1
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Tashev SA, Euchner J, Yserentant K, Hänselmann S, Hild F, Chmielewicz W, Hummert J, Schwörer F, Tsopoulidis N, Germer S, Saßmannshausen Z, Fackler OT, Klingmüller U, Herten DP. ProDOL: a general method to determine the degree of labeling for staining optimization and molecular counting. Nat Methods 2024:10.1038/s41592-024-02376-6. [PMID: 39117875 DOI: 10.1038/s41592-024-02376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 06/24/2024] [Indexed: 08/10/2024]
Abstract
Determining the label to target ratio, also known as the degree of labeling (DOL), is crucial for quantitative fluorescence microscopy and a high DOL with minimal unspecific labeling is beneficial for fluorescence microscopy in general. Yet robust, versatile and easy-to-use tools for measuring cell-specific labeling efficiencies are not available. Here we present a DOL determination technique named protein-tag DOL (ProDOL), which enables fast quantification and optimization of protein-tag labeling. With ProDOL various factors affecting labeling efficiency, including substrate type, incubation time and concentration, as well as sample fixation and cell type can be easily assessed. We applied ProDOL to investigate how human immunodeficiency virus-1 pathogenesis factor Nef modulates CD4 T cell activation measuring total and activated copy numbers of the adapter protein SLP-76 in signaling microclusters. ProDOL proved to be a versatile and robust tool for labeling calibration, enabling determination of labeling efficiencies, optimization of strategies and quantification of protein stoichiometry.
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Affiliation(s)
- Stanimir Asenov Tashev
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Chemistry, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham, Birmingham, UK
| | - Jonas Euchner
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Chemistry, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham, Birmingham, UK
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Klaus Yserentant
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Chemistry, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham, Birmingham, UK
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | - Felix Hild
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Wioleta Chmielewicz
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Johan Hummert
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Chemistry, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham, Birmingham, UK
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- PicoQuant GmbH, Berlin, Germany
| | - Florian Schwörer
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nikolaos Tsopoulidis
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Germer
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Zoe Saßmannshausen
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk-Peter Herten
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- School of Chemistry, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, UK.
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham, Birmingham, UK.
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany.
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2
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Hou Y, Treanor B. DNA origami: Interrogating the nano-landscape of immune receptor activation. Biophys J 2024; 123:2211-2223. [PMID: 37838832 PMCID: PMC11331043 DOI: 10.1016/j.bpj.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
The immune response is orchestrated by elaborate protein interaction networks that interweave ligand-mediated receptor reorganization with signaling cascades. While the biochemical processes have been extensively investigated, delineating the biophysical principles governing immune receptor activation has remained challenging due to design limitations of traditional ligand display platforms. These constraints have been overcome by advances in DNA origami nanotechnology, enabling unprecedented control over ligand geometry on configurable scaffolds. It is now possible to systematically dissect the independent roles of ligand stoichiometry, spatial distribution, and rigidity in immune receptor activation, signaling, and cooperativity. In this review, we highlight pioneering efforts in manipulating the ligand presentation landscape to understand immune receptor triggering and to engineer functional immune responses.
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Affiliation(s)
- Yuchen Hou
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario.
| | - Bebhinn Treanor
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario; Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario; Department of Immunology, University of Toronto, Toronto, Ontario.
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3
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Prikhodko IV, Guria GT. The method for assessing the specificity of developing CAR therapies. BIOPHYSICAL REPORTS 2024; 4:100172. [PMID: 39025235 PMCID: PMC11344002 DOI: 10.1016/j.bpr.2024.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
The effectiveness of antitumor chimeric antigen receptor (CAR) therapy mainly dealt with an elevated sensitivity of CAR cells to target cells. However, CAR therapies are associated with nonspecific side effects: on-target off-tumor toxicity. Sensitivity and specificity of CAR cells are the most important properties of the recognition process of target cells among other cells. Current developments are mainly concentrated on exploring molecular biology methods for designing CAR cells with the highest sensitivity, while the problem of the CAR cell specificity is rarely considered. For the assessment of CAR cell specificity, we suggest that, in addition to an elevated level of CAR-antigen affinity, the ability of CARs for clustering should be taken into account. We assume that the CAR cell cytotoxicity is determined by CAR clustering. The latter is treated within the framework of nucleation theory. The master equation for the probability of CAR cell cytotoxicity is derived. The size of a critical CAR cluster is found to be one of two most essential parameters. The conditions for necessary sensitivity and sufficient specificity are explored. Relevant parametric diagrams are derived. Possible applications of the method for assessing the specificity of developing CAR therapies are discussed.
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Affiliation(s)
- Ivan V Prikhodko
- Laboratory for Mathematical Modelling of Biological Processes, National Medical Research Center for Hematology, Moscow, Russia
| | - Georgy Th Guria
- Laboratory for Mathematical Modelling of Biological Processes, National Medical Research Center for Hematology, Moscow, Russia; Chair of the Living Systems Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
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4
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Cárdenas-García SP, Ijaz S, Pereda AE. The components of an electrical synapse as revealed by expansion microscopy of a single synaptic contact. eLife 2024; 13:e91931. [PMID: 38994821 PMCID: PMC11333041 DOI: 10.7554/elife.91931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 07/08/2024] [Indexed: 07/13/2024] Open
Abstract
Most nervous systems combine both transmitter-mediated and direct cell-cell communication, known as 'chemical' and 'electrical' synapses, respectively. Chemical synapses can be identified by their multiple structural components. Electrical synapses are, on the other hand, generally defined by the presence of a 'gap junction' (a cluster of intercellular channels) between two neuronal processes. However, while gap junctions provide the communicating mechanism, it is unknown whether electrical transmission requires the contribution of additional cellular structures. We investigated this question at identifiable single synaptic contacts on the zebrafish Mauthner cells, at which gap junctions coexist with specializations for neurotransmitter release and where the contact unequivocally defines the anatomical limits of a synapse. Expansion microscopy of these single contacts revealed a detailed map of the incidence and spatial distribution of proteins pertaining to various synaptic structures. Multiple gap junctions of variable size were identified by the presence of their molecular components. Remarkably, most of the synaptic contact's surface was occupied by interleaving gap junctions and components of adherens junctions, suggesting a close functional association between these two structures. In contrast, glutamate receptors were confined to small peripheral portions of the contact, indicating that most of the synaptic area functions as an electrical synapse. Thus, our results revealed the overarching organization of an electrical synapse that operates with not one, but multiple gap junctions, in close association with structural and signaling molecules known to be components of adherens junctions. The relationship between these intercellular structures will aid in establishing the boundaries of electrical synapses found throughout animal connectomes and provide insight into the structural organization and functional diversity of electrical synapses.
