-92 μM). Furthermore, we showed that the response range of the LUCOS sensor can be adjusted by attenuating the affinity of the tethered NT-proBNP competitor, which enabled detection in the nanomolar concentration range (KD,app = 317 ± 26 nM). Overall, the LUCOS platform offers a highly versatile and easy method to convert commercially available monoclonal antibodies into bioluminescent biosensors that provide a homogeneous alternative for the competitive immunoassay.
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Affiliation(s)
- Eva A van Aalen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Joep J J Lurvink
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Leandra Vermeulen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Benice van Gerven
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Yan Ni
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Remco Arts
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
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2
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de Stigter Y, van der Veer HJ, Rosier BJHM, Merkx M. Bioluminescent Intercalating Dyes for Ratiometric Nucleic Acid Detection. ACS Chem Biol 2024; 19:575-583. [PMID: 38315567 PMCID: PMC10877566 DOI: 10.1021/acschembio.3c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Rapid and sensitive DNA detection methods that can be conducted at the point of need may aid in disease diagnosis and monitoring. However, translation of current assays has proven challenging, as they typically require specialized equipment or probe-specific modifications for every new target DNA. Here, we present Luminescent Multivalent Intercalating Dye (LUMID), off-the-shelf bioluminescent sensors consisting of intercalating dyes conjugated to a NanoLuc luciferase, which allow for nonspecific detection of double-stranded DNA through a blue-to-green color change. Through the incorporation of multiple, tandem-arranged dyes separated by positively charged linkers, DNA-binding affinities were improved by over 2 orders of magnitude, detecting nanomolar DNA concentrations with an 8-fold change in green/blue ratio. We show that LUMID is easily combined with loop-mediated isothermal amplification (LAMP), enabling sequence-specific detection of viral DNA with attomolar sensitivity and a smartphone-based readout. With LUMID, we have thus developed a tool for simple and sensitive DNA detection that is particularly attractive for point-of-need applications.
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Affiliation(s)
- Yosta de Stigter
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Harmen J. van der Veer
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J. H. M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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3
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Gräwe A, Spruit CM, de Vries RP, Merkx M. Bioluminescent detection of viral surface proteins using branched multivalent protein switches. RSC Chem Biol 2024; 5:148-157. [PMID: 38333197 PMCID: PMC10849123 DOI: 10.1039/d3cb00164d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/22/2023] [Indexed: 02/10/2024] Open
Abstract
Fast and reliable virus diagnostics is key to prevent the spread of viruses in populations. A hallmark of viruses is the presence of multivalent surface proteins, a property that can be harnessed to control conformational switching in sensor proteins. Here, we introduce a new sensor platform (dark-LUX) for the detection of viral surface proteins consisting of a general bioluminescent framework that can be post-translationally functionalized with separately expressed binding domains. The platform relies on (1) plug-and-play bioconjugation of different binding proteins via SpyTag/SpyCatcher technology to create branched protein structures, (2) an optimized turn-on bioluminescent switch based on complementation of the split-luciferase NanoBiT upon target binding and (3) straightforward exploration of the protein linker space. The influenza A virus (IAV) surface proteins hemagglutinin (HA) and neuraminidase (NA) were used as relevant multivalent targets to establish proof of principle and optimize relevant parameters such as linker properties, choice of target binding domains and the optimal combination of the competing NanoBiT components SmBiT and DarkBiT. The sensor framework allows rapid conjugation and exchange of various binding domains including scFvs, nanobodies and de novo designed binders for a variety of targets, including the construction of a heterobivalent switch that targets the head and stem region of hemagglutinin. The modularity of the platform thus allows straightforward optimization of binding domains and scaffold properties for existing viral targets, and is well suited to quickly adapt bioluminescent sensor proteins to effectively detect newly evolving viral epitopes.
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Affiliation(s)
- Alexander Gräwe
- Laboratory of Protein Engineering, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Cindy M Spruit
- Utrecht Institute for Pharmaceutical Sciences, Department of Chemical Biology and Drug Discovery Utrecht The Netherlands
| | - Robert P de Vries
- Utrecht Institute for Pharmaceutical Sciences, Department of Chemical Biology and Drug Discovery Utrecht The Netherlands
| | - Maarten Merkx
- Laboratory of Protein Engineering, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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Biewenga L, Vermathen R, Rosier BJHM, Merkx M. A Generic Antibody-Blocking Protein That Enables pH-Switchable Activation of Antibody Activity. ACS Chem Biol 2024; 19:48-57. [PMID: 38110237 PMCID: PMC10804362 DOI: 10.1021/acschembio.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Molecular strategies that allow for reversible control of antibody activity have drawn considerable interest for both therapeutic and diagnostic applications. Protein M is a generic antibody-binding protein that binds to the Fv domain of IgGs and, in doing so, blocks antigen binding. However, the dissociation of protein M is essentially irreversible, which has precluded its use as an antibody affinity reagent and molecular mask to control antibody activity. Here, we show that introduction of 8 histidine residues on the Fv binding interface of protein M results in a variant that shows pH-switchable IgG binding. This protein M-8his variant provides an attractive and universal affinity resin for the purification of IgGs, antibody fragments (Fab and single-chain variable fragments (scFv)), and antibody conjugates. Moreover, protein M-8his enables the pH-dependent blocking of therapeutic antibodies, allowing the selective targeting of cells at pH 6.0.
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Affiliation(s)
- Lieuwe Biewenga
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Robin Vermathen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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5
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van Aalen EA, de Vries IR, Hanckmann ETL, Stevens JRF, Romagnoli TR, Derijks LJJ, Broeren MAC, Merkx M. Point-of-care therapeutic drug monitoring of tumour necrosis factor-α inhibitors using a single step immunoassay. Sens Diagn 2023; 2:1492-1500. [PMID: 38013761 PMCID: PMC10633107 DOI: 10.1039/d3sd00131h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/04/2023] [Indexed: 11/29/2023]
Abstract
Therapeutic drug monitoring (TDM) of tumor necrosis factor-α (TNFα)-inhibitors adalimumab and infliximab is important to establish optimal drug dose and maximize treatment efficacy. Currently, TDM is primarily performed with ELISA techniques in clinical laboratories, resulting in a long sample-to-result workflow. Point-of-care (POC) detection of these therapeutic antibodies could significantly decrease turnaround times and allow for user-friendly home-testing. Here, we adapted the recently developed bioluminescent dRAPPID (dimeric Ratiometric Plug-and-Play Immunodiagnostics) sensor platform to allow POC TDM of infliximab and adalimumab. We applied the two best performing dRAPPID sensors, with limit-of-detections of 1 pM and 17 pM, to measure the infliximab and adalimumab levels in 49 and 40 patient serum samples, respectively. The analytical performance of dRAPPID was benchmarked with commercial ELISAs and yielded Pearson's correlation coefficients of 0.93 and 0.94 for infliximab and adalimumab, respectively. Furthermore, a dedicated bioluminescence reader was fabricated and used as a readout device for the TDM dRAPPID sensors. Subsequently, infliximab and adalimumab patient serum samples were measured with the TDM dRAPPID sensors and bioluminescence reader, yielding Pearson's correlation coefficients of 0.97 and 0.86 for infliximab and adalimumab, respectively, and small proportional differences with ELISA (slope was 0.97 ± 0.09 and 0.96 ± 0.20, respectively). The adalimumab and infliximab dRAPPID sensors, in combination with the dedicated bioluminescence reader, allow for ease-of-use TDM with a fast turnaround time and show potential for POC TDM outside of clinical laboratories.
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Affiliation(s)
- Eva A van Aalen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Ivar R de Vries
- Department of Electrical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Eva T L Hanckmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Jeannot R F Stevens
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Thomas R Romagnoli
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Luc J J Derijks
- Department of Clinical Pharmacy and Pharmacology, Máxima Medical Center P.O. Box 7777 5500 MB Veldhoven The Netherlands
- Department of Clinical Pharmacy and Toxicology, Maastricht University Medical Center P.O. Box 5800 6202 AZ Maastricht The Netherlands
| | - Maarten A C Broeren
- Laboratory of Clinical Chemistry and Haematology, Máxima Medical Center P.O. Box 7777 5500 MB Veldhoven The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
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6
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Makri Pistikou AM, Cremers GAO, Nathalia BL, Meuleman TJ, Bögels BWA, Eijkens BV, de Dreu A, Bezembinder MTH, Stassen OMJA, Bouten CCV, Merkx M, Jerala R, de Greef TFA. Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells. Nat Commun 2023; 14:7001. [PMID: 37919273 PMCID: PMC10622552 DOI: 10.1038/s41467-023-42810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
The rational design and implementation of synthetic mammalian communication systems can unravel fundamental design principles of cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics. Here, we develop the foundations of an orthogonal, and scalable mammalian synthetic communication platform that exploits the programmability of synthetic receptors and selective affinity and tunability of diffusing coiled-coil peptides. Leveraging the ability of coiled-coils to exclusively bind to a cognate receptor, we demonstrate orthogonal receptor activation and Boolean logic operations at the receptor level. We show intercellular communication based on synthetic receptors and secreted multidomain coiled-coils and demonstrate a three-cell population system that can perform AND gate logic. Finally, we show CC-GEMS receptor-dependent therapeutic protein expression. Our work provides a modular and scalable framework for the engineering of complex cell consortia, with the potential to expand the aptitude of cell therapeutics and diagnostics.
