1
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Beyer HM, Kumar S, Nieke M, Diehl CMC, Tang K, Shumka S, Koh CS, Fleck C, Davies JA, Khammash M, Zurbriggen MD. Genetically-stable engineered optogenetic gene switches modulate spatial cell morphogenesis in two- and three-dimensional tissue cultures. Nat Commun 2024; 15:10470. [PMID: 39622829 PMCID: PMC11612184 DOI: 10.1038/s41467-024-54350-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 11/08/2024] [Indexed: 12/06/2024] Open
Abstract
Recent advances in tissue engineering have been remarkable, yet the precise control of cellular behavior in 2D and 3D cultures remains challenging. One approach to address this limitation is to genomically engineer optogenetic control of cellular processes into tissues using gene switches that can operate with only a few genomic copies. Here, we implement blue and red light-responsive gene switches to engineer genomically stable two- and three-dimensional mammalian tissue models. Notably, we achieve precise control of cell death and morphogen-directed patterning in 2D and 3D tissues by optogenetically regulating cell necroptosis and synthetic WNT3A signaling at high spatiotemporal resolution. This is accomplished using custom-built patterned LED systems, including digital mirrors and photomasks, as well as laser techniques. These advancements demonstrate the capability of precise spatiotemporal modulation in tissue engineering and open up new avenues for developing programmable 3D tissue and organ models, with significant implications for biomedical research and therapeutic applications.
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Affiliation(s)
- Hannes M Beyer
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
| | - Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Klingelbergstrasse 48, Basel, Switzerland
| | - Marius Nieke
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
| | - Carroll M C Diehl
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
| | - Kun Tang
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
| | - Sara Shumka
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
| | - Cha San Koh
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Ernst-Zermelo-Straße 1, Freiburg im Breisgau, Germany
| | - Jamie A Davies
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Klingelbergstrasse 48, Basel, Switzerland.
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany.
- CEPLAS - Cluster of Excellence on Plant Sciences, Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany.
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2
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Idstein V, Ehret AK, Yousefi OS, Schamel WW. Engineering of an Optogenetic T Cell Receptor Compatible with Fluorescence-Based Readouts. ACS Synth Biol 2023; 12:2857-2864. [PMID: 37781987 DOI: 10.1021/acssynbio.3c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Optogenetics offers a set of tools for the precise manipulation of signaling pathways. Here we exploit optogenetics to experimentally change the kinetics of protein-protein interactions on demand. We had developed a system in which the interaction of a modified T cell receptor (TCR) with an engineered ligand can be controlled by light. The ligand was the plant photoreceptor phytochrome B (PhyB) and the TCR included a TCRβ chain fused to GFP and a mutated PhyB-interacting factor (PIFS), resulting in the GFP-PIFS-TCR. We failed to engineer a nonfluorescent PIFS-fused TCR, since PIFS did not bind to PhyB when omitting GFP. Here we tested nine different versions of PIFS-fused TCRs. We found that the SNAP-PIFS-TCR was expressed well on the surface, bound to PhyB, and subsequently elicited activation signals. This receptor could be combined with a GFP reporter system in which the expression of GFP is driven by the transcription factor NF-AT.
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Affiliation(s)
- Vincent Idstein
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, and Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19a, 79104 Freiburg, Germany
| | - Anna K Ehret
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, and Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19a, 79104 Freiburg, Germany
| | - O Sascha Yousefi
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Wolfgang W Schamel
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, and Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106 Freiburg, Germany
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3
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Nzigou Mombo B, Bijonowski BM, Raab CA, Niland S, Brockhaus K, Müller M, Eble JA, Wegner SV. Reversible photoregulation of cell-cell adhesions with opto-E-cadherin. Nat Commun 2023; 14:6292. [PMID: 37813868 PMCID: PMC10562482 DOI: 10.1038/s41467-023-41932-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
E-cadherin-based cell-cell adhesions are dynamically and locally regulated in many essential processes, including embryogenesis, wound healing and tissue organization, with dysregulation manifesting as tumorigenesis and metastasis. However, the lack of tools that would provide control of the high spatiotemporal precision observed with E-cadherin adhesions hampers investigation of the underlying mechanisms. Here, we present an optogenetic tool, opto-E-cadherin, that allows reversible control of E-cadherin-mediated cell-cell adhesions with blue light. With opto-E-cadherin, functionally essential calcium binding is photoregulated such that cells expressing opto-E-cadherin at their surface adhere to each other in the dark but not upon illumination. Consequently, opto-E-cadherin provides remote control over multicellular aggregation, E-cadherin-associated intracellular signalling and F-actin organization in 2D and 3D cell cultures. Opto-E-cadherin also allows switching of multicellular behaviour between single and collective cell migration, as well as of cell invasiveness in vitro and in vivo. Overall, opto-E-cadherin is a powerful optogenetic tool capable of controlling cell-cell adhesions at the molecular, cellular and behavioural level that opens up perspectives for the study of dynamics and spatiotemporal control of E-cadherin in biological processes.