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Affiliation(s)
- Sandra P Cárdenas-García
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
| | - Sundas Ijaz
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
| | - Alberto E Pereda
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
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5
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Sánchez MF, Faria S, Frühschulz S, Werkmann L, Winter C, Karimian T, Lanzerstorfer P, Plochberger B, Weghuber J, Tampé R. Engineering Mesoscale T Cell Receptor Clustering by Plug-and-Play Nanotools. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2310407. [PMID: 38924642 DOI: 10.1002/adma.202310407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 06/10/2024] [Indexed: 06/28/2024]
Abstract
T cell receptor (TCR) clustering and formation of an immune synapse are crucial for TCR signaling. However, limited information is available about these dynamic assemblies and their connection to transmembrane signaling. In this work, TCR clustering is controlled via plug-and-play nanotools based on an engineered irreversible conjugation pair and a peptide-loaded major histocompatibility complex (pMHC) molecule to compare receptor assembly in a ligand (pMHC)-induced or ligand-independent manner. A streptavidin-binding peptide displayed in both tools enabled their anchoring in streptavidin-pre-structured matrices. Strikingly, pMHC-induced clustering in the confined regions exhibit higher density and dynamics than the ligand-free approach, indicating that the size and architecture of the pMHC ligand influences TCR assembly. This approach enables the control of membrane receptor clustering with high specificity and provides the possibility to explore different modalities of receptor activation.
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Affiliation(s)
- M Florencia Sánchez
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Sevi Faria
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Stefan Frühschulz
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Lars Werkmann
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Tina Karimian
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Peter Lanzerstorfer
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, 4600, Austria
| | - Birgit Plochberger
- University of Applied Sciences Upper Austria, Campus Linz, Linz, 4020, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstr. 13, Vienna, 1200, Austria
| | - Julian Weghuber
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Wels, 4600, Austria
- FFoQSI - Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, FFoQSI GmbH, Technopark 1D, Tulln an der Donau, 3430, Austria
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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6
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability. SCIENCE ADVANCES 2024; 10:eadi0707. [PMID: 38905351 PMCID: PMC11192083 DOI: 10.1126/sciadv.adi0707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of deterministic bistability but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts deterministic bistability and may be more resistant to pharmacological inhibition.
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Affiliation(s)
- Albert A. Lee
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Neil H. Kim
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Steven Alvarez
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - He Ren
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - L. J. Nugent Lew
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jay T. Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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7
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Jain K, Pandey A, Wang H, Chung T, Nemati A, Kanchanawong P, Sheetz MP, Cai H, Changede R. TiO 2 Nano-Biopatterning Reveals Optimal Ligand Presentation for Cell-Matrix Adhesion Formation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309284. [PMID: 38340044 PMCID: PMC11126362 DOI: 10.1002/adma.202309284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Nanoscale organization of transmembrane receptors is critical for cellular functions, enabled by the nanoscale engineering of bioligand presentation. Previously, a spatial threshold of ≤60 nm for integrin binding ligands in cell-matrix adhesion is demonstrated using monoliganded gold nanoparticles. However, the ligand geometric arrangement is limited to hexagonal arrays of monoligands, while plasmonic quenching limits further investigation by fluorescence-based high-resolution imaging. Here, these limitations are overcome with dielectric TiO2 nanopatterns, eliminating fluorescence quenching, thus enabling super-resolution fluorescence microscopy on nanopatterns. By dual-color super-resolution imaging, high precision and consistency among nanopatterns, bioligands, and integrin nanoclusters are observed, validating the high quality and integrity of both nanopattern functionalization and passivation. By screening TiO2 nanodiscs with various diameters, an increase in fibroblast cell adhesion, spreading area, and Yes-associated protein (YAP) nuclear localization on 100 nm diameter compared with smaller diameters was observed. Focal adhesion kinase is identified as the regulatory signal. These findings explore the optimal ligand presentation when the minimal requirements are sufficiently fulfilled in the heterogenous extracellular matrix network of isolated binding regions with abundant ligands. Integration of high-fidelity nano-biopatterning with super-resolution imaging allows precise quantitative studies to address early signaling events in response to receptor clustering and their nanoscale organization.
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Affiliation(s)
- Kashish Jain
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Ashish Pandey
- Tech4Health Institute and Department of Radiology, NYU Langone Health, New York, NY, USA
| | - Hao Wang
- Tech4Health Institute and Department of Radiology, NYU Langone Health, New York, NY, USA
| | - Taerin Chung
- Tech4Health Institute and Department of Radiology, NYU Langone Health, New York, NY, USA
| | - Arash Nemati
- Tech4Health Institute and Department of Radiology, NYU Langone Health, New York, NY, USA
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Michael P. Sheetz
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Molecular Mechanomedicine Program, Biochemistry and Molecular Biology Department, University of Texas Medical Branch, Galveston, TX, USA
| | - Haogang Cai
- Tech4Health Institute and Department of Radiology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, New York University, Brooklyn, NY, USA
| | - Rishita Changede
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- TeOra Pte. Ltd, Singapore, Singapore
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8
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Trollmann MFW, Böckmann RA. Characterization of domain formation in complex membranes. Methods Enzymol 2024; 701:1-46. [PMID: 39025569 DOI: 10.1016/bs.mie.2024.03.006] [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: 07/20/2024]
Abstract
A widely known property of lipid membranes is their tendency to undergo a separation into disordered (Ld) and ordered (Lo) domains. This impacts the local structure of the membrane relevant for the physical (e.g., enhanced electroporation) and biological (e.g., protein sorting) significance of these regions. The increase in computing power, advancements in simulation software, and more detailed information about the composition of biological membranes shifts the study of these domains into the focus of classical molecular dynamics simulations. In this chapter, we present a versatile yet robust analysis pipeline that can be easily implemented and adapted for a wide range of lipid compositions. It employs Gaussian-based Hidden Markov Models to predict the hidden order states of individual lipids by describing their structure through the area per lipid and the average SCC order parameters per acyl chain. Regions of the membrane with a high correlation between ordered lipids are identified by employing the Getis-Ord local spatial autocorrelation statistic on a Voronoi tessellation of the lipids. As an example, the approach is applied to two distinct systems at a coarse-grained resolution, demonstrating either a strong tendency towards phase separation (1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DIPC), cholesterol) or a weak tendency toward phase separation (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PUPC), cholesterol). Explanations of the steps are complemented by coding examples written in Python, providing both a comprehensive understanding and practical guidance for a seamless integration of the workflow into individual projects.
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Affiliation(s)
- Marius F W Trollmann
- Computational Biology-Theoretical & Computational Membrane Biophysics, Department of Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Erlangen National High Performance Computing Center (NHR@FAU)
| | - Rainer A Böckmann
- Computational Biology-Theoretical & Computational Membrane Biophysics, Department of Biology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Erlangen National High Performance Computing Center (NHR@FAU); FAU Profile Center Immunomedicine (FAU I-MED), FAU Erlangen-Nürnberg.
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9
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Qiu Y, Xiao Q, Wang Y, Cao Y, Wang J, Wan Z, Chen X, Liu W, Ma L, Xu C. Mechanical force determines chimeric antigen receptor microclustering and signaling. Mol Ther 2024; 32:1016-1032. [PMID: 38327049 PMCID: PMC11163199 DOI: 10.1016/j.ymthe.2024.02.006] [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] [Received: 08/28/2023] [Revised: 01/03/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024] Open
Abstract
Chimeric antigen receptor (CAR) T cells are activated to trigger the lytic machinery after antigen engagement, and this has been successfully applied clinically as therapy. The mechanism by which antigen binding leads to the initiation of CAR signaling remains poorly understood. Here, we used a set of short double-stranded DNA (dsDNA) tethers with mechanical forces ranging from ∼12 to ∼51 pN to manipulate the mechanical force of antigen tether and decouple the microclustering and signaling events. Our results revealed that antigen-binding-induced CAR microclustering and signaling are mechanical force dependent. Additionally, the mechanical force delivered to the antigen tether by the CAR for microclustering is generated by autonomous cell contractility. Mechanistically, the mechanical-force-induced strong adhesion and CAR diffusion confinement led to CAR microclustering. Moreover, cytotoxicity may have a lower mechanical force threshold than cytokine generation. Collectively, these results support a model of mechanical-force-induced CAR microclustering for signaling.