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Affiliation(s)
- Anna-Maria Makri Pistikou
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Glenn A O Cremers
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bryan L Nathalia
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Theodorus J Meuleman
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bruno V Eijkens
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Anne de Dreu
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten T H Bezembinder
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Oscar M J A Stassen
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Carlijn C V Bouten
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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7
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Schrijver DP, Röring RJ, Deckers J, de Dreu A, Toner YC, Prevot G, Priem B, Munitz J, Nugraha EG, van Elsas Y, Azzun A, Anbergen T, Groh LA, Becker AMD, Pérez-Medina C, Oosterwijk RS, Novakovic B, Moorlag SJCFM, Jansen A, Pickkers P, Kox M, Beldman TJ, Kluza E, van Leent MMT, Teunissen AJP, van der Meel R, Fayad ZA, Joosten LAB, Fisher EA, Merkx M, Netea MG, Mulder WJM. Resolving sepsis-induced immunoparalysis via trained immunity by targeting interleukin-4 to myeloid cells. Nat Biomed Eng 2023; 7:1097-1112. [PMID: 37291433 PMCID: PMC10504080 DOI: 10.1038/s41551-023-01050-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/02/2023] [Indexed: 06/10/2023]
Abstract
Immunoparalysis is a compensatory and persistent anti-inflammatory response to trauma, sepsis or another serious insult, which increases the risk of opportunistic infections, morbidity and mortality. Here, we show that in cultured primary human monocytes, interleukin-4 (IL4) inhibits acute inflammation, while simultaneously inducing a long-lasting innate immune memory named trained immunity. To take advantage of this paradoxical IL4 feature in vivo, we developed a fusion protein of apolipoprotein A1 (apoA1) and IL4, which integrates into a lipid nanoparticle. In mice and non-human primates, an intravenously injected apoA1-IL4-embedding nanoparticle targets myeloid-cell-rich haematopoietic organs, in particular, the spleen and bone marrow. We subsequently demonstrate that IL4 nanotherapy resolved immunoparalysis in mice with lipopolysaccharide-induced hyperinflammation, as well as in ex vivo human sepsis models and in experimental endotoxemia. Our findings support the translational development of nanoparticle formulations of apoA1-IL4 for the treatment of patients with sepsis at risk of immunoparalysis-induced complications.
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Affiliation(s)
- David P Schrijver
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rutger J Röring
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen Deckers
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anne de Dreu
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Yohana C Toner
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Geoffrey Prevot
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bram Priem
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Angiogenesis Laboratory, Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Jazz Munitz
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eveline G Nugraha
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Yuri van Elsas
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anthony Azzun
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tom Anbergen
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Laszlo A Groh
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anouk M D Becker
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Tumor Immunology, RIMLS, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carlos Pérez-Medina
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Roderick S Oosterwijk
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Boris Novakovic
- Epigenetics Group, Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Aron Jansen
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Peter Pickkers
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Matthijs Kox
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Thijs J Beldman
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ewelina Kluza
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mandy M T van Leent
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abraham J P Teunissen
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roy van der Meel
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Zahi A Fayad
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Edward A Fisher
- Division of Cardiology, Department of Medicine, Marc and Ruti Bell Program in Vascular Biology, New York University School of Medicine, New York, NY, USA
| | - Maarten Merkx
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
| | - Willem J M Mulder
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands.
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands.
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8
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Tholen MME, Rosier BJHM, Vermathen RT, Sewnath CAN, Storm C, Woythe L, Izquierdo-Lozano C, Riera R, van Egmond M, Merkx M, Albertazzi L. Mapping Antibody Domain Exposure on Nanoparticle Surfaces Using DNA-PAINT. ACS Nano 2023. [PMID: 37283555 DOI: 10.1021/acsnano.3c02195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Decorating nanoparticles with antibodies (Ab) is a key strategy for targeted drug delivery and imaging. For this purpose, the orientation of the antibody on the nanoparticle is crucial to maximize fragment antibody-binding (Fab) exposure and thus antigen binding. Moreover, the exposure of the fragment crystallizable (Fc) domain may lead to the engagement of immune cells through one of the Fc receptors. Therefore, the choice of the chemistry for nanoparticle-antibody conjugation is key for the biological performance, and methods have been developed for orientation-selective functionalization. Despite the importance of this issue, there is a lack of direct methods to quantify the antibodies' orientation on the nanoparticle's surface. Here, we present a generic methodology that enables for multiplexed, simultaneous imaging of both Fab and Fc exposure on the surface of nanoparticles, based on super-resolution microscopy. Fab-specific Protein M and Fc-specific Protein G probes were conjugated to single stranded DNAs and two-color DNA-PAINT imaging was performed. Hereby, we quantitatively addressed the number of sites per particle and highlight the heterogeneity in the Ab orientation and compared the results with a geometrical computational model to validate data interpretation. Moreover, super-resolution microscopy can resolve particle size, allowing the study of how particle dimensions affect antibody coverage. We show that different conjugation strategies modulate the Fab and Fc exposure which can be tuned depending on the application of choice. Finally, we explored the biomedical importance of antibody domain exposure in antibody dependent cell mediated phagocytosis (ADCP). This method can be used universally to characterize antibody-conjugated nanoparticles, improving the understanding of relationships between structure and targeting capacities in targeted nanomedicine.
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Affiliation(s)
- Marrit M E Tholen
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Robin T Vermathen
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Céline A N Sewnath
- Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Cancer Immunology, Amsterdam Institute for Infection and Immunity, 1081 HV Amsterdam, The Netherlands
| | - Cornelis Storm
- Department of Applied Physics, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Laura Woythe
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Cristina Izquierdo-Lozano
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Roger Riera
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Marjolein van Egmond
- Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Cancer Immunology, Amsterdam Institute for Infection and Immunity, 1081 HV Amsterdam, The Netherlands
- Department of Surgery, Amsterdam UMC, Vrije Universtiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Maarten Merkx
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands
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9
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van Aalen EA, Rosier BJHM, Jansen T, Wouters SFA, Vermathen RT, van der Veer HJ, Yeste Lozano J, Mughal S, Fernández-Costa JM, Ramón-Azcón J, den Toonder JMJ, Merkx M. Integrated Bioluminescent Immunoassays for High-Throughput Sampling and Continuous Monitoring of Cytokines. Anal Chem 2023. [PMID: 37253113 DOI: 10.1021/acs.analchem.3c00745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immunoassays show great potential for the detection of low levels of cytokines, due to their high sensitivity and excellent specificity. There is a particular demand for biosensors that enable both high-throughput screening and continuous monitoring of clinically relevant cytokines such as interleukin-6 (IL-6) and tumor necrosis factor-α (TNFα). To this end, we here introduce a novel bioluminescent immunoassay based on the ratiometric plug-and-play immunodiagnostics (RAPPID) platform, with an improved intrinsic signal-to-background and an >80-fold increase in the luminescent signal. The new dRAPPID assay, comprising a dimeric protein G adapter connected via a semiflexible linker, was applied to detect the secretion of IL-6 by breast carcinoma cells upon TNFα stimulation and the production of low concentrations of IL-6 (∼18 pM) in an endotoxin-stimulated human 3D muscle tissue model. Moreover, we integrated the dRAPPID assay in a newly developed microfluidic device for the simultaneous and continuous monitoring of changes in IL-6 and TNFα in the low-nanomolar range. The luminescence-based read-out and the homogeneous nature of the dRAPPID platform allowed for detection with a simple measurement setup, consisting of a digital camera and a light-sealed box. This permits the usage of the continuous dRAPPID monitoring chip at the point of need, without the requirement for complex or expensive detection techniques.