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Affiliation(s)
- Brice Nzigou Mombo
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Brent M Bijonowski
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Christopher A Raab
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Stephan Niland
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Katrin Brockhaus
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Marc Müller
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany.
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4
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Russ M, Ehret AK, Hörner M, Peschkov D, Bohnert R, Idstein V, Minguet S, Weber W, Lillemeier BF, Yousefi OS, Schamel WW. Opto-APC: Engineering of cells that display phytochrome B on their surface for optogenetic studies of cell-cell interactions. Front Mol Biosci 2023; 10:1143274. [PMID: 36936981 PMCID: PMC10016228 DOI: 10.3389/fmolb.2023.1143274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
The kinetics of a ligand-receptor interaction determine the responses of the receptor-expressing cell. One approach to experimentally and reversibly change this kinetics on demand is optogenetics. We have previously developed a system in which the interaction of a modified receptor with an engineered ligand can be controlled by light. In this system the ligand is a soluble Phytochrome B (PhyB) tetramer and the receptor is fused to a mutated PhyB-interacting factor (PIFS). However, often the natural ligand is not soluble, but expressed as a membrane protein on another cell. This allows ligand-receptor interactions in two dimensions. Here, we developed a strategy to generate cells that display PhyB as a membrane-bound protein by expressing the SpyCatcher fused to a transmembrane domain in HEK-293T cells and covalently coupling purified PhyB-SpyTag to these cells. As proof-of-principle, we use Jurkat T cells that express a GFP-PIFS-T cell receptor and show that these cells can be stimulated by the PhyB-coupled HEK-293T cells in a light dependent manner. Thus, we call the PhyB-coupled cells opto-antigen presenting cells (opto-APCs). Our work expands the toolbox of optogenetic technologies, allowing two-dimensional ligand-receptor interactions to be controlled by light.
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Affiliation(s)
- Marissa Russ
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna K. Ehret
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Maximilian Hörner
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Peschkov
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Rebecca Bohnert
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Vincent Idstein
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Susana Minguet
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Björn F. Lillemeier
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - O. Sascha Yousefi
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wolfgang W. Schamel
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- *Correspondence: Wolfgang W. Schamel,
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5
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Engineered Allosteric Regulation of Protein Function. J Mol Biol 2022; 434:167620. [PMID: 35513109 DOI: 10.1016/j.jmb.2022.167620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/27/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
Allosteric regulation of proteins has been utilized to study various aspects of cell signaling, from unicellular events to organism-wide phenotypes. However, traditional methods of allosteric regulation, such as constitutively active mutants and inhibitors, lack tight spatiotemporal control. This often leads to unintended signaling consequences that interfere with data interpretation. To overcome these obstacles, researchers employed protein engineering approaches that enable tight control of protein function through allosteric mechanisms. These methods provide high specificity as well as spatial and temporal precision in regulation of protein activity in vitro and in vivo. In this review, we focus on the recent advancements in engineered allosteric regulation and discuss the various bioengineered allosteric techniques available now, from chimeric GPCRs to chemogenetic and optogenetic switches. We highlight the benefits and pitfalls of each of these techniques as well as areas in which future improvements can be made. Additionally, we provide a brief discussion on implementation of engineered allosteric regulation approaches, demonstrating that these tools can shed light on elusive biological events and have the potential to be utilized in precision medicine.
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6
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Abstract
Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically-encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated "optophysiology"), and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
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7
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Lehtinen K, Nokia MS, Takala H. Red Light Optogenetics in Neuroscience. Front Cell Neurosci 2022; 15:778900. [PMID: 35046775 PMCID: PMC8761848 DOI: 10.3389/fncel.2021.778900] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used in studying brain function. A multitude of optogenetic tools for neuroscience have been created that, for example, enable the control of action potential generation via light-activated ion channels. Other optogenetic proteins have been used in the brain, for example, to control long-term potentiation or to ablate specific subtypes of neurons. In in vivo applications, however, the majority of optogenetic tools are operated with blue, green, or yellow light, which all have limited penetration in biological tissues compared to red light and especially infrared light. This difference is significant, especially considering the size of the rodent brain, a major research model in neuroscience. Our review will focus on the utilization of red light-operated optogenetic tools in neuroscience. We first outline the advantages of red light for in vivo studies. Then we provide a brief overview of the red light-activated optogenetic proteins and systems with a focus on new developments in the field. Finally, we will highlight different tools and applications, which further facilitate the use of red light optogenetics in neuroscience.