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Affiliation(s)
- Yue Qiu
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Qingyue Xiao
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Yucai Wang
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Yichen Cao
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Jing Wang
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zhengpeng Wan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xiangjun Chen
- Center for Infectious Disease Research, School of Medicine, Westlake University, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Wanli Liu
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Li Ma
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Chenguang Xu
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
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10
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Hou F, Guo Z, Ho MT, Hui Y, Zhao CX. Particle-Based Artificial Antigen-Presenting Cell Systems for T Cell Activation in Adoptive T Cell Therapy. ACS NANO 2024; 18:8571-8599. [PMID: 38483840 DOI: 10.1021/acsnano.3c10180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
T cell-based adoptive cell therapy (ACT) has emerged as a promising treatment for various diseases, particularly cancers. Unlike other immunotherapy modalities, ACT involves directly transferring engineered T cells into patients to eradicate diseased cells; hence, it necessitates methods for effectively activating and expanding T cells in vitro. Artificial antigen-presenting cells (aAPCs) have been widely developed based on biomaterials, particularly micro- and nanoparticles, and functionalized with T cell stimulatory antibodies to closely mimic the natural T cell-APC interactions. Due to their vast clinical utility, aAPCs have been employed as an off-the-shelf technology for T cell activation in FDA-approved ACTs, and the development of aAPCs is constantly advancing with the emergence of aAPCs with more sophisticated designs and additional functionalities. Here, we review the recent advancements in particle-based aAPCs for T cell activation in ACTs. Following a brief introduction, we first describe the manufacturing processes of ACT products. Next, the design and synthetic strategies for micro- and nanoparticle-based aAPCs are discussed separately to emphasize their features, advantages, and limitations. Then, the impact of design parameters of aAPCs, such as size, shape, ligand density/mobility, and stiffness, on their functionality and biomedical performance is explored to provide deeper insights into the design concepts and principles for more efficient and safer aAPCs. The review concludes by discussing current challenges and proposing future perspectives for the development of more advanced aAPCs.
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Affiliation(s)
- Fei Hou
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Zichao Guo
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Minh Trang Ho
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yue Hui
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Chun-Xia Zhao
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia 5005, Australia
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11
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Kocyła AM, Czogalla A, Wessels I, Rink L, Krężel A. A combined biochemical and cellular approach reveals Zn 2+-dependent hetero- and homodimeric CD4 and Lck assemblies in T cells. Structure 2024; 32:292-303.e7. [PMID: 38157858 DOI: 10.1016/j.str.2023.11.013] [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] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
The CD4 or CD8 co-receptors' interaction with the protein-tyrosine kinase Lck initiates the tyrosine phosphorylation cascade leading to T cell activation. A critical question is: to what extent are co-receptors and Lck coupled? Our contribution concerns Zn2+, indispensable for CD4- and CD8-Lck formation. We combined biochemical and cellular approaches to show that dynamic fluctuations of free Zn2+ in physiological ranges influence Zn(CD4)2 and Zn(CD4)(Lck) species formation and their ratio, although the same Zn(Cys)2(Cys)2 cores. Moreover, we demonstrated that the affinity of Zn2+ to CD4 and CD4-Lck species differs significantly. Increased intracellular free Zn2+ concentration in T cells causes higher CD4 partitioning in the plasma membrane. We additionally found that CD4 palmitoylation decreases the specificity of CD4-Lck formation in the reconstituted membrane model. Our findings help elucidate co-receptor-Lck coupling stoichiometry and demonstrate that intracellular free Zn2+ has a major role in the interplay between CD4 dimers and CD4-Lck assembly.
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Affiliation(s)
- Anna M Kocyła
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Inga Wessels
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Lothar Rink
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland.
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12
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Mayer I, Karimian T, Gordiyenko K, Angelin A, Kumar R, Hirtz M, Mikut R, Reischl M, Stegmaier J, Zhou L, Ma R, Nienhaus GU, Rabe KS, Lanzerstorfer P, Domínguez CM, Niemeyer CM. Surface-Patterned DNA Origami Rulers Reveal Nanoscale Distance Dependency of the Epidermal Growth Factor Receptor Activation. NANO LETTERS 2024; 24:1611-1619. [PMID: 38267020 PMCID: PMC10853960 DOI: 10.1021/acs.nanolett.3c04272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The nanoscale arrangement of ligands can have a major effect on the activation of membrane receptor proteins and thus cellular communication mechanisms. Here we report on the technological development and use of tailored DNA origami-based molecular rulers to fabricate "Multiscale Origami Structures As Interface for Cells" (MOSAIC), to enable the systematic investigation of the effect of the nanoscale spacing of epidermal growth factor (EGF) ligands on the activation of the EGF receptor (EGFR). MOSAIC-based analyses revealed that EGF distances of about 30-40 nm led to the highest response in EGFR activation of adherent MCF7 and Hela cells. Our study emphasizes the significance of DNA-based platforms for the detailed investigation of the molecular mechanisms of cellular signaling cascades.
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Affiliation(s)
- Ivy Mayer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Tina Karimian
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Klavdiya Gordiyenko
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Alessandro Angelin
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ravi Kumar
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Michael Hirtz
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ralf Mikut
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Johannes Stegmaier
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute
of Imaging and Computer Vision, RWTH Aachen
University, 52074 Aachen, Germany
| | - Lu Zhou
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Rui Ma
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
- Institute
of Biological and Chemical Systems (IBCS) and Institute of Nanotechnology
(INT), Karlsruhe Institute of Technology
(KIT), 76021 Karlsruhe, Germany
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kersten S. Rabe
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Peter Lanzerstorfer
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Carmen M. Domínguez
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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13
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L Bello M, Mendes GEM, Silva ACR, Faria RX. Virtual screening indicates potential inhibitors of the P2X7 receptor. Comput Biol Med 2023; 164:107299. [PMID: 37552915 DOI: 10.1016/j.compbiomed.2023.107299] [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] [Received: 03/22/2023] [Revised: 07/11/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023]
Abstract
Anti-inflammatory agents can be synthetic or natural compounds and are often used to attenuate different levels of inflammation. Inflammatory diseases, due to the involvement of multiple systems, are becoming difficult to treat, involve long durations of therapy where applicable, have a high cost of management and have a deleterious impact on public health. The search for natural and synthetic compounds with anti-inflammatory activity is an important strategy in drug design. Bioactive synthetic drugs may be repurposed for other pharmacological applications, and natural product chemical structures offer unlimited opportunities for new drug discoveries due to the unparalleled availability of chemical diversity. Virtual screening of 2774 molecules on the mouse P2X7 protein showed that potential ligands are composed of five flavonoids (narirutin, diosmin, complanatuside, hesperidin, and oroxin B) and other drugs such as velpatasvir, itacitinib and lifitegrast. In vitro studies in mouse cells confirmed the inhibitory activity of the indicated ligands on the P2X7 receptor by applying virtual screening. The behavior of protein bonded to the ligands was verified by analysis of the molecular dynamic simulation trajectories for four of the most potent inhibitor compounds, indicating that the ligands velpatasvir, itacitinib, lithospermic acid and narirutin remained in the binding site indicated by molecular docking.