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Affiliation(s)
- Eva A van Aalen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tom Jansen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F A Wouters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Robin T Vermathen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Harmen J van der Veer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - José Yeste Lozano
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
| | - Sheeza Mughal
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
| | - Juan M Fernández-Costa
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
| | - Javier Ramón-Azcón
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23,O Barcelona E08010, Spain
| | - Jaap M J den Toonder
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Microsystems, Department of Mechanical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
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10
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van der Veer H, van Aalen EA, Michielsen CMS, Hanckmann ETL, Deckers J, van Borren MMGJ, Flipse J, Loonen AJM, Schoeber JPH, Merkx M. Glow-in-the-Dark Infectious Disease Diagnostics Using CRISPR-Cas9-Based Split Luciferase Complementation. ACS Cent Sci 2023; 9:657-667. [PMID: 37122471 PMCID: PMC10141630 DOI: 10.1021/acscentsci.2c01467] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Indexed: 05/03/2023]
Abstract
Nucleic acid detection methods based on CRISPR and isothermal amplification techniques show great potential for point-of-care diagnostic applications. However, most current methods rely on fluorescent or lateral flow assay readout, requiring external excitation or postamplification reaction transfer. Here, we developed a bioluminescent nucleic acid sensor (LUNAS) platform in which target dsDNA is sequence-specifically detected by a pair of dCas9-based probes mediating split NanoLuc luciferase complementation. LUNAS is easily integrated with recombinase polymerase amplification (RPA), providing attomolar sensitivity in a rapid one-pot assay. A calibrator luciferase is included for a robust ratiometric readout, enabling real-time monitoring of the RPA reaction using a simple digital camera. We designed an RT-RPA-LUNAS assay that allows SARS-CoV-2 RNA detection without the need for cumbersome RNA isolation and demonstrated its diagnostic performance for COVID-19 patient nasopharyngeal swab samples. Detection of SARS-CoV-2 from samples with viral RNA loads of ∼200 cp/μL was achieved within ∼20 min, showing that RPA-LUNAS is attractive for point-of-care infectious disease testing.
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Affiliation(s)
- Harmen
J. van der Veer
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Eva A. van Aalen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Claire M. S. Michielsen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Eva T. L. Hanckmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Jeroen Deckers
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | | | - Jacky Flipse
- Laboratory
for Medical Microbiology and Immunology, Rijnstate Hospital, P.O. Box 8, Velp 6880 AA, The Netherlands
| | - Anne J. M. Loonen
- Research
Group Applied Natural Sciences, Fontys University
of Applied Sciences, Eindhoven 5612 AP, The Netherlands
- Pathologie-DNA,
Lab for Molecular Diagnostics, Location
Jeroen Bosch Hospital, ’s-Hertogenbosch 5223 GZ, The Netherlands
| | - Joost P. H. Schoeber
- Research
Group Applied Natural Sciences, Fontys University
of Applied Sciences, Eindhoven 5612 AP, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
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11
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van Veldhuisen TW, Altenburg WJ, Verwiel MAM, Lemmens LJM, Mason AF, Merkx M, Brunsveld L, van Hest JCM. Enzymatic Regulation of Protein-Protein Interactions in Artificial Cells. Adv Mater 2023:e2300947. [PMID: 37027309 DOI: 10.1002/adma.202300947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Indexed: 06/02/2023]
Abstract
Membraneless organelles are important for spatial organization of proteins and regulation of intracellular processes. Proteins can be recruited to these condensates by specific protein-protein or protein-nucleic acid interactions, which are often regulated by post-translational modifications. However, the mechanisms behind these dynamic, affinity-based protein recruitment events are not well understood. Here, a coacervate system that incorporates the 14-3-3 scaffold protein to study enzymatically regulated recruitment of 14-3-3-binding proteins is presented, which mostly bind in a phosphorylation-dependent manner. Synthetic coacervates are efficiently loaded with 14-3-3, and phosphorylated binding partners, such as the c-Raf pS233/pS259 peptide (c-Raf), show 14-3-3-dependent sequestration with up to 161-fold increase in local concentration. The c-Raf domain is fused to green fluorescent protein (GFP-c-Raf) to demonstrate recruitment of proteins. In situ phosphorylation of GFP-c-Raf by a kinase leads to enzymatically regulated uptake. The introduction of a phosphatase into coacervates preloaded with the phosphorylated 14-3-3-GFP-c-Raf complex results in a significant cargo efflux mediated by dephosphorylation. Finally, the general applicability of this platform to study protein-protein interactions is demonstrated by the phosphorylation-dependent and 14-3-3-mediated active reconstitution of a split-luciferase inside artificial cells. This work presents an approach to study dynamically regulated protein recruitment in condensates, using native interaction domains.
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Affiliation(s)
- Thijs W van Veldhuisen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
| | - Wiggert J Altenburg
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
| | - Madelief A M Verwiel
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
| | - Lenne J M Lemmens
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
| | - Alexander F Mason
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
| | - Jan C M van Hest
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, The Netherlands
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12
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Deckers J, Anbergen T, Hokke AM, de Dreu A, Schrijver DP, de Bruin K, Toner YC, Beldman TJ, Spangler JB, de Greef TFA, Grisoni F, van der Meel R, Joosten LAB, Merkx M, Netea MG, Mulder WJM. Engineering cytokine therapeutics. Nat Rev Bioeng 2023; 1:286-303. [PMID: 37064653 PMCID: PMC9933837 DOI: 10.1038/s44222-023-00030-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Cytokines have pivotal roles in immunity, making them attractive as therapeutics for a variety of immune-related disorders. However, the widespread clinical use of cytokines has been limited by their short blood half-lives and severe side effects caused by low specificity and unfavourable biodistribution. Innovations in bioengineering have aided in advancing our knowledge of cytokine biology and yielded new technologies for cytokine engineering. In this Review, we discuss how the development of bioanalytical methods, such as sequencing and high-resolution imaging combined with genetic techniques, have facilitated a better understanding of cytokine biology. We then present an overview of therapeutics arising from cytokine re-engineering, targeting and delivery, mRNA therapeutics and cell therapy. We also highlight the application of these strategies to adjust the immunological imbalance in different immune-mediated disorders, including cancer, infection and autoimmune diseases. Finally, we look ahead to the hurdles that must be overcome before cytokine therapeutics can live up to their full potential.
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Affiliation(s)
- Jeroen Deckers
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Tom Anbergen
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Ayla M. Hokke
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Anne de Dreu
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - David P. Schrijver
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Koen de Bruin
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Yohana C. Toner
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Thijs J. Beldman
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jamie B. Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Centre for Living Technologies, Alliance Eindhoven University of Technology, Wageningen University & Research, Utrecht University and University Medical Center Utrecht (EWUU), Utrecht, Netherlands
| | - Francesca Grisoni
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
- Centre for Living Technologies, Alliance Eindhoven University of Technology, Wageningen University & Research, Utrecht University and University Medical Center Utrecht (EWUU), Utrecht, Netherlands
| | - Roy van der Meel
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Present Address: Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Leo A. B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Centre, Nijmegen, Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Present Address: Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Centre, Nijmegen, Netherlands
- Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Willem J. M. Mulder
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Present Address: Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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13
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Gräwe A, Merkx M. Bioluminescence Goes Dark: Boosting the Performance of Bioluminescent Sensor Proteins Using Complementation Inhibitors. ACS Sens 2022; 7:3800-3808. [PMID: 36450135 PMCID: PMC9791688 DOI: 10.1021/acssensors.2c01726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Bioluminescent sensor proteins have recently gained popularity in both basic research and point-of-care diagnostics. Sensor proteins based on intramolecular complementation of split NanoLuc are particularly attractive because their intrinsic modular design enables for systematic tuning of sensor properties. Here we show how the sensitivity of these sensors can be enhanced by the introduction of catalytically inactive variants of the small SmBiT subunit (DarkBiTs) as intramolecular inhibitors. Starting from previously developed bioluminescent antibody sensor proteins (LUMABS), we developed single component, biomolecular switches with a strongly reduced background signal for the detection of three clinically relevant antibodies, anti-HIV1-p17, cetuximab (CTX), and an RSV neutralizing antibody (101F). These new dark-LUMABS sensors showed 5-13-fold increases in sensitivity which translated into lower limits of detection. The use of DarkBiTs as competitive intramolecular inhibitor domains is not limited to the LUMABS sensor family and might be used to boost the performance of other bioluminescent sensor proteins based on split luciferase complementation.