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Affiliation(s)
- Kimmo Lehtinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Miriam S. Nokia
- Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
- Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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8
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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9
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Lavrador P, Gaspar VM, Mano JF. Engineering mammalian living materials towards clinically relevant therapeutics. EBioMedicine 2021; 74:103717. [PMID: 34839265 PMCID: PMC8628209 DOI: 10.1016/j.ebiom.2021.103717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
Engineered living materials represent a new generation of human-made biotherapeutics that are highly attractive for a myriad of medical applications. In essence, such cell-rich platforms provide encodable bioactivities with extended lifetimes and environmental multi-adaptability currently unattainable in conventional biomaterial platforms. Emerging cell bioengineering tools are herein discussed from the perspective of materializing living cells as cooperative building blocks that drive the assembly of multiscale living materials. Owing to their living character, pristine cellular units can also be imparted with additional therapeutically-relevant biofunctionalities. On this focus, the most recent advances on the engineering of mammalian living materials and their biomedical applications are herein outlined, alongside with a critical perspective on major roadblocks hindering their realistic clinical translation. All in all, transposing the concept of leveraging living materials as autologous tissue-building entities and/or self-regulated biotherapeutics opens new realms for improving precision and personalized medicine strategies in the foreseeable future.
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Affiliation(s)
- Pedro Lavrador
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Vítor M Gaspar
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - João F Mano
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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10
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Luo Y, Li J, Li B, Xia Y, Wang H, Fu C. Physical Cues of Matrices Reeducate Nerve Cells. Front Cell Dev Biol 2021; 9:731170. [PMID: 34646825 PMCID: PMC8502847 DOI: 10.3389/fcell.2021.731170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/20/2021] [Indexed: 11/15/2022] Open
Abstract
The behavior of nerve cells plays a crucial role in nerve regeneration. The mechanical, topographical, and electrical microenvironment surrounding nerve cells can activate cellular signaling pathways of mechanical transduction to affect the behavior of nerve cells. Recently, biological scaffolds with various physical properties have been developed as extracellular matrix to regulate the behavior conversion of nerve cell, such as neuronal neurite growth and directional differentiation of neural stem cells, providing a robust driving force for nerve regeneration. This review mainly focused on the biological basis of nerve cells in mechanical transduction. In addition, we also highlighted the effect of the physical cues, including stiffness, mechanical tension, two-dimensional terrain, and electrical conductivity, on neurite outgrowth and differentiation of neural stem cells and predicted their potential application in clinical nerve tissue engineering.
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Affiliation(s)
- Yiqian Luo
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jie Li
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Baoqin Li
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yuanliang Xia
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Hengyi Wang
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Changfeng Fu
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
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11
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Wichert N, Witt M, Blume C, Scheper T. Clinical applicability of optogenetic gene regulation. Biotechnol Bioeng 2021; 118:4168-4185. [PMID: 34287844 DOI: 10.1002/bit.27895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/27/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022]
Abstract
The field of optogenetics is rapidly growing in relevance and number of developed tools. Among other things, the optogenetic repertoire includes light-responsive ion channels and methods for gene regulation. This review will be confined to the optogenetic control of gene expression in mammalian cells as suitable models for clinical applications. Here optogenetic gene regulation might offer an excellent method for spatially and timely regulated gene and protein expression in cell therapeutic approaches. Well-known systems for gene regulation, such as the LOV-, CRY2/CIB-, PhyB/PIF-systems, as well as other, in mammalian cells not yet fully established systems, will be described. Advantages and disadvantages with regard to clinical applications are outlined in detail. Among the many unanswered questions concerning the application of optogenetics, we discuss items such as the use of exogenous chromophores and their effects on the biology of the cells and methods for a gentle, but effective gene transfection method for optogenetic tools for in vivo applications.
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Affiliation(s)
- Nina Wichert
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Martin Witt
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Cornelia Blume
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Thomas Scheper
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
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12
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Wagner HJ, Mohsenin H, Weber W. Synthetic Biology-Empowered Hydrogels for Medical Diagnostics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 178:197-226. [PMID: 33582837 DOI: 10.1007/10_2020_158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Synthetic biology is strongly inspired by concepts of engineering science and aims at the design and generation of artificial biological systems in different fields of research such as diagnostics, analytics, biomedicine, or chemistry. To this aim, synthetic biology uses an engineering approach relying on a toolbox of molecular sensors and switches that endows cellular hosts with non-natural computing functions and circuits. Importantly, this concept is not only limited to cellular approaches. Synthetic biological building blocks have also conferred sensing and switching capability to otherwise inactive materials. This principle has attracted high interest for the development of biohybrid materials capable of sensing and responding to specific molecular stimuli, such as disease biomarkers, antibiotics, or heavy metals. Moreover, the interconnection of individual sense-and-respond materials to complex materials systems has enabled the processing of, for example, multiple inputs or the amplification of signals using feedback topologies. Such systems holding high potential for applications in the analytical and diagnostic sectors will be described in this chapter.