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Affiliation(s)
- Murilo L Bello
- Pharmaceutical Planning and Computer Simulation Laboratory, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme Eduardo M Mendes
- Pharmaceutical Planning and Computer Simulation Laboratory, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil; Postgraduate Program in Sciences and Biotechnology, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Ana Cláudia R Silva
- Laboratory for Environmental Health Assessment and Promotion, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Robson X Faria
- Laboratory for Environmental Health Assessment and Promotion, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil.
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14
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Cárdenas-García SP, Ijaz S, Pereda AE. The components of an electrical synapse as revealed by expansion microscopy of a single synaptic contact. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550347. [PMID: 37546897 PMCID: PMC10402082 DOI: 10.1101/2023.07.25.550347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Most nervous systems combine both transmitter-mediated and direct cell-cell communication, known as 'chemical' and 'electrical' synapses, respectively. Chemical synapses can be identified by their multiple structural components. Electrical synapses are, on the other hand, generally defined by the presence of a 'gap junction' (a cluster of intercellular channels) between two neuronal processes. However, while gap junctions provide the communicating mechanism, it is unknown whether electrical transmission requires the contribution of additional cellular structures. We investigated this question at identifiable single synaptic contacts on the zebrafish Mauthner cells, at which gap junctions coexist with specializations for neurotransmitter release and where the contact defines the anatomical limits of a synapse. Expansion microscopy of these contacts revealed a detailed map of the incidence and spatial distribution of proteins pertaining to various synaptic structures. Multiple gap junctions of variable size were identified by the presence of their molecular components. Remarkably, most of the synaptic contact's surface was occupied by interleaving gap junctions and components of adherens junctions, suggesting a close functional association between these two structures. In contrast, glutamate receptors were confined to small peripheral portions of the contact, indicating that most of the synaptic area works as an electrical synapse. Thus, our results revealed the overarching organization of an electrical synapse that operates with not one, but multiple gap junctions, in close association with structural and signaling molecules known to be components of AJs. The relationship between these intercellular structures will aid in establishing the boundaries of electrical synapses found throughout animal connectomes and provide insight into the structural organization and functional diversity of electrical synapses.
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Affiliation(s)
- Sandra P. Cárdenas-García
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sundas Ijaz
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alberto E. Pereda
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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15
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Zhao L, Zhao G, Feng J, Zhang Z, Zhang J, Guo H, Lin M. T Cell engineering for cancer immunotherapy by manipulating mechanosensitive force-bearing receptors. Front Bioeng Biotechnol 2023; 11:1220074. [PMID: 37560540 PMCID: PMC10407658 DOI: 10.3389/fbioe.2023.1220074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023] Open
Abstract
T cell immune responses are critical for in both physiological and pathological processes. While biochemical cues are important, mechanical cues arising from the microenvironment have also been found to act a significant role in regulating various T cell immune responses, including activation, cytokine production, metabolism, proliferation, and migration. The immune synapse contains force-sensitive receptors that convert these mechanical cues into biochemical signals. This phenomenon is accepted in the emerging research field of immunomechanobiology. In this review, we provide insights into immunomechanobiology, with a specific focus on how mechanosensitive receptors are bound and triggered, and ultimately resulting T cell immune responses.
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Affiliation(s)
- Lingzhu Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
| | - Guoqing Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
| | - Jinteng Feng
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
- Department of Thoracic Surgery, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zheng Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
| | - Jiayu Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
| | - Hui Guo
- Department of Medical Oncology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Min Lin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, China
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16
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without classic kinetic bistability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549263. [PMID: 37503094 PMCID: PMC10370109 DOI: 10.1101/2023.07.17.549263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal, or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of classic kinetic bistability, but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts classic kinetic bistability and is distinctly more resistant to pharmacological inhibition.
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17
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Li Y, Peng J, Xia Y, Pan C, Li Y, Gu W, Wang J, Wang C, Wang Y, Song J, Zhou X, Ma L, Jiang Y, Liu B, Feng Q, Wang W, Jiao S, An L, Li D, Zhou Z, Zhao Y. Sufu limits sepsis-induced lung inflammation via regulating phase separation of TRAF6. Theranostics 2023; 13:3761-3780. [PMID: 37441604 PMCID: PMC10334838 DOI: 10.7150/thno.83676] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023] Open
Abstract
Rationale: Sepsis is a potentially life-threatening condition caused by the body's response to a severe infection. Although the identification of multiple pathways involved in inflammation, tissue damage and aberrant healing during sepsis, there remain unmet needs for the development of new therapeutic strategies essential to prevent the reoccurrence of infection and organ injuries. Methods: Expression of Suppressor of Fused (Sufu) was evaluated by qRT-PCR, western blotting, and immunofluorescence in murine lung and peritoneal macrophages. The significance of Sufu expression in prognosis was assessed by Kaplan-Meier survival analysis. The GFP-TRAF6-expressing stable cell line (GFP-TRAF6 Blue cells) were constructed to evaluate phase separation of TRAF6. Phase separation of TRAF6 and the roles of Sufu in repressing TRAF6 droplet aggregation were analyzed by co-immunoprecipitation, immunofluorescence, Native-PAGE, FRAP and in vitro assays using purified proteins. The effects of Sufu on sepsis-induced lung inflammation were evaluated by cell function assays, LPS-induced septic shock model and polymicrobial sepsis-CLP mice model. Results: We found that Sufu expression is reduced in early response to lipopolysaccharide (LPS)-induced acute inflammation in murine lung and peritoneal macrophages. Deletion of Sufu aggravated LPS-induced and CLP (cecal ligation puncture)-induced lung injury and lethality in mice, and augmented LPS-induced proinflammatory gene expression in cultured macrophages. In addition, we identified the role of Sufu as a negative regulator of the Toll-Like Receptor (TLR)-triggered inflammatory response. We further demonstrated that Sufu directly interacts with TRAF6, thereby preventing oligomerization and autoubiquitination of TRAF6. Importantly, TRAF6 underwent phase separation during LPS-induced inflammation, which is essential for subsequent ubiquitination activation and NF-κB activity. Sufu inhibits the phase-separated TRAF6 droplet formation, preventing NF-κB activation upon LPS stimulation. In a septic shock model, TRAF6 depletion rescued the augmented inflammatory phenotype in mice with myeloid cell-specific deletion of Sufu. Conclusions: These findings implicated Sufu as an important inhibitor of TRAF6 in sepsis and suggest that therapeutics targeting Sufu-TRAF6 may greatly benefit the treatment of sepsis.