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14
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Gräwe A, Merkx M, Stein V. iFLinkC-X: A Scalable Framework to Assemble Bespoke Genetically Encoded Co-polymeric Linkers of Variable Lengths and Amino Acid Composition. Bioconjug Chem 2022; 33:1415-1421. [PMID: 35815527 DOI: 10.1021/acs.bioconjchem.2c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Linker engineering is rapidly gaining prominence as protein engineers and synthetic biologists construct increasingly sophisticated protein assemblies capable of executing complex molecular functions in the context of biosensing, biocatalysis, or biotherapeutics. Depending on the application, the structural and functional requirements imposed on the underlying linkers can differ vastly. At the same time, there is a distinct lack of methods to effectively code linkers at the level of DNA and tailor them to the functional requirements of different fusion proteins. Addressing these limitations, a scalable framework is presented to compose co-polymeric linkers of variable lengths and amino acid composition based on a limited number of linker fragments stored in sequence-verified entry plasmids. The assembly process is exemplified for Pro-rich linkers in the context of a Zn2+-responsive dual-readout BRET/FRET sensor while examining how linker composition impacts key functional properties such as ligand affinity, dynamic range, and their ability to separate structurally distinct domains.
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Affiliation(s)
- Alexander Gräwe
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany.,Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology (TU/e), 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology (TU/e), 5600 MB Eindhoven, The Netherlands
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
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15
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Hazegh Nikroo A, Lemmens LJM, Wezeman T, Ottmann C, Merkx M, Brunsveld L. Switchable Control of Scaffold Protein Activity via Engineered Phosphoregulated Autoinhibition. ACS Synth Biol 2022; 11:2464-2472. [PMID: 35765959 PMCID: PMC9295147 DOI: 10.1021/acssynbio.2c00122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/08/2023]
Abstract
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Scaffold proteins
operate as organizing hubs to enable high-fidelity
signaling, fulfilling crucial roles in the regulation of cellular
processes. Bottom-up construction of controllable scaffolding platforms
is attractive for the implementation of regulatory processes in synthetic
biology. Here, we present a modular and switchable synthetic scaffolding
system, integrating scaffold-mediated signaling with switchable kinase/phosphatase
input control. Phosphorylation-responsive inhibitory peptide motifs
were fused to 14-3-3 proteins to generate dimeric protein scaffolds
with appended regulatory peptide motifs. The availability of the scaffold
for intermolecular partner protein binding could be lowered up to
35-fold upon phosphorylation of the autoinhibition motifs, as demonstrated
using three different kinases. In addition, a hetero-bivalent autoinhibitory
platform design allowed for dual-kinase input regulation of scaffold
activity. Reversibility of the regulatory platform was illustrated
through phosphatase-controlled abrogation of autoinhibition, resulting
in full recovery of 14-3-3 scaffold activity.
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Affiliation(s)
- Arjan Hazegh Nikroo
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Lenne J M Lemmens
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Tim Wezeman
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
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16
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Merkx M. The Benefit of Being Gracious. ACS Sens 2022; 7:1614. [PMID: 35748051 DOI: 10.1021/acssensors.2c01181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Abstract
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Fluorescent Zn2+ sensors play a pivotal role in zinc
biology, but their application in complex media such as blood serum
or plate reader-based cellular assays is hampered by autofluorescence
and light scattering. Bioluminescent sensor proteins provide an attractive
alternative to fluorescent sensors for these applications, but the
only bioluminescent sensor protein developed so far, BLZinCh, has
a limited sensor response and a suboptimal Zn2+ affinity.
In this work, we expanded the toolbox of bioluminescent Zn2+ sensors by developing two new sensor families that show a large
change in the emission ratio and cover a range of physiologically
relevant Zn2+ affinities. The LuZi platform relies on competitive
complementation of split NanoLuc luciferase and displays a robust,
2-fold change in red-to-blue emission, allowing quantification of
free Zn2+ between 2 pM and 1 nM. The second platform was
developed by replacing the long flexible GGS linker in the original
BLZinCh sensor by rigid polyproline linkers, yielding a series of
BLZinCh-Pro sensors with a 3–4-fold improved ratiometric response
and physiologically relevant Zn2+ affinities between 0.5
and 1 nM. Both the LuZi and BLZinCh-Pro sensors allowed the direct
determination of low nM concentrations of free Zn2+ in
serum, providing an attractive alternative to more laborious and/or
indirect approaches to measure serum zinc levels. Furthermore, the
genetic encoding of the BLZinCh-Pro sensors allowed their use as intracellular
sensors, where the sensor occupancy of 40–50% makes them ideally
suited to monitor both increases and decreases in intracellular free
Zn2+ concentration in simple, plate reader-based measurements,
without the need for fluorescence microscopy.
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18
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van Aalen EA, Wouters SFA, Verzijl D, Merkx M. Bioluminescent RAPPID Sensors for the Single-Step Detection of Soluble Axl and Multiplex Analysis of Cell Surface Cancer Biomarkers. Anal Chem 2022; 94:6548-6556. [PMID: 35438976 PMCID: PMC9069438 DOI: 10.1021/acs.analchem.2c00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Indexed: 11/29/2022]
Abstract
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Early diagnosis of
cancer is essential for the efficacy of treatment.
Our group recently developed RAPPID, a bioluminescent immunoassay
platform capable of measuring a wide panel of biomarkers directly
in solution. Here, we developed and systematically screened different
RAPPID sensors for sensitive detection of the soluble fraction of
Axl (sAxl), a cell surface receptor that is overexpressed in several
types of cancer. The best-performing RAPPID sensor, with a limit of
detection of 8 pM and a >9-fold maximal change in
emission
ratio, was applied to measure Axl in three different contexts: clinically
relevant sAxl levels (∼0.5 and ∼1 nM) in diluted blood
plasma, proteolytically cleaved Axl in the cell culture medium of
A431 and HeLa cancer cells, and Axl on the membrane of A431 cells.
We further extended the sensor toolbox by developing dual-color RAPPID
for simultaneous detection of Axl and EGFR on A431 and HeLa cells,
as well as an AND-gate RAPPID that measures the concurrent presence
of these two cell surface receptors on the same cell. These new RAPPID
sensors provide attractive alternatives for more laborious protein
detection and quantification methods such as FACS and immunostainings,
due to their simple practical implantation and low intrinsic background
signal.
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Affiliation(s)
- Eva A van Aalen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F A Wouters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | | | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
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19
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Merkx M. Computational Design of Sensor Proteins; It May Actually Work. ACS Sens 2021; 6:2783-2784. [PMID: 34445871 DOI: 10.1021/acssensors.1c01482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Affiliation(s)
- Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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21
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Pille J, Aloi A, Le DHT, Vialshin I, van de Laar N, Kevenaar K, Merkx M, Voets IK, van Hest JCM. Pathway-Dependent Co-Assembly of Elastin-Like Polypeptides. Small 2021; 17:e2007234. [PMID: 33690936 DOI: 10.1002/smll.202007234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/22/2021] [Indexed: 06/12/2023]
Abstract
In natural systems, temperature-induced assembly of biomolecules can lead to the formation of distinct assembly states, created out of the same set of starting compounds, based on the heating trajectory followed. Until now it has been difficult to achieve similar behavior in synthetic polymer mixtures. Here, a novel pathway-dependent assembly based on stimulus-responsive polymers is shown. When a mixture of mono- and diblock copolymers, based on elastin-like polypeptides, is heated with a critical heating rate co-assembled particles are created that are monodisperse, stable, and have tunable hydrodynamic radii between 20 and 120 nm. Below this critical heating rate, the constituents separately form polymer assemblies. This process is kinetically driven and reversible in thermodynamically closed systems. Using the co-assembly pathway, fluorescent proteins and bioluminescent enzymes are encapsulated with high efficiency. Encapsulated cargo shows unperturbed function even after delivery into cells. The pathway-dependent co-assembly of elastin-like polypeptides is not only of fundamental interest from a materials science perspective, allowing the formation of multiple distinct assemblies from the same starting compounds, which can be interconverted by going back to the molecularly dissolved states. It also enables a versatile way for constructing highly effective vehicles for the cellular delivery of biomolecular cargo.