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Affiliation(s)
- Hanna J Wagner
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Hasti Mohsenin
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wilfried Weber
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.
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13
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Burgos-Morales O, Gueye M, Lacombe L, Nowak C, Schmachtenberg R, Hörner M, Jerez-Longres C, Mohsenin H, Wagner H, Weber W. Synthetic biology as driver for the biologization of materials sciences. Mater Today Bio 2021; 11:100115. [PMID: 34195591 PMCID: PMC8237365 DOI: 10.1016/j.mtbio.2021.100115] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 01/16/2023] Open
Abstract
Materials in nature have fascinating properties that serve as a continuous source of inspiration for materials scientists. Accordingly, bio-mimetic and bio-inspired approaches have yielded remarkable structural and functional materials for a plethora of applications. Despite these advances, many properties of natural materials remain challenging or yet impossible to incorporate into synthetic materials. Natural materials are produced by living cells, which sense and process environmental cues and conditions by means of signaling and genetic programs, thereby controlling the biosynthesis, remodeling, functionalization, or degradation of the natural material. In this context, synthetic biology offers unique opportunities in materials sciences by providing direct access to the rational engineering of how a cell senses and processes environmental information and translates them into the properties and functions of materials. Here, we identify and review two main directions by which synthetic biology can be harnessed to provide new impulses for the biologization of the materials sciences: first, the engineering of cells to produce precursors for the subsequent synthesis of materials. This includes materials that are otherwise produced from petrochemical resources, but also materials where the bio-produced substances contribute unique properties and functions not existing in traditional materials. Second, engineered living materials that are formed or assembled by cells or in which cells contribute specific functions while remaining an integral part of the living composite material. We finally provide a perspective of future scientific directions of this promising area of research and discuss science policy that would be required to support research and development in this field.
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Affiliation(s)
- O. Burgos-Morales
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Gueye
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - L. Lacombe
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - C. Nowak
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - R. Schmachtenberg
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Hörner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - C. Jerez-Longres
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
| | - H. Mohsenin
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - H.J. Wagner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Department of Biosystems Science and Engineering - D-BSSE, ETH Zurich, Basel, 4058, Switzerland
| | - W. Weber
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
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14
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Kramer MM, Lataster L, Weber W, Radziwill G. Optogenetic Approaches for the Spatiotemporal Control of Signal Transduction Pathways. Int J Mol Sci 2021; 22:5300. [PMID: 34069904 PMCID: PMC8157557 DOI: 10.3390/ijms22105300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Biological signals are sensed by their respective receptors and are transduced and processed by a sophisticated intracellular signaling network leading to a signal-specific cellular response. Thereby, the response to the signal depends on the strength, the frequency, and the duration of the stimulus as well as on the subcellular signal progression. Optogenetic tools are based on genetically encoded light-sensing proteins facilitating the precise spatiotemporal control of signal transduction pathways and cell fate decisions in the absence of natural ligands. In this review, we provide an overview of optogenetic approaches connecting light-regulated protein-protein interaction or caging/uncaging events with steering the function of signaling proteins. We briefly discuss the most common optogenetic switches and their mode of action. The main part deals with the engineering and application of optogenetic tools for the control of transmembrane receptors including receptor tyrosine kinases, the T cell receptor and integrins, and their effector proteins. We also address the hallmarks of optogenetics, the spatial and temporal control of signaling events.
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Affiliation(s)
- Markus M. Kramer
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Levin Lataster
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
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15
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Oh TJ, Fan H, Skeeters SS, Zhang K. Steering Molecular Activity with Optogenetics: Recent Advances and Perspectives. Adv Biol (Weinh) 2021; 5:e2000180. [PMID: 34028216 PMCID: PMC8218620 DOI: 10.1002/adbi.202000180] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/14/2020] [Indexed: 12/24/2022]
Abstract
Optogenetics utilizes photosensitive proteins to manipulate the localization and interaction of molecules in living cells. Because light can be rapidly switched and conveniently confined to the sub-micrometer scale, optogenetics allows for controlling cellular events with an unprecedented resolution in time and space. The past decade has witnessed an enormous progress in the field of optogenetics within the biological sciences. The ever-increasing amount of optogenetic tools, however, can overwhelm the selection of appropriate optogenetic strategies. Considering that each optogenetic tool may have a distinct mode of action, a comparative analysis of the current optogenetic toolbox can promote the further use of optogenetics, especially by researchers new to this field. This review provides such a compilation that highlights the spatiotemporal accuracy of current optogenetic systems. Recent advances of optogenetics in live cells and animal models are summarized, the emerging work that interlinks optogenetics with other research fields is presented, and exciting clinical and industrial efforts to employ optogenetic strategy toward disease intervention are reported.