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Affiliation(s)
- Yehua Li
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu 730070, P. R. China
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Jiayin Peng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Yuanxin Xia
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chenyu Pan
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, P. R. China
| | - Yu Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Weijie Gu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jia Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chaoxiong Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yuang Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiawen Song
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xuan Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Liya Ma
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yiao Jiang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Biao Liu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qiongni Feng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wenjia Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, P. R. China
| | - Shi Jiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, P. R. China
| | - Liwei An
- Department of Medical Ultrasound, Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai 200072, P. R. China
| | - Dianfan Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, P. R. China
| | - Yun Zhao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, P. R. China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, P. R. China
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18
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Comerci CJ, McCarthy DG, Nosrati M, Kim KB, Kashani-Sabet M, Moerner WE, Leong SP. Nanometer-scale distribution of PD-1 in the melanoma tumor microenvironment. JOURNAL OF RADIOLOGY AND ONCOLOGY 2023; 7:20-25. [PMID: 37539093 PMCID: PMC10399701 DOI: 10.29328/journal.jro.1001048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The nanometer-scale spatial organization of immune receptors plays a role in cell activation and suppression. While the connection between this spatial organization and cell signaling events is emerging from cell culture experiments, how these results translate to more physiologically relevant settings like the tumor microenvironment remains poorly understood due to the challenges of high-resolution imaging in vivo. Here we perform super-resolution immunofluorescence microscopy of human melanoma tissue sections to examine the spatial organization of the immune checkpoint inhibitor programmed cell death 1 (PD-1). We show that PD-1 exhibits a variety of organizations ranging from nanometer-scale clusters to more uniform membrane labeling. Our results demonstrate the capability of super-resolution imaging to examine the spatial organization of immune checkpoint markers in the tumor microenvironment, suggesting a future direction for both clinical and immunology research.
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Affiliation(s)
- Colin J Comerci
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Biophysics Program, Stanford University, Stanford, CA, 94305, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dannielle G McCarthy
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Chan-Zuckerberg Initiative, 801 Jefferson Ave, Redwood City, CA, 94063, USA
| | - Mehdi Nosrati
- Center for Melanoma Research and Treatment, California Pacific Medical Center, Research Institute, San Francisco, CA, 94107, USA
| | - Kevin B Kim
- Center for Melanoma Research and Treatment, California Pacific Medical Center, Research Institute, San Francisco, CA, 94107, USA
| | - Mohammed Kashani-Sabet
- Center for Melanoma Research and Treatment, California Pacific Medical Center, Research Institute, San Francisco, CA, 94107, USA
| | - WE Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Stanley P Leong
- Center for Melanoma Research and Treatment, California Pacific Medical Center, Research Institute, San Francisco, CA, 94107, USA
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19
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Shil S, Tsuruta M, Kawauchi K, Miyoshi D. Biomolecular Liquid-Liquid Phase Separation for Biotechnology. BIOTECH 2023; 12:26. [PMID: 37092470 PMCID: PMC10123627 DOI: 10.3390/biotech12020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The liquid-liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies.
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Affiliation(s)
| | | | | | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
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20
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Du G, Zhao L, Zheng Y, Belfetmi A, Cai T, Xu B, Heyninck K, Van Den Heede K, Buyse MA, Fontana P, Bowman M, Lin LL, Wu H, Chou JJ. Autoinhibitory structure of preligand association state implicates a new strategy to attain effective DR5 receptor activation. Cell Res 2023; 33:131-146. [PMID: 36604598 PMCID: PMC9892523 DOI: 10.1038/s41422-022-00755-2] [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: 09/18/2022] [Accepted: 11/15/2022] [Indexed: 01/07/2023] Open
Abstract
Members of the tumor necrosis factor receptor superfamily (TNFRSF) are important therapeutic targets that can be activated to induce death of cancer cells or stimulate proliferation of immune cells. Although it has long been implicated that these receptors assemble preligand associated states that are required for dominant interference in human disease, such states have so far eluded structural characterization. Here, we find that the ectodomain of death receptor 5 (DR5-ECD), a representative member of TNFRSF, can specifically self-associate when anchored to lipid bilayer, and we report this self-association structure determined by nuclear magnetic resonance (NMR). Unexpectedly, two non-overlapping interaction interfaces are identified that could propagate to higher-order clusters. Structure-guided mutagenesis indicates that the observed preligand association structure is represented on DR5-expressing cells. The DR5 preligand association serves an autoinhibitory role as single-domain antibodies (sdAbs) that partially dissociate the preligand cluster can sensitize the receptor to its ligand TRAIL and even induce substantial receptor signaling in the absence of TRAIL. Unlike most agonistic antibodies that require multivalent binding to aggregate receptors for activation, these agonistic sdAbs are monovalent and act specifically on an oligomeric, autoinhibitory configuration of the receptor. Our data indicate that receptors such as DR5 can form structurally defined preclusters incompatible with signaling and that true agonists should disrupt the preligand cluster while converting it to signaling-productive cluster. This mechanism enhances our understanding of a long-standing question in TNFRSF signaling and suggests a new opportunity for developing agonistic molecules by targeting receptor preligand clustering.
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Affiliation(s)
- Gang Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Linlin Zhao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yumei Zheng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Anissa Belfetmi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tiantian Cai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Boying Xu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | | | | | | | - Pietro Fontana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Michael Bowman
- Checkpoint Immunology, Immunology & Inflammation, Sanofi, Cambridge, MA, USA
| | - Lih-Ling Lin
- Checkpoint Immunology, Immunology & Inflammation, Sanofi, Cambridge, MA, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
| | - James Jeiwen Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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21
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Sarkar S, Goswami D. Lifetime of actin-dependent protein nanoclusters. Biophys J 2023; 122:290-300. [PMID: 36518075 PMCID: PMC9892618 DOI: 10.1016/j.bpj.2022.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/23/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein nanoclusters (PNCs) are dynamic collections of a few proteins that spatially organize in nanometer-length clusters. PNCs are one of the principal forms of spatial organization of membrane proteins, and they have been shown or hypothesized to be important in various cellular processes, including cell signaling. PNCs show remarkable diversity in size, shape, and lifetime. In particular, the lifetime of PNCs can vary over a wide range of timescales. The diversity in size and shape can be explained by the interaction of the clustering proteins with the actin cytoskeleton or the lipid membrane, but very little is known about the processes that determine the lifetime of the nanoclusters. In this paper, using mathematical modeling of the cluster dynamics, we model the biophysical processes that determine the lifetime of actin-dependent PNCs. In particular, we investigated the role of actin aster fragmentation, which had been suggested to be a key determinant of the PNC lifetime, and we found that it is important only for a small class of PNCs. A simple extension of our model allowed us to investigate the kinetics of protein-ligand interaction near PNCs. We found an anomalous increase in the lifetime of ligands near PNCs, which agrees remarkably well with experimental data on RAS-RAF kinetics. In particular, analysis of the RAS-RAF data through our model provides falsifiable predictions and novel hypotheses that will not only shed light on the role of RAS-RAF kinetics in various cancers, but also will be useful in studying membrane protein clustering in general.
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Affiliation(s)
- Sumantra Sarkar
- The Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico; Theoretical Biophysics (T-6) Group, Los Alamos National Laboratory, Los Alamos, New Mexico; Department of Physics, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
| | - Debanjan Goswami
- NCI RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland.