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Affiliation(s)
- Jan Pille
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Antonio Aloi
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Duc H T Le
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Ilia Vialshin
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Nathalie van de Laar
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Kirsten Kevenaar
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Maarten Merkx
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Ilja K Voets
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
| | - Jan C M van Hest
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems Eindhoven University of Technology, PO Box 513, Eindhoven, 5600 MB, the Netherlands
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22
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Gooding JJ, Camasso N, Bakker E, Kelley S, Sailor M, Merkx M, Mao L, Clark H, Maboudian R, Masson JF, deMello A, Li M, Liu SM. 2021: A Year Starting Full of Hope. ACS Sens 2021; 6:1-2. [PMID: 33478226 DOI: 10.1021/acssensors.0c02726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Affiliation(s)
- Maarten Merkx
- Technische Universiteit Eindhoven, Eindhoven, The Netherlands
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24
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Tomimuro K, Tenda K, Ni Y, Hiruta Y, Merkx M, Citterio D. Thread-Based Bioluminescent Sensor for Detecting Multiple Antibodies in a Single Drop of Whole Blood. ACS Sens 2020; 5:1786-1794. [PMID: 32441095 DOI: 10.1021/acssensors.0c00564] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 12/20/2022]
Abstract
Antibodies are important biomarkers in clinical diagnostics in addition to being increasingly used for therapeutic purposes. Although numerous methods for their detection and quantification exist, they predominantly require benchtop instruments operated by specialists. To enable the detection of antibodies at point-of-care (POC), the development of simple and rapid assay methods independent of laboratory equipment is of high relevance. In this study, we demonstrate microfluidic thread-based analytical devices (μTADs) as a new platform for antibody detection by means of bioluminescence resonance energy-transfer (BRET) switching sensor proteins. The devices consist of vertically assembled layers including a blood separation membrane and a plastic film with a sewn-in cotton thread, onto which the BRET sensor proteins together with the substrate furimazine have been predeposited. In contrast to intensity-based signaling, the BRET mechanism enables time-independent, ratiometric readout of bioluminescence signals with a digital camera in a darkroom or a smartphone camera with a 3D-printed lens adapter. The device design allows spatially separated deposition of multiple bioluminescent proteins on a single sewn thread, enabling quantification of multiple antibodies in 5 μL of whole blood within 5 min. The bioluminescence response is independent of the applied sample volume within the range of 5-15 μL. Therefore, μTADs in combination with BRET-based sensor proteins represent user-friendly analytical tools for POC quantification of antibodies without any laboratory equipment in a finger prick (5 μL) of whole blood.
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Affiliation(s)
- Kosuke Tomimuro
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
| | - Keisuke Tenda
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
| | - Yan Ni
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yuki Hiruta
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
| | - Maarten Merkx
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Daniel Citterio
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, 223-8522 Yokohama, Japan
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25
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Xu X, Lemmens LJM, den Hamer A, Merkx M, Ottmann C, Brunsveld L. Modular bioengineered kinase sensors via scaffold protein-mediated split-luciferase complementation. Chem Sci 2020; 11:5532-5536. [PMID: 32874496 PMCID: PMC7446724 DOI: 10.1039/d0sc00074d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 01/06/2020] [Accepted: 05/11/2020] [Indexed: 01/07/2023] Open
Abstract
Phosphorylation is a key regulation event in cellular signaling. To sense the underlying kinase activity, we engineered modular and easy adaptable serine kinase sensors for the exemplary kinases PKA, PKB and CHK1.
Phosphorylation is a key regulation event in cellular signaling. Sensing the underlying kinase activity is of crucial importance for its fundamental understanding and for drug development. For this, modular kinase activity sensing concepts are urgently needed. We engineered modular serine kinase sensors based on complementation of split NanoBiT luciferase on protein assembly platforms generated from the scaffold protein 14-3-3. The bioengineered platforms are modular and easy adaptable as exemplary shown using novel sensors for the kinases PKA, PKB, and CHK1. Two designs were conceptualized, both relying on binding of defined mono- or bivalent kinase recognition motifs to the 14-3-3 platform upon phosphorylation, resulting in reconstitution of active split-luciferase. Especially the design based on double phosphorylation and bivalent 14-3-3 binding exhibits high efficiency for signal amplification (>1000-fold) and sensitivity to specific kinases, including in cellular lysates.
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Affiliation(s)
- Xiaolu Xu
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Lenne J M Lemmens
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Anniek den Hamer
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Maarten Merkx
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Christian Ottmann
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Luc Brunsveld
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
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Abstract
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The
ability to continuously measure concentrations of small molecules
is important for biomedical, environmental, and industrial monitoring.
However, because of their low molecular mass, it is difficult to quantify
concentrations of such molecules, particularly at low concentrations.
Here, we describe a small-molecule sensor that is generalizable, sensitive,
specific, reversible, and suited for continuous monitoring over long
durations. The sensor consists of particles attached to a sensing
surface via a double-stranded DNA tether. The particles transiently
bind to the sensing surface via single-molecular affinity interactions,
and the transient binding is optically detected as digital binding
events via the Brownian motion of the particles. The rate of binding
events decreases with increasing analyte concentration because analyte
molecules inhibit binding of the tethered particle to the surface.
The sensor enables continuous measurements of analyte concentrations
because of the reversibility of the intermolecular bonds and digital
read-out of particle motion. We show results for the monitoring of
short single-stranded DNA sequences and creatinine, a small-molecule
biomarker (113 Da) for kidney function, demonstrating a temporal resolution
of a few minutes. The precision of the sensor is determined by the
statistics of the digital switching events, which means that the precision
is tunable by the number of particles and the measurement time.
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Affiliation(s)
- Junhong Yan
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Laura van Smeden
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Maarten Merkx
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Peter Zijlstra
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Menno W. J. Prins
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
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27
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Gooding JJ, Mazur A, Bakker E, Kelley S, Sailor M, Merkx M, Mao L, Clark H, Maboudian R, Long Y. Remembering NJ. ACS Sens 2020; 5:887-888. [PMID: 32326707 DOI: 10.1021/acssensors.0c00660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J Justin Gooding
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Antonella Mazur
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Eric Bakker
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Shana Kelley
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Michael Sailor
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Maarten Merkx
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Lanqun Mao
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Heather Clark
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Roya Maboudian
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
| | - Yitao Long
- The University of New South Wales, Sydney, Australia.,ACS Publications, Washington, D.C., United States.,The University of Geneva, Geneva, Switzerland.,The University of Toronto, Toronto, Ontario, Canada.,University of California, San Diego, San Diego, California United States.,Technische Universiteit Eindhoven, Eindhoven, The Netherlands.,Institute of Chemistry, Chinese Academy of Sciences Beijing, China.,Northeastern University, Boston, Massachusetts, United States.,University of California, Berkeley, California, United States.,Nanjing University, Nanjing, China
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Guo S, Dubuc E, Rave Y, Verhagen M, Twisk SAE, van der Hek T, Oerlemans GJM, van den Oetelaar MCM, van Hazendonk LS, Brüls M, Eijkens BV, Joostens PL, Keij SR, Xing W, Nijs M, Stalpers J, Sharma M, Gerth M, Boonen RJEA, Verduin K, Merkx M, Voets IK, de Greef TFA. Engineered Living Materials Based on Adhesin-Mediated Trapping of Programmable Cells. ACS Synth Biol 2020; 9:475-485. [PMID: 32105449 PMCID: PMC7091533 DOI: 10.1021/acssynbio.9b00404] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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] [Indexed: 01/01/2023]
Abstract
Engineered living materials have the potential for wide-ranging applications such as biosensing and treatment of diseases. Programmable cells provide the functional basis for living materials; however, their release into the environment raises numerous biosafety concerns. Current designs that limit the release of genetically engineered cells typically involve the fabrication of multilayer hybrid materials with submicrometer porous matrices. Nevertheless the stringent physical barriers limit the diffusion of macromolecules and therefore the repertoire of molecules available for actuation in response to communication signals between cells and their environment. Here, we engineer a novel living material entitled "Platform for Adhesin-mediated Trapping of Cells in Hydrogels" (PATCH). This technology is based on engineered E. coli that displays an adhesion protein derived from an Antarctic bacterium with a high affinity for glucose. The adhesin stably anchors E. coli in dextran-based hydrogels with large pore diameters (10-100 μm) and reduces the leakage of bacteria into the environment by up to 100-fold. As an application of PATCH, we engineered E. coli to secrete the bacteriocin lysostaphin which specifically kills Staphyloccocus aureus with low probability of raising antibiotic resistance. We demonstrated that living materials containing this lysostaphin-secreting E. coli inhibit the growth of S. aureus, including the strain resistant to methicillin (MRSA). Our tunable platform allows stable integration of programmable cells in dextran-based hydrogels without compromising free diffusion of macromolecules and could have potential applications in biotechnology and biomedicine.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Martijn Nijs
- Stichting PAMM, Laboratory for Pathology and Medical Microbiology, De Run 6250, Veldhoven, 5504 DL, The Netherlands
| | - Jitske Stalpers
- Stichting PAMM, Laboratory for Pathology and Medical Microbiology, De Run 6250, Veldhoven, 5504 DL, The Netherlands
| | | | | | | | - Kees Verduin
- Stichting PAMM, Laboratory for Pathology and Medical Microbiology, De Run 6250, Veldhoven, 5504 DL, The Netherlands
| | | | | | - Tom F. A. de Greef
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
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29
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Wouters SA, Vugs WJP, Arts R, de Leeuw NM, Teeuwen RWH, Merkx M. Bioluminescent Antibodies through Photoconjugation of Protein G-Luciferase Fusion Proteins. Bioconjug Chem 2020; 31:656-662. [PMID: 31909607 PMCID: PMC7086395 DOI: 10.1021/acs.bioconjchem.9b00804] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/06/2020] [Indexed: 12/18/2022]
Abstract
Bioluminescent antibodies represent attractive detection agents in both bioanalytical assays and imaging. Currently, their preparation relies on genetic fusion of luciferases to antibodies or nonspecific chemical conjugation strategies. Here, we report a generic method to generate well-defined covalent antibody-luciferase conjugates starting from commercially available monoclonal antibodies. Our approach uses fusion proteins consisting of the bright blue light-emitting luciferase NanoLuc (NL) and an Fc-binding protein domain (Gx) that can be photo-cross-linked to the antibody using UV light illumination. Green and red color variants were constructed by tight fusion of the NanoLuc with a green fluorescent acceptor domain and introduction of Cy3, respectively. To increase the already bright NanoLuc emission, tandem fusions were successfully developed in which the Gx domain is fused to two or three copies of the NanoLuc domain. The Gx-NL fusion proteins can be efficiently photo-cross-linked to all human immunoglobulin G (IgG) isotypes and most mammalian IgG's using 365 nm light, yielding antibodies with either one or two luciferase domains. The bioluminescent antibodies were successfully used in cell immunostaining and bioanalytical assays such as enzyme-linked immunosorbent assay (ELISA) and Western blotting.