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Affiliation(s)
- Teak-Jung Oh
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Huaxun Fan
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Savanna S Skeeters
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Kai Zhang
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
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16
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Bretherton RC, DeForest CA. The Art of Engineering Biomimetic Cellular Microenvironments. ACS Biomater Sci Eng 2021; 7:3997-4008. [PMID: 33523625 DOI: 10.1021/acsbiomaterials.0c01549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cells and their surrounding microenvironment exist in dynamic reciprocity, where bidirectional feedback and feedforward crosstalk drives essential processes in development, homeostasis, and disease. With the ongoing explosion of customizable biomaterial innovation for dynamic cell culture, an ever-expanding suite of user-programmable scaffolds now exists to probe cell fate in response to spatiotemporally controlled biophysical and biochemical cues. Here, we highlight emerging trends in these efforts, emphasizing strategies that offer tunability over complex network mechanics, present biomolecular cues anisotropically, and harness cells as physiochemical actuators of the pericellular niche. Altogether, these material advances will lead to breakthroughs in our basic understanding of how cells interact with, integrate signals from, and influence their surrounding microenvironment.
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Affiliation(s)
- Ross C Bretherton
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States.,Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States.,Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington 98109, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,Molecular Engineering & Sciences Institute, University of Washington, Seattle, Washington 98195, United States
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17
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Kim S, Uroz M, Bays JL, Chen CS. Harnessing Mechanobiology for Tissue Engineering. Dev Cell 2021; 56:180-191. [PMID: 33453155 PMCID: PMC7855912 DOI: 10.1016/j.devcel.2020.12.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/10/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022]
Abstract
A primary challenge in tissue engineering is to recapitulate both the structural and functional features of whole tissues and organs. In vivo, patterning of the body plan and constituent tissues emerges from the carefully orchestrated interactions between the transcriptional programs that give rise to cell types and the mechanical forces that drive the bending, twisting, and extensions critical to morphogenesis. Substantial recent progress in mechanobiology-understanding how mechanics regulate cell behaviors and what cellular machineries are responsible-raises the possibility that one can begin to use these insights to help guide the strategy and design of functional engineered tissues. In this perspective, we review and propose the development of different approaches, from providing appropriate extracellular mechanical cues to interfering with cellular mechanosensing machinery, to aid in controlling cell and tissue structure and function.
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Affiliation(s)
- Sudong Kim
- Department of Biomedical Engineering and the Biological Design Center, Boston University, Boston, MA 02215, USA; The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
| | - Marina Uroz
- Department of Biomedical Engineering and the Biological Design Center, Boston University, Boston, MA 02215, USA; The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
| | - Jennifer L Bays
- Department of Biomedical Engineering and the Biological Design Center, Boston University, Boston, MA 02215, USA; The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
| | - Christopher S Chen
- Department of Biomedical Engineering and the Biological Design Center, Boston University, Boston, MA 02215, USA; The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA.
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18
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Özkale B, Sakar MS, Mooney DJ. Active biomaterials for mechanobiology. Biomaterials 2021; 267:120497. [PMID: 33129187 PMCID: PMC7719094 DOI: 10.1016/j.biomaterials.2020.120497] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023]
Abstract
Active biomaterials offer novel approaches to study mechanotransduction in mammalian cells. These material systems probe cellular responses by dynamically modulating their resistance to endogenous forces or applying exogenous forces on cells in a temporally controlled manner. Stimuli-responsive molecules, polymers, and nanoparticles embedded inside cytocompatible biopolymer networks transduce external signals such as light, heat, chemicals, and magnetic fields into changes in matrix elasticity (few kPa to tens of kPa) or forces (few pN to several μN) at the cell-material interface. The implementation of active biomaterials in mechanobiology has generated scientific knowledge and therapeutic potential relevant to a variety of conditions including but not limited to cancer metastasis, fibrosis, and tissue regeneration. We discuss the repertoire of cellular responses that can be studied using these platforms including receptor signaling as well as downstream events namely, cytoskeletal organization, nuclear shuttling of mechanosensitive transcriptional regulators, cell migration, and differentiation. We highlight recent advances in active biomaterials and comment on their future impact.