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22
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Le Saux G, Toledo-Ashkenazi E, Schvartzman M. Fabrication of Nanoscale Arrays to Study the Effect of Ligand Arrangement on Inhibitory Signaling in NK Cells. Methods Mol Biol 2023; 2654:313-325. [PMID: 37106191 DOI: 10.1007/978-1-0716-3135-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Molecular scale nanopatterns of bioactive molecules have been used to study the effect of transmembrane receptor arrangement on a variety of cell types, including immune cells and their immune response in particular. However, state-of-the-art fabrication approaches have thus far enabled the production of patterns with control over one receptor type only. Herein, we describe a protocol to fabricate arrays for the molecular scale control of the segregation between activating and inhibitory receptors in NK cells. We used this platform to study how ligand segregation regulates NK cell inhibitory signaling and function. The arrays are based on patterns of nanodots of two metals, selectively functionalized with activating and inhibitory ligands. Due to the versatility of our functionalization approach, this protocol can be applied to configurate virtually any combination of extracellular ligands into controlled multifunctional arrays.
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Affiliation(s)
- Guillaume Le Saux
- Department of Materials Engineering, Isle Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Esti Toledo-Ashkenazi
- Department of Materials Engineering, Isle Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mark Schvartzman
- Department of Materials Engineering, Isle Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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23
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McAffee DB, O'Dair MK, Lin JJ, Low-Nam ST, Wilhelm KB, Kim S, Morita S, Groves JT. Discrete LAT condensates encode antigen information from single pMHC:TCR binding events. Nat Commun 2022; 13:7446. [PMID: 36460640 PMCID: PMC9718779 DOI: 10.1038/s41467-022-35093-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
LAT assembly into a two-dimensional protein condensate is a prominent feature of antigen discrimination by T cells. Here, we use single-molecule imaging techniques to resolve the spatial position and temporal duration of each pMHC:TCR molecular binding event while simultaneously monitoring LAT condensation at the membrane. An individual binding event is sufficient to trigger a LAT condensate, which is self-limiting, and neither its size nor lifetime is correlated with the duration of the originating pMHC:TCR binding event. Only the probability of the LAT condensate forming is related to the pMHC:TCR binding dwell time. LAT condenses abruptly, but after an extended delay from the originating binding event. A LAT mutation that facilitates phosphorylation at the PLC-γ1 recruitment site shortens the delay time to LAT condensation and alters T cell antigen specificity. These results identify a function for the LAT protein condensation phase transition in setting antigen discrimination thresholds in T cells.
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Affiliation(s)
- Darren B McAffee
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Mark K O'Dair
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jenny J Lin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Shalini T Low-Nam
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kiera B Wilhelm
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sungi Kim
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Shumpei Morita
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
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24
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Kwak M, Southard KM, Kim WR, Lin A, Kim NH, Gopalappa R, Lee HJ, An M, Choi SH, Jung Y, Noh K, Farlow J, Georgakopoulos A, Robakis NK, Kang MK, Kutys ML, Seo D, Kim HH, Kim YH, Cheon J, Gartner ZJ, Jun YW. Adherens junctions organize size-selective proteolytic hotspots critical for Notch signalling. Nat Cell Biol 2022; 24:1739-1753. [PMID: 36456828 PMCID: PMC10665132 DOI: 10.1038/s41556-022-01031-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/19/2022] [Indexed: 12/02/2022]
Abstract
Adherens junctions (AJs) create spatially, chemically and mechanically discrete microdomains at cellular interfaces. Here, using a mechanogenetic platform that generates artificial AJs with controlled protein localization, clustering and mechanical loading, we find that AJs also organize proteolytic hotspots for γ-secretase with a spatially regulated substrate selectivity that is critical in the processing of Notch and other transmembrane proteins. Membrane microdomains outside of AJs exclusively organize Notch ligand-receptor engagement (LRE microdomains) to initiate receptor activation. Conversely, membrane microdomains within AJs exclusively serve to coordinate regulated intramembrane proteolysis (RIP microdomains). They do so by concentrating γ-secretase and primed receptors while excluding full-length Notch. AJs induce these functionally distinct microdomains by means of lipid-dependent γ-secretase recruitment and size-dependent protein segregation. By excluding full-length Notch from RIP microdomains, AJs prevent inappropriate enzyme-substrate interactions and suppress spurious Notch activation. Ligand-induced ectodomain shedding eliminates size-dependent segregation, releasing Notch to translocate into AJs for processing by γ-secretase. This mechanism directs radial differentiation of ventricular zone-neural progenitor cells in vivo and more broadly regulates the proteolysis of other large cell-surface receptors such as amyloid precursor protein. These findings suggest an unprecedented role of AJs in creating size-selective spatial switches that choreograph γ-secretase processing of multiple transmembrane proteins regulating development, homeostasis and disease.
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Affiliation(s)
- Minsuk Kwak
- Department of Otolaryngology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Helen Diller Family Cancer Comprehensive Center (HDFCCC), University of California, San Francisco, CA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, Republic of Korea
| | - Kaden M Southard
- Department of Otolaryngology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Woon Ryoung Kim
- Department of Otolaryngology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Helen Diller Family Cancer Comprehensive Center (HDFCCC), University of California, San Francisco, CA, USA
| | - Annie Lin
- Department of Otolaryngology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Helen Diller Family Cancer Comprehensive Center (HDFCCC), University of California, San Francisco, CA, USA
| | - Nam Hyeong Kim
- Department of Otolaryngology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Helen Diller Family Cancer Comprehensive Center (HDFCCC), University of California, San Francisco, CA, USA
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, Republic of Korea
- Department of Nano Engineering, Sungkyunkwan University, Suwon, Republic of Korea
- Imnewrun Inc., Suwon, Republic of Korea
| | - Ramu Gopalappa
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Lee
- Department of Otolaryngology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Helen Diller Family Cancer Comprehensive Center (HDFCCC), University of California, San Francisco, CA, USA
| | - Minji An
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Seo Hyun Choi
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Yunmin Jung
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Kunwoo Noh
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Justin Farlow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Anastasios Georgakopoulos
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nikolaos K Robakis
- Department of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Min K Kang
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Matthew L Kutys
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu, Republic of Korea
| | - Hyongbum Henry Kim
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Plus Project, Yonsei University College of Medicine, Seoul, Republic of Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, Republic of Korea
- Department of Nano Engineering, Sungkyunkwan University, Suwon, Republic of Korea
- Imnewrun Inc., Suwon, Republic of Korea
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Young-Wook Jun
- Department of Otolaryngology, University of California, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Helen Diller Family Cancer Comprehensive Center (HDFCCC), University of California, San Francisco, CA, USA.