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Affiliation(s)
- Simone
F. A. Wouters
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Willem J. P. Vugs
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Remco Arts
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Nynke M. de Leeuw
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Roy W. H. Teeuwen
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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30
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Gooding JJ, Mazur A, Bakker E, Kelley S, Tao N, Sailor M, Merkx M, Mao L, Clark H. Happy 5th Anniversary for ACS Sensors. ACS Sens 2020; 5:1-2. [PMID: 31973528 DOI: 10.1021/acssensors.0c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J Justin Gooding
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Antonella Mazur
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Eric Bakker
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Shana Kelley
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Nongjian Tao
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Michael Sailor
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Maarten Merkx
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Lanqun Mao
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
| | - Heather Clark
- The University of New South Wales , Sydney , Australia.,ACS Publications , Washington , DC , United States.,The University of Geneva , Geneva , Switzerland.,The University of Toronto , Toronto , Ontario Canada.,Arizona State University , Tempe , Arizona United States.,University of California, San Diego , San Diego , California United States.,Technische Universiteit Eindhoven , Eindhoven , The Netherlands.,Institute of Chemistry , Chinese Academy of Sciences Beijing , China.,Northeastern University , Boston , Massachusetts United States
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31
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Engelen W, Zhu K, Subedi N, Idili A, Ricci F, Tel J, Merkx M. Programmable Bivalent Peptide-DNA Locks for pH-Based Control of Antibody Activity. ACS Cent Sci 2020; 6:22-31. [PMID: 31989023 PMCID: PMC6978833 DOI: 10.1021/acscentsci.9b00964] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Indexed: 05/11/2023]
Abstract
The ability to control antibody activity by pH has important applications in diagnostics, therapeutic antibody targeting, and antibody-guided imaging. Here, we report the rational design of bivalent peptide-DNA ligands that allow pH-dependent control of antibody activity. Our strategy uses a pH-responsive DNA triple helix to control switching from a tight-binding bivalent peptide-DNA lock into a weaker-binding monovalent ligand. Different designs are introduced that allow antibody activation at both basic and acidic pHs, either autonomously or in the presence of an additional oligonucleotide trigger. The pH of antibody activation could be precisely tuned by changing the DNA triple helix sequence. The peptide-DNA locks allowed pH-dependent antibody targeting of tumor cells both in bulk and for single cells confined in water-in-oil microdroplets. The latter approach enables high-throughput antibody-mediated detection of single tumor cells based on their distinctive metabolic activity.
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Affiliation(s)
- Wouter Engelen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Kwankwan Zhu
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Nikita Subedi
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- Laboratory
of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Andrea Idili
- Dipartimento
di Scienze e Tecnologie Chimiche, University
of Rome, Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Dipartimento
di Scienze e Tecnologie Chimiche, University
of Rome, Tor Vergata, Rome 00133, Italy
| | - Jurjen Tel
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- Laboratory
of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
- E-mail:
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32
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Oudejans S, de Weert-van Oene G, Spits M, de Wildt W, Merkx M, Dekker J, Visch I, Goudriaan A. A Self-Reported Version of the Measurements in the Addictions for Triage and Evaluation-Q: Concurrent Validity with the MATE 2.1. Eur Addict Res 2020; 26:20-27. [PMID: 31639811 PMCID: PMC6979419 DOI: 10.1159/000503625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Substance abuse treatment centers require reliable and valid instruments to monitor treatment progress, to evaluate treatment effectiveness, and to initiate clinical trials. Currently the Measurements in the Addictions for Triage and Evaluation (MATE) 2.1, an instrument that serves these purposes, is considered quite lengthy and intensive, especially in the case of allocation to milder treatment intensity. Therefore, a self-reported version of the MATE-Q was designed for patients with mild to moderate substance-abuse and co-occurring problems. The aim of the present study was to assess concurrent validity with the interviewer version of the MATE (version 2.1). MATERIALS AND METHODS Data were collected at 2 locations of a Dutch substance abuse treatment center, one location in a large city and one in a suburban area. A correlational design was employed, where each included participant completed a MATE-Q and a MATE 2.1 within 3 days or less (administered at intake, before treatment initiation). A total of 98 treatment-seeking patients were included (51.0% alcohol as a primary problem, 19.4% cannabis, 14.3% gambling and 6.1% cocaine). Measurements included the MATE-Q and the MATE 2.1. Intraclass correlation coefficients (ICCs) for single measures were calculated, deploying the 2-way mixed procedure with absolute agreement. Descriptives of scores comprise means and Cronbach's alpha for internal consistency. RESULTS For the majority (15 out of 24) of the scores ICCs were equal or above 0.7. For 93 patients (95%), the primary problem substance or problem behavior was reported correspondingly. Nine MATE-Q mean scores differed significantly from their MATE 2.1 counterparts. DISCUSSION/CONCLUSION For the majority of scores, the MATE-Q has acceptable concurrent validity for the assessment of patients with mild to moderate substance abuse and co-occurring problems.
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Affiliation(s)
- Suzan Oudejans
- aMark Bench, Amsterdam, The Netherlands,bAmsterdam UMC Department of Psychiatry, Amsterdam Institute for Addiction Research, Amsterdam, The Netherlands,fPhrenos Center of Expertise, Utrecht, The Netherlands,*Suzan Oudejans, Mark Bench, Rhôneweg 16, NL–1043AH Amsterdam (The Netherlands), E-Mail
| | - Gerdien de Weert-van Oene
- dArkin Mental Healthcare Services, Amsterdam, The Netherlands,gNovadic-Kentron, Network for Addiction Treatment, Vught, The Netherlands
| | - Masha Spits
- aMark Bench, Amsterdam, The Netherlands,bAmsterdam UMC Department of Psychiatry, Amsterdam Institute for Addiction Research, Amsterdam, The Netherlands,eDutch Addiction Association, Amersfoort, The Netherlands
| | - Wencke de Wildt
- cJellinek Substance Abuse Treatment Center, Amsterdam, The Netherlands,dArkin Mental Healthcare Services, Amsterdam, The Netherlands
| | - Maarten Merkx
- bAmsterdam UMC Department of Psychiatry, Amsterdam Institute for Addiction Research, Amsterdam, The Netherlands,hHSK, Arnhem, The Netherlands
| | - Jack Dekker
- dArkin Mental Healthcare Services, Amsterdam, The Netherlands,iVrije Universiteit, Faculty of Behavioral and Movement Science, Amsterdam, The Netherlands
| | - Irene Visch
- dArkin Mental Healthcare Services, Amsterdam, The Netherlands
| | - Anneke Goudriaan
- bAmsterdam UMC Department of Psychiatry, Amsterdam Institute for Addiction Research, Amsterdam, The Netherlands,dArkin Mental Healthcare Services, Amsterdam, The Netherlands
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34
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Abstract
Antibody‐based molecular recognition plays a central role in today's life sciences, ranging from immunoassays to molecular imaging and antibody‐based therapeutics. Control over antibody activity by using external triggers such as light could further increase the specificity of antibody‐based targeting. Here we present bivalent peptide–DNA ligands containing photocleavable linkers as a noncovalent approach by which to allow photoactivation of antibody activity. Light‐triggered cleavage of the 3‐amino‐3‐(2‐nitrophenyl)propionic acid peptide linker converted the high‐affinity bivalent peptide–DNA lock into weakly binding monovalent ligands, effectively restoring antibody targeting of cell‐surface receptors. In this work, a proof of principle was provided with an anti‐hemagglutinin antibody, but the molecular design of the lock is generic and applicable to any monoclonal antibody for which an epitope or mimotope of sufficient affinity is available.