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Affiliation(s)
- Berna Özkale
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA; Wyss Institute for Biologically Inspired Engineering, Cambridge, MA, 02138, USA
| | - Mahmut Selman Sakar
- Institute of Mechanical Engineering and Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
| | - David J Mooney
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA; Wyss Institute for Biologically Inspired Engineering, Cambridge, MA, 02138, USA.
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19
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Mumford TR, Roth L, Bugaj LJ. Reverse and Forward Engineering Multicellular Structures with Optogenetics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020; 16:61-71. [PMID: 33718689 PMCID: PMC7945718 DOI: 10.1016/j.cobme.2020.100250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding how cells self-organize into functional higher-order structures is of great interest, both towards deciphering animal development, as well as for our ability to predictably build custom tissues to meet research and therapeutic needs. The proper organization of cells across length-scales results from interconnected and dynamic networks of molecules and cells. Optogenetic probes provide dynamic and tunable control over molecular events within cells, and thus represent a powerful approach to both dissect and control collective cell behaviors. Here we emphasize the breadth of the optogenetic toolkit and discuss how these methods have already been used to reverse-engineer the design rules of developing organisms. We also offer our perspective on the rich potential for optogenetics to power forward-engineering of tissue assembly towards the generation of bespoke tissues with user-defined properties.
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Affiliation(s)
- Thomas R. Mumford
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lee Roth
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lukasz J. Bugaj
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
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20
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Wittmann T, Dema A, van Haren J. Lights, cytoskeleton, action: Optogenetic control of cell dynamics. Curr Opin Cell Biol 2020; 66:1-10. [PMID: 32371345 PMCID: PMC7577957 DOI: 10.1016/j.ceb.2020.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/29/2023]
Abstract
Cell biology is moving from observing molecules to controlling them in real time, a critical step towards a mechanistic understanding of how cells work. Initially developed from light-gated ion channels to control neuron activity, optogenetics now describes any genetically encoded protein system designed to accomplish specific light-mediated tasks. Recent photosensitive switches use many ingenious designs that bring spatial and temporal control within reach for almost any protein or pathway of interest. This next generation optogenetics includes light-controlled protein-protein interactions and shape-shifting photosensors, which in combination with live microscopy enable acute modulation and analysis of dynamic protein functions in living cells. We provide a brief overview of various types of optogenetic switches. We then discuss how diverse approaches have been used to control cytoskeleton dynamics with light through Rho GTPase signaling, microtubule and actin assembly, mitotic spindle positioning and intracellular transport and highlight advantages and limitations of different experimental strategies.
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Affiliation(s)
- Torsten Wittmann
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
| | - Alessandro Dema
- Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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21
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Xu D, Ricken J, Wegner SV. Turning Cell Adhesions ON or OFF with High Spatiotemporal Precision Using the Green Light Responsive Protein CarH. Chemistry 2020; 26:9859-9863. [PMID: 32270892 PMCID: PMC7496717 DOI: 10.1002/chem.202001238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/31/2020] [Indexed: 01/09/2023]
Abstract
Spatiotemporal control of integrin-mediated cell adhesions to extracellular matrix regulates cell behavior with has numerous implications for biotechnological applications. In this work, two approaches for regulating cell adhesions in space and time with high precision are reported, both of which utilize green light. In the first design, CarH, which is a tetramer in the dark, is used to mask cRGD adhesion-peptides on a surface. Upon green light illumination, the CarH tetramer dissociates into its monomers, revealing the adhesion peptide so that cells can adhere. In the second design, the RGD motif is incorporated into the CarH protein tetramer such that cells can adhere to surfaces functionalized with this protein. The cell adhesions can be disrupted with green light, due to the disassembly of the CarH-RGD protein. Both designs allow for photoregulation with noninvasive visible light and open new possibilities to investigate the dynamical regulation of cell adhesions in cell biology.
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Affiliation(s)
- Dongdong Xu
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Julia Ricken
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Max Planck Institute for Medical ResearchJahnstraße 2969120HeidelbergGermany
| | - Seraphine V. Wegner
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Physiological Chemistry and PathobiochemistryUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
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22
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Abstract
As the crucial non-cellular component of tissues, the extracellular matrix (ECM) provides both physical support and signaling regulation to cells. Some ECM molecules provide a fibrillar environment around cells, while others provide a sheet-like basement membrane scaffold beneath epithelial cells. In this Review, we focus on recent studies investigating the mechanical, biophysical and signaling cues provided to developing tissues by different types of ECM in a variety of developing organisms. In addition, we discuss how the ECM helps to regulate tissue morphology during embryonic development by governing key elements of cell shape, adhesion, migration and differentiation. Summary: This Review discusses our current understanding of how the extracellular matrix helps guide developing tissues by influencing cell adhesion, migration, shape and differentiation, emphasizing the biophysical cues it provides.