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (Nano BME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
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25
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Role of the membrane anchor in the regulation of Lck activity. J Biol Chem 2022; 298:102663. [PMID: 36372231 PMCID: PMC9763865 DOI: 10.1016/j.jbc.2022.102663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Theoretical work suggests that collective spatiotemporal behavior of integral membrane proteins should be modulated by boundary lipids sheathing their membrane anchors. Here, we show evidence for this prediction while investigating the mechanism for maintaining a steady amount of the active form of integral membrane protein Lck kinase (LckA) by Lck trans-autophosphorylation regulated by the phosphatase CD45. We used super-resolution microscopy, flow cytometry, and pharmacological and genetic perturbation to gain insight into the spatiotemporal context of this process. We found that LckA is generated exclusively at the plasma membrane, where CD45 maintains it in a ceaseless dynamic equilibrium with its unphosphorylated precursor. Steady LckA shows linear dependence, after an initial threshold, over a considerable range of Lck expression levels. This behavior fits a phenomenological model of trans-autophosphorylation that becomes more efficient with increasing LckA. We then challenged steady LckA formation by genetically swapping the Lck membrane anchor with structurally divergent ones, such as that of Src or the transmembrane domains of LAT, CD4, palmitoylation-defective CD4 and CD45 that were expected to drastically modify Lck boundary lipids. We observed small but significant changes in LckA generation, except for the CD45 transmembrane domain that drastically reduced LckA due to its excessive lateral proximity to CD45. Comprehensively, LckA formation and maintenance can be best explained by lipid bilayer critical density fluctuations rather than liquid-ordered phase-separated nanodomains, as previously thought, with "like/unlike" boundary lipids driving dynamical proximity and remoteness of Lck with itself and with CD45.
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26
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Philippi M, Richter CP, Kappen M, Watrinet I, Miao Y, Runge M, Jorde L, Korneev S, Holtmannspötter M, Kurre R, Holthuis JCM, Garcia KC, Plückthun A, Steinhart M, Piehler J, You C. Biofunctional Nanodot Arrays in Living Cells Uncover Synergistic Co-Condensation of Wnt Signalodroplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203723. [PMID: 36266931 DOI: 10.1002/smll.202203723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Qualitative and quantitative analysis of transient signaling platforms in the plasma membrane has remained a key experimental challenge. Here, biofunctional nanodot arrays (bNDAs) are developed to spatially control dimerization and clustering of cell surface receptors at the nanoscale. High-contrast bNDAs with spot diameters of ≈300 nm are obtained by capillary nanostamping of bovine serum albumin bioconjugates, which are subsequently biofunctionalized by reaction with tandem anti-green fluorescence protein (GFP) clamp fusions. Spatially controlled assembly of active Wnt signalosomes is achieved at the nanoscale in the plasma membrane of live cells by capturing the co-receptor Lrp6 into bNDAs via an extracellular GFP tag. Strikingly, co-recruitment is observed of co-receptor Frizzled-8 as well as the cytosolic scaffold proteins Axin-1 and Disheveled-2 into Lrp6 nanodots in the absence of ligand. Density variation and the high dynamics of effector proteins uncover highly cooperative liquid-liquid phase separation (LLPS)-driven assembly of Wnt "signalodroplets" at the plasma membrane, pinpointing the synergistic effects of LLPS for Wnt signaling amplification. These insights highlight the potential of bNDAs for systematically interrogating nanoscale signaling platforms and condensation at the plasma membrane of live cells.
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Affiliation(s)
- Michael Philippi
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Christian P Richter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Marie Kappen
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Isabelle Watrinet
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mercedes Runge
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Lara Jorde
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Sergej Korneev
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Michael Holtmannspötter
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Joost C M Holthuis
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, Zurich, 8057, Switzerland
| | - Martin Steinhart
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Changjiang You
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
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27
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West SJ, Boehning D, Akimzhanov AM. Regulation of T cell function by protein S-acylation. Front Physiol 2022; 13:1040968. [PMID: 36467682 PMCID: PMC9709458 DOI: 10.3389/fphys.2022.1040968] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/02/2022] [Indexed: 10/26/2023] Open
Abstract
S-acylation, the reversible lipidation of free cysteine residues with long-chain fatty acids, is a highly dynamic post-translational protein modification that has recently emerged as an important regulator of the T cell function. The reversible nature of S-acylation sets this modification apart from other forms of protein lipidation and allows it to play a unique role in intracellular signal transduction. In recent years, a significant number of T cell proteins, including receptors, enzymes, ion channels, and adaptor proteins, were identified as S-acylated. It has been shown that S-acylation critically contributes to their function by regulating protein localization, stability and protein-protein interactions. Furthermore, it has been demonstrated that zDHHC protein acyltransferases, the family of enzymes mediating this modification, also play a prominent role in T cell activation and differentiation. In this review, we aim to highlight the diversity of proteins undergoing S-acylation in T cells, elucidate the mechanisms by which reversible lipidation can impact protein function, and introduce protein acyltransferases as a novel class of regulatory T cell proteins.
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Affiliation(s)
- Savannah J. West
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center and University of Texas Health Science at Houston Graduate School, Houston, TX, United States
| | - Darren Boehning
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Askar M. Akimzhanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center and University of Texas Health Science at Houston Graduate School, Houston, TX, United States
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28
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A bead-based method for high-throughput mapping of the sequence- and force-dependence of T cell activation. Nat Methods 2022; 19:1295-1305. [PMID: 36064771 DOI: 10.1038/s41592-022-01592-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/21/2022] [Indexed: 11/08/2022]
Abstract
Adaptive immunity relies on T lymphocytes that use αβ T cell receptors (TCRs) to discriminate among peptides presented by major histocompatibility complex molecules (pMHCs). Identifying pMHCs capable of inducing robust T cell responses will not only enable a deeper understanding of the mechanisms governing immune responses but could also have broad applications in diagnosis and treatment. T cell recognition of sparse antigenic pMHCs in vivo relies on biomechanical forces. However, in vitro screening methods test potential pMHCs without force and often at high (nonphysiological) pMHC densities and thus fail to predict potent agonists in vivo. Here, we present a technology termed BATTLES (biomechanically assisted T cell triggering for large-scale exogenous-pMHC screening) that uses biomechanical force to initiate T cell triggering for peptides and cells in parallel. BATTLES displays candidate pMHCs on spectrally encoded beads composed of a thermo-responsive polymer capable of applying shear loads to T cells, facilitating exploration of the force- and sequence-dependent landscape of T cell responses. BATTLES can be used to explore basic T cell mechanobiology and T cell-based immunotherapies.
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29
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Lanna A, Vaz B, D'Ambra C, Valvo S, Vuotto C, Chiurchiù V, Devine O, Sanchez M, Borsellino G, Akbar AN, De Bardi M, Gilroy DW, Dustin ML, Blumer B, Karin M. An intercellular transfer of telomeres rescues T cells from senescence and promotes long-term immunological memory. Nat Cell Biol 2022; 24:1461-1474. [PMID: 36109671 PMCID: PMC7613731 DOI: 10.1038/s41556-022-00991-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 08/11/2022] [Indexed: 02/06/2023]
Abstract
The common view is that T lymphocytes activate telomerase to delay senescence. Here we show that some T cells (primarily naïve and central memory cells) elongated telomeres by acquiring telomere vesicles from antigen-presenting cells (APCs) independently of telomerase action. Upon contact with these T cells, APCs degraded shelterin to donate telomeres, which were cleaved by the telomere trimming factor TZAP, and then transferred in extracellular vesicles at the immunological synapse. Telomere vesicles retained the Rad51 recombination factor that enabled telomere fusion with T-cell chromosome ends lengthening them by an average of ~3,000 base pairs. Thus, there are antigen-specific populations of T cells whose ageing fate decisions are based on telomere vesicle transfer upon initial contact with APCs. These telomere-acquiring T cells are protected from senescence before clonal division begins, conferring long-lasting immune protection.