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Affiliation(s)
- Simone F A Wouters
- Laboratory of Chemical Biology and, Institute of Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 4500 MB, Eindhoven, The Netherlands
| | - Elvira Wijker
- Laboratory of Chemical Biology and, Institute of Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 4500 MB, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and, Institute of Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 4500 MB, Eindhoven, The Netherlands
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35
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Merkx M. Too Creative for Our Own Good: Reframing Sensors as Chemical Clickbait. ACS Sens 2019; 4:1452. [PMID: 31248262 DOI: 10.1021/acssensors.9b01046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maarten Merkx
- Eindhoven University of Technology, Eindhoven, The Netherlands
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36
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Abstract
![]()
Recent
years have witnessed an increasing interest in hybrid
molecular systems in which the programmability of DNA hybridization
is used to introduce enhanced molecular control in synthetic systems.
The first examples of DNA-functionalized supramolecular polymers have
been reported only recently, but have already revealed structural
and functional properties that are not easily obtained in either synthetic
supramolecular polymers or DNA-only based systems. In this Topical
Review, we provide an overview of the various forms of additional
control offered by DNA hybridization for different types of supramolecular
polymers and discuss how orthogonal supramolecular interactions in
these hybrid systems can give rise to emergent structural and functional
properties.
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37
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Abstract
Bioluminescent sensor proteins provide attractive tools for applications ranging from in vivo imaging to point-of-care testing. Here we introduce a new class of ratiometric bioluminescent sensor proteins that do not rely on direct modulation of BRET efficiency, but are based on competitive intramolecular complementation of split NanoLuc luciferase. Proof of concept for the feasibility of this sensor principle was provided by developing a blue-red light emitting sensor protein for the detection of anti-HIV1-p17 antibodies with a 500% change in emission ratio and a Kd of 10 pM. The new sensor design also improved the dynamic response of a sensor for the therapeutic antibody cetuximab 4-fold, allowing the direct quantification of this anti-EGFR antibody in undiluted blood plasma. The modular sensor architecture allows easy and systematic tuning of a sensor's dynamic range and should be generally applicable to allow rational engineering of bioluminescent sensor proteins.
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Affiliation(s)
- Yan Ni
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Remco Arts
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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38
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Tenda K, van Gerven B, Arts R, Hiruta Y, Merkx M, Citterio D. Rücktitelbild: Paper‐Based Antibody Detection Devices Using Bioluminescent BRET‐Switching Sensor Proteins (Angew. Chem. 47/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Keisuke Tenda
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
| | - Benice van Gerven
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Remco Arts
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Yuki Hiruta
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
| | - Maarten Merkx
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Daniel Citterio
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
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39
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Tenda K, van Gerven B, Arts R, Hiruta Y, Merkx M, Citterio D. Paper‐Based Antibody Detection Devices Using Bioluminescent BRET‐Switching Sensor Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Keisuke Tenda
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
| | - Benice van Gerven
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Remco Arts
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Yuki Hiruta
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
| | - Maarten Merkx
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Daniel Citterio
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
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40
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Tenda K, van Gerven B, Arts R, Hiruta Y, Merkx M, Citterio D. Back Cover: Paper‐Based Antibody Detection Devices Using Bioluminescent BRET‐Switching Sensor Proteins (Angew. Chem. Int. Ed. 47/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201811030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Keisuke Tenda
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
| | - Benice van Gerven
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Remco Arts
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Yuki Hiruta
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
| | - Maarten Merkx
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS)Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven The Netherlands
| | - Daniel Citterio
- Department of Applied ChemistryKeio University 3-14-1 Hiyoshi Kohoku-ku 223-8522 Yokohama Japan
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41
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Aper SJA, den Hamer A, Wouters SFA, Lemmens LJM, Ottmann C, Brunsveld L, Merkx M. Protease-Activatable Scaffold Proteins as Versatile Molecular Hubs in Synthetic Signaling Networks. ACS Synth Biol 2018; 7:2216-2225. [PMID: 30125482 PMCID: PMC6154215 DOI: 10.1021/acssynbio.8b00217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 12/29/2022]
Abstract
Protease signaling and scaffold-induced control of protein-protein interactions represent two important mechanisms for intracellular signaling. Here we report a generic and modular approach to control the activity of scaffolding proteins by protease activity, creating versatile molecular platforms to construct synthetic signaling networks. Using 14-3-3 proteins as a structurally well-characterized and important class of scaffold proteins, three different architectures were explored to achieve optimal protease-mediated control of scaffold activity, fusing either one or two monovalent inhibitory ExoS peptides or a single bivalent ExoS peptide to T14-3-3 using protease-cleavable linkers. Analysis of scaffolding activity before and after protease-induced cleavage revealed optimal control of 14-3-3 activity for the system that contained monovalent ExoS peptides fused to both the N-and C-terminus, each blocking a single T14-3-3 binding site. The protease-activatable 14-3-3 scaffolds were successfully applied to construct a three-step signaling cascade in which dimerization and activation of FGG-caspase-9 on an orthogonal supramolecular platform resulted in activation of a 14-3-3 scaffold, which in turn allowed 14-3-3-templated complementation of a split-luciferase. In addition, by combining 14-3-3-templated activation of caspase-9 with a caspase-9-activatable 14-3-3 scaffold, the first example of a synthetic self-activating protease signaling network was created. Protease-activatable 14-3-3 proteins thus represent a modular platform whose properties can be rationally engineered to fit different applications, both to create artificial in vitro synthetic molecular networks and as a novel signaling hub to re-engineer intracellular signaling pathways.
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Affiliation(s)
- Stijn J. A. Aper
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Anniek den Hamer
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F. A. Wouters
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lenne J. M. Lemmens
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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42
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Tenda K, van Gerven B, Arts R, Hiruta Y, Merkx M, Citterio D. Paper-Based Antibody Detection Devices Using Bioluminescent BRET-Switching Sensor Proteins. Angew Chem Int Ed Engl 2018; 57:15369-15373. [PMID: 30168634 PMCID: PMC6282528 DOI: 10.1002/anie.201808070] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [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] [Received: 07/15/2018] [Indexed: 12/04/2022]
Abstract
This work reports on fully integrated “sample‐in‐signal‐out” microfluidic paper‐based analytical devices (μPADs) relying on bioluminescence resonance energy transfer (BRET) switches for analyte recognition and colorimetric signal generation. The devices use BRET‐based antibody sensing proteins integrated into vertically assembled layers of functionalized paper, and their design enables sample volume‐independent and fully reagent‐free operation, including on‐device blood plasma separation. User operation is limited to the application of a single drop (20–30 μL) of sample (serum, whole blood) and the acquisition of a photograph 20 min after sample introduction, with no requirement for precise pipetting, liquid handling, or analytical equipment except for a camera. Simultaneous detection of three different antibodies (anti‐HIV1, anti‐HA, and anti‐DEN1) in whole blood was achieved. Given its simplicity, this type of device is ideally suited for user‐friendly point‐of‐care testing in low‐resource environments.