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Affiliation(s)
- David A Cruz Walma
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892-4370, USA
| | - Kenneth M Yamada
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892-4370, USA
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23
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Yousefi OS, Hörner M, Wess M, Idstein V, Weber W, Schamel WWA. Optogenetic Tuning of Ligand Binding to The Human T cell Receptor Using The opto-ligand-TCR System. Bio Protoc 2020; 10:e3540. [PMID: 33659514 PMCID: PMC7842703 DOI: 10.21769/bioprotoc.3540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 11/02/2022] Open
Abstract
T cells are one major cell type of the immune system that use their T cell antigen receptor (TCR) to bind and respond to foreign molecules derived from pathogens. The ligand-TCR interaction half-lives determine stimulation outcome. Until recently, scientists relied on mutating either the TCR or its ligands to investigate how varying TCR-ligand interaction durations impacted on T cell activation. Our newly created opto-ligand-TCR system allowed us to precisely and reversibly control ligand binding to the TCR by light illumination. This system uses phytochrome B (PhyB) tetramers as a light-regulated TCR ligand. PhyB can be photoconverted between a binding (ON) and non-binding (OFF) conformation by 660 nm and 740 nm light illumination, respectively. PhyB ON is able to bind to a synthetic TCR, generated by fusing the PhyB interacting factor (PIF) to the TCRβ chain. Switching PhyB to the OFF conformation disrupts this interaction. Sufficiently long binding of PhyB tetramers to the PIF-TCR led to T cell activation as measured by calcium influx. Here, we describe protocols for how to generate the tetrameric ligand for our opto-ligand-TCR system, how to measure ligand-TCR binding by flow cytometry and how to quantify T cell activation via calcium influx.
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Affiliation(s)
- O. Sascha Yousefi
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Maximilian Hörner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Maximilian Wess
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Vincent Idstein
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Wolfgang W. A. Schamel
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center Freiburg and Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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24
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Hörner M, Yousefi OS, Schamel WWA, Weber W. Production, Purification and Characterization of Recombinant Biotinylated Phytochrome B for Extracellular Optogenetics. Bio Protoc 2020; 10:e3541. [PMID: 33659515 PMCID: PMC7842835 DOI: 10.21769/bioprotoc.3541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
In the field of extracellular optogenetics, photoreceptors are applied outside of cells to obtain systems with a desired functionality. Among the diverse applied photoreceptors, phytochromes are the only ones that can be actively and reversibly switched between the active and inactive photostate by the illumination with cell-compatible red and far-red light. In this protocol, we describe the production of a biotinylated variant of the photosensory domain of A. thaliana phytochrome B (PhyB-AviTag) in E. coli with a single, optimized expression plasmid. We give detailed instructions for the purification of the protein by immobilized metal affinity chromatography and the characterization of the protein in terms of purity, biotinylation, spectral photoswitching and the light-dependent interaction with its interaction partner PIF6. In comparison to previous studies applying PhyB-AviTag, the optimized expression plasmid used in this protocol simplifies the production process and shows an increased yield and purity.
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Affiliation(s)
- Maximilian Hörner
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - O. Sascha Yousefi
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Wolfgang W. A. Schamel
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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25
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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26
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Hörner M, Gerhardt K, Salavei P, Hoess P, Härrer D, Kaiser J, Tabor JJ, Weber W. Production of Phytochromes by High-Cell-Density E. coli Fermentation. ACS Synth Biol 2019; 8:2442-2450. [PMID: 31526004 DOI: 10.1021/acssynbio.9b00267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phytochromes are important photoreceptors of plants, bacteria, and fungi responsive to light in the red and far-red spectrum. For increasing applications in basic research, synthetic biology, and materials sciences, it is required to recombinantly produce and purify phytochromes in high amounts. An ideal host organism for this purpose is E. coli due to its widespread use, fast growth, and ability for high-cell-density fermentation. Here, we describe the development of a generic platform for the production of phytochromes in E. coli that is compatible with high-cell-density fermentation. We exemplify our approach by the production of the photosensory domains of phytochrome B (PhyB) from A. thaliana and of the cyanobacterial phytochrome 1 (Cph1) from Synechocystis PCC 6803 in the multigram scale per 10 L fermentation run.