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Affiliation(s)
- Keisuke Tenda
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 223-8522, Yokohama, Japan
| | - Benice van Gerven
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands
| | - Remco Arts
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands
| | - Yuki Hiruta
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 223-8522, Yokohama, Japan
| | - Maarten Merkx
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands
| | - Daniel Citterio
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 223-8522, Yokohama, Japan
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Gooding JJ, Mazur A, Merkx M, Kelley S, Tao N, Long YT, Bakker E, Sailor M. First Impact Factor for ACS Sensors - 5.711. ACS Sens 2018; 3:1218-1219. [PMID: 30049217 DOI: 10.1021/acssensors.8b00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Maarten Merkx
- Technische Universiteit Eindhoven, Eindhoven, Netherlands
| | | | | | - Yi-Tao Long
- East China University of Science and Technology, Shanghai, China
| | - Eric Bakker
- The University of Geneva, Geneva, Switzerland
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Abstract
![]()
Dynamic
DNA-based circuits represent versatile systems to perform
complex computing operations at the molecular level. However, the
majority of DNA circuits relies on freely diffusing reactants, which
slows down their rate of operation substantially. Here we introduce
the use of DNA-functionalized benzene-1,3,5-tricarboxamide (BTA) supramolecular
polymers as dynamic scaffolds to template DNA-based molecular computing.
By selectively recruiting DNA circuit components to a supramolecular
BTA polymer functionalized with 10-nucleotide handle strands, the
kinetics of strand displacement and strand exchange reactions were
accelerated 100-fold. In addition, strand exchange reactions were
also favored thermodynamically by bivalent interactions between the
reaction product and the supramolecular polymer. The noncovalent assembly
of the supramolecular polymers enabled straightforward optimization
of the polymer composition to best suit various applications. The
ability of supramolecular BTA polymers to increase the efficiency
of DNA-based computing was demonstrated for three well-known and practically
important DNA-computing operations: multi-input AND gates, Catalytic
Hairpin Assembly and Hybridization Chain Reactions. This work thus
establishes supramolecular BTA polymers as an efficient platform for
DNA-based molecular operations, paving the way for the construction
of autonomous bionanomolecular systems that confine and combine molecular
sensing, computation, and actuation.
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Affiliation(s)
- Wouter Engelen
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Sjors P W Wijnands
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Maarten Merkx
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
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Affiliation(s)
- Maarten Merkx
- Technische Universiteit Eindhoven, Eindhoven, Netherlands
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46
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Rosier BJHM, Cremers GAO, Engelen W, Merkx M, Brunsveld L, de Greef TFA. Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy. Chem Commun (Camb) 2018; 53:7393-7396. [PMID: 28617516 PMCID: PMC5708335 DOI: 10.1039/c7cc04178k] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A photocrosslinkable protein G adapter was used to site-specifically conjugate complex native proteins to oligonucleotides, allowing for efficient incorporation on DNA origami nanostructures.
A photocrosslinkable protein G variant was used as an adapter protein to covalently and site-specifically conjugate an antibody and an Fc-fusion protein to an oligonucleotide. This modular approach enables straightforward decoration of DNA nanostructures with complex native proteins while retaining their innate binding affinity, allowing precise control over the nanoscale spatial organization of such proteins for in vitro and in vivo biomedical applications.
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Affiliation(s)
- Bas J H M Rosier
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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47
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Engelen W, van de Wiel KM, Meijer LHH, Saha B, Merkx M. Nucleic acid detection using BRET-beacons based on bioluminescent protein-DNA hybrids. Chem Commun (Camb) 2018; 53:2862-2865. [PMID: 28217801 PMCID: PMC5436041 DOI: 10.1039/c6cc10032e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Bioluminescent molecular beacons have been developed using a modular design approach that relies on BRET between the bright luciferase NanoLuc and a Cy3 acceptor.
Bioluminescent molecular beacons have been developed using a modular design approach that relies on BRET between the bright luciferase NanoLuc and a Cy3 acceptor. While classical molecular beacons are hampered by background fluorescence and scattering, these BRET-beacons allow detection of low pM concentrations of nucleic acids directly in complex media.
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Affiliation(s)
- Wouter Engelen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands.
| | - Kayleigh M van de Wiel
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands.
| | - Lenny H H Meijer
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands.
| | - Bedabrata Saha
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600 MB, Eindhoven, The Netherlands.
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48
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van Rosmalen M, Ni Y, Vervoort DFM, Arts R, Ludwig SKJ, Merkx M. Dual-Color Bioluminescent Sensor Proteins for Therapeutic Drug Monitoring of Antitumor Antibodies. Anal Chem 2018; 90:3592-3599. [PMID: 29443503 PMCID: PMC5843950 DOI: 10.1021/acs.analchem.8b00041] [Citation(s) in RCA: 38] [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] [Indexed: 12/21/2022]
Abstract
Monitoring the levels of therapeutic antibodies in individual patients would allow patient-specific dose optimization, with the potential for major therapeutic and financial benefits. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor) that allow antibody detection directly in blood plasma. In this study, we targeted four clinically important therapeutic antibodies, the Her2-receptor targeting trastuzumab, the anti-CD20 antibodies rituximab and obinutuzumab, and the EGFR-blocking cetuximab. A strong correlation was found between the affinity of the antibody binding peptide and sensor performance. LUMABS sensors with physiologically relevant affinities and decent sensor responses were obtained for trastuzumab and cetuximab using mimotope and meditope peptides, respectively, with affinities in the 10-7 M range. The lower affinity of the CD20-derived cyclic peptide employed in the anti-CD20 LUMABS sensor ( Kd = 10-5 M), translated in a LUMABS sensor with a strongly attenuated sensor response. The trastuzumab and cetuximab sensors were further characterized with respect to binding kinetics and their performance in undiluted blood plasma. For both antibodies, LUMABS-based detection directly in plasma compared well to the analytical performance of commercial ELISA kits. Besides identifying important design parameters for the development of new LUMABS sensors, this work demonstrates the potential of the LUMABS platform for point-of-care detection of therapeutic antibodies.
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Affiliation(s)
- Martijn van Rosmalen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Yan Ni
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Daan F M Vervoort
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Remco Arts
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Susann K J Ludwig
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
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49
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Gooding JJ, Mazur A, Sailor M, Merkx M, Kelley S, Tao N, Long Y, Bakker E. An Exciting Year Ahead for ACS Sensors. ACS Sens 2018; 3:1-2. [PMID: 29370705 DOI: 10.1021/acssensors.8b00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Michael Sailor
- University of California , San Diego, California United States
| | - Maarten Merkx
- Technische Universiteit Eindhoven , Eindhoven, The Netherlands
| | - Shana Kelley
- The University of Toronto , Toronto, Ontario Canada
| | - Nongjian Tao
- Arizona State University , Tempe, Arizona, United States
| | - Yitao Long
- East China University of Science and Technology , Shanghai, China
| | - Eric Bakker
- The University of Geneva , Geneva, Switzerland
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50
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Wijnands SPW, Engelen W, Lafleur RPM, Meijer EW, Merkx M. Controlling protein activity by dynamic recruitment on a supramolecular polymer platform. Nat Commun 2018; 9:65. [PMID: 29302054 PMCID: PMC5754363 DOI: 10.1038/s41467-017-02559-0] [Citation(s) in RCA: 38] [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: 08/30/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022] Open
Abstract
Nature uses dynamic molecular platforms for the recruitment of weakly associating proteins into higher-order assemblies to achieve spatiotemporal control of signal transduction. Nanostructures that emulate this dynamic behavior require features such as plasticity, specificity and reversibility. Here we introduce a synthetic protein recruitment platform that combines the dynamics of supramolecular polymers with the programmability offered by DNA-mediated protein recruitment. Assembly of benzene-1,3,5-tricarboxamide (BTA) derivatives functionalized with a 10-nucleotide receptor strand into µm-long supramolecular BTA polymers is remarkably robust, even with high contents of DNA-functionalized BTA monomers and associated proteins. Specific recruitment of DNA-conjugated proteins on the supramolecular polymer results in a 1000-fold increase in protein complex formation, while at the same time enabling their rapid exchange along the BTA polymer. Our results establish supramolecular BTA polymers as a generic protein recruitment platform and demonstrate how assembly of protein complexes along the supramolecular polymer allows efficient and dynamic control of protein activity. DNA-origami allows the precise recruitment of DNA-protein conjugates but lacks the dynamics found in natural protein assemblies. Here the authors present a synthetic polymer platform that combines the dynamics of supramolecular polymers with the programmability of DNA-mediated protein recruitment.
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Affiliation(s)
- Sjors P W Wijnands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Wouter Engelen
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - René P M Lafleur
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.
| | - Maarten Merkx
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands. .,Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.
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