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Wang Y, Barnett SFH, Le S, Guo Z, Zhong X, Kanchanawong P, Yan J. Label-free Single-Molecule Quantification of Rapamycin-induced FKBP-FRB Dimerization for Direct Control of Cellular Mechanotransduction. NANO LETTERS 2019; 19:7514-7525. [PMID: 31466449 DOI: 10.1021/acs.nanolett.9b03364] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chemically induced dimerization (CID) has been applied to study numerous biological processes and has important pharmacological applications. However, the complex multistep interactions under various physical constraints involved in CID impose a great challenge for the quantification of the interactions. Furthermore, the mechanical stability of the ternary complexes has not been characterized; hence, their potential application in mechanotransduction studies remains unclear. Here, we report a single-molecule detector that can accurately quantify almost all key interactions involved in CID and the mechanical stability of the ternary complex, in a label-free manner. Its application is demonstrated using rapamycin-induced heterodimerization of FRB and FKBP as an example. We revealed the sufficient mechanical stability of the FKBP/rapamycin/FRB ternary complex and demonstrated its utility in the precise switching of talin-mediated force transmission in integrin-based cell adhesions.
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Affiliation(s)
- Yinan Wang
- Department of Physics , National University of Singapore , Singapore 117546
| | - Samuel F H Barnett
- Mechanobiology Institute , National University of Singapore , Singapore 117411
| | - Shimin Le
- Department of Physics , National University of Singapore , Singapore 117546
| | - Zhenhuan Guo
- Mechanobiology Institute , National University of Singapore , Singapore 117411
| | - Xueying Zhong
- Mechanobiology Institute , National University of Singapore , Singapore 117411
| | - Pakorn Kanchanawong
- Mechanobiology Institute , National University of Singapore , Singapore 117411
- Department of Biomedical Engineering , National University of Singapore , Singapore 117583
| | - Jie Yan
- Department of Physics , National University of Singapore , Singapore 117546
- Mechanobiology Institute , National University of Singapore , Singapore 117411
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28
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Mohammed D, Versaevel M, Bruyère C, Alaimo L, Luciano M, Vercruysse E, Procès A, Gabriele S. Innovative Tools for Mechanobiology: Unraveling Outside-In and Inside-Out Mechanotransduction. Front Bioeng Biotechnol 2019; 7:162. [PMID: 31380357 PMCID: PMC6646473 DOI: 10.3389/fbioe.2019.00162] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/20/2019] [Indexed: 12/26/2022] Open
Abstract
Cells and tissues can sense and react to the modifications of the physico-chemical properties of the extracellular environment (ECM) through integrin-based adhesion sites and adapt their physiological response in a process called mechanotransduction. Due to their critical localization at the cell-ECM interface, transmembrane integrins are mediators of bidirectional signaling, playing a key role in “outside-in” and “inside-out” signal transduction. After presenting the basic conceptual fundamentals related to cell mechanobiology, we review the current state-of-the-art technologies that facilitate the understanding of mechanotransduction signaling pathways. Finally, we highlight innovative technological developments that can help to advance our understanding of the mechanisms underlying nuclear mechanotransduction.
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Affiliation(s)
- Danahe Mohammed
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Marie Versaevel
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Céline Bruyère
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laura Alaimo
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Marine Luciano
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Eléonore Vercruysse
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Anthony Procès
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium.,Department of Neurosciences, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Sylvain Gabriele
- Mechanobiology and Soft Matter Group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
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29
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Yousefi OS, Günther M, Hörner M, Chalupsky J, Wess M, Brandl SM, Smith RW, Fleck C, Kunkel T, Zurbriggen MD, Höfer T, Weber W, Schamel WW. Optogenetic control shows that kinetic proofreading regulates the activity of the T cell receptor. eLife 2019; 8:42475. [PMID: 30947807 PMCID: PMC6488296 DOI: 10.7554/elife.42475] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/05/2019] [Indexed: 12/18/2022] Open
Abstract
The immune system distinguishes between self and foreign antigens. The kinetic proofreading (KPR) model proposes that T cells discriminate self from foreign ligands by the different ligand binding half-lives to the T cell receptor (TCR). It is challenging to test KPR as the available experimental systems fall short of only altering the binding half-lives and keeping other parameters of the interaction unchanged. We engineered an optogenetic system using the plant photoreceptor phytochrome B (PhyB) as a ligand to selectively control the dynamics of ligand binding to the TCR by light. This opto-ligand-TCR system was combined with the unique property of PhyB to continuously cycle between the binding and non-binding states under red light, with the light intensity determining the cycling rate and thus the binding duration. Mathematical modeling of our experimental datasets showed that indeed the ligand-TCR interaction half-life is the decisive factor for activating downstream TCR signaling, substantiating KPR.
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Affiliation(s)
- O Sascha Yousefi
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Günther
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Maximilian Hörner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Julia Chalupsky
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Wess
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Simon M Brandl
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Robert W Smith
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Christian Fleck
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Tim Kunkel
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Matias D Zurbriggen
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences, University of Düsseldorf, Düsseldorf, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wolfgang Wa Schamel
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
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