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Affiliation(s)
- Alessio Lanna
- Sentcell UK Laboratories, IRCCS Fondazione Santa Lucia, Rome, Italy.
- Department of Experimental and Translational Medicine, Division of Medicine, University College London, London, UK.
| | - Bruno Vaz
- Sentcell UK Laboratories, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Clara D'Ambra
- Sentcell UK Laboratories, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Salvatore Valvo
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Claudia Vuotto
- Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Valerio Chiurchiù
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
- Laboratory of Resolution of Neuroinflammation, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Oliver Devine
- Division of Infection and Immunity, University College London, London, UK
| | | | | | - Arne N Akbar
- Department of Experimental and Translational Medicine, Division of Medicine, University College London, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Marco De Bardi
- NeuroImmunology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Derek W Gilroy
- Department of Experimental and Translational Medicine, Division of Medicine, University College London, London, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Brendan Blumer
- Block.one, George Town, Cayman Islands
- Block.one, Hong Kong, Hong Kong
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, University California, San Diego, CA, USA
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30
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Casanellas I, Samitier J, Lagunas A. Recent advances in engineering nanotopographic substrates for cell studies. Front Bioeng Biotechnol 2022; 10:1002967. [PMID: 36147534 PMCID: PMC9486185 DOI: 10.3389/fbioe.2022.1002967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cells sense their environment through the cell membrane receptors. Interaction with extracellular ligands induces receptor clustering at the nanoscale, assembly of the signaling complexes in the cytosol and activation of downstream signaling pathways, regulating cell response. Nanoclusters of receptors can be further organized hierarchically in the cell membrane at the meso- and micro-levels to exert different biological functions. To study and guide cell response, cell culture substrates have been engineered with features that can interact with the cells at different scales, eliciting controlled cell responses. In particular, nanoscale features of 1–100 nm in size allow direct interaction between the material and single cell receptors and their nanoclusters. Since the first “contact guidance” experiments on parallel microstructures, many other studies followed with increasing feature resolution and biological complexity. Here we present an overview of the advances in the field summarizing the biological scenario, substrate fabrication techniques and applications, highlighting the most recent developments.
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Affiliation(s)
- Ignasi Casanellas
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona (UB), Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Josep Samitier
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, University of Barcelona (UB), Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Anna Lagunas
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid, Spain
- *Correspondence: Anna Lagunas,
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Abstract
Immune signalling pathways convert pathogenic stimuli into cytosolic events that lead to the resolution of infection. Upon ligand engagement, immune receptors together with their downstream adaptors and effectors undergo substantial conformational changes and spatial reorganization. During this process, nanometre-to-micrometre-sized signalling clusters have been commonly observed that are believed to be hotspots for signal transduction. Because of their large size and heterogeneous composition, it remains a challenge to fully understand the mechanisms by which these signalling clusters form and their functional consequences. Recently, phase separation has emerged as a new biophysical principle for organizing biomolecules into large clusters with fluidic properties. Although the field is still in its infancy, studies of phase separation in immunology are expected to provide new perspectives for understanding immune responses. Here, we present an up-to-date view of how liquid-liquid phase separation drives the formation of signalling condensates and regulates immune signalling pathways, including those downstream of T cell receptor, B cell receptor and the innate immune receptors cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) and retinoic acid-inducible gene I protein (RIG-I). We conclude with a summary of the current challenges the field is facing and outstanding questions for future studies.
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Affiliation(s)
- Qian Xiao
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Ceara K. McAtee
- Yale Combined Program in the Biological and Biomedical Sciences, New Haven, CT, USA
| | - Xiaolei Su
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA,Yale Cancer Center, Yale University, New Haven, CT, USA,
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32
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Dam T, Chouliara M, Junghans V, Jönsson P. Supported Lipid Bilayers and the Study of Two-Dimensional Binding Kinetics. Front Mol Biosci 2022; 9:833123. [PMID: 35252352 PMCID: PMC8896763 DOI: 10.3389/fmolb.2022.833123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Binding between protein molecules on contacting cells is essential in initiating and regulating several key biological processes. In contrast to interactions between molecules in solution, these events are restricted to the two-dimensional (2D) plane of the meeting cell surfaces. However, converting between the more commonly available binding kinetics measured in solution and the so-called 2D binding kinetics has proven a complicated task since for the latter several factors other than the protein-protein interaction per se have an impact. A few important examples of these are: protein density, membrane fluctuations, force on the bond and the use of auxiliary binding molecules. The development of model membranes, and in particular supported lipid bilayers (SLBs), has made it possible to simplify the studied contact to analyze these effects and to measure 2D binding kinetics of individual protein-protein interactions. We will in this review give an overview of, and discuss, how different SLB systems have been used for this and compare different methods to measure binding kinetics in cell-SLB contacts. Typically, the SLB is functionalized with fluorescently labelled ligands whose interaction with the corresponding receptor on a binding cell can be detected. This interaction can either be studied 1) by an accumulation of ligands in the cell-SLB contact, whose magnitude depends on the density of the proteins and binding affinity of the interaction, or 2) by tracking single ligands in the SLB, which upon interaction with a receptor result in a change of motion of the diffusing ligand. The advantages and disadvantages of other methods measuring 2D binding kinetics will also be discussed and compared to the fluorescence-based methods. Although binding kinetic measurements in cell-SLB contacts have provided novel information on how ligands interact with receptors in vivo the number of these measurements is still limited. This is influenced by the complexity of the system as well as the required experimental time. Moreover, the outcome can vary significantly between studies, highlighting the necessity for continued development of methods to study 2D binding kinetics with higher precision and ease.
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Affiliation(s)
- Tommy Dam
- Department of Chemistry, Lund University, Lund, Sweden
| | | | - Victoria Junghans
- Nuffield Department of Medicine, CAMS Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Peter Jönsson
- Department of Chemistry, Lund University, Lund, Sweden
- *Correspondence: Peter Jönsson,
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33
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Li W, Jiang C, Zhang E. Advances in the phase separation-organized membraneless organelles in cells: a narrative review. Transl Cancer Res 2022; 10:4929-4946. [PMID: 35116344 PMCID: PMC8797891 DOI: 10.21037/tcr-21-1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/29/2021] [Indexed: 11/26/2022]
Abstract
Membraneless organelles (MLOs) are micro-compartments that lack delimiting membranes, concentrating several macro-molecules with a high local concentration in eukaryotic cells. Recent studies have shown that MLOs have pivotal roles in multiple biological processes, including gene transcription, RNA metabolism, translation, protein modification, and signal transduction. These biological processes in cells have essential functions in many diseases, such as cancer, neurodegenerative diseases, and virus-related diseases. The liquid-liquid phase separation (LLPS) microenvironment within cells is thought to be the driving force for initiating the formation of micro-compartments with a liquid-like property, becoming an important organizing principle for MLOs to mediate organism responses. In this review, we comprehensively elucidated the formation of these MLOs and the relationship between biological functions and associated diseases. The mechanisms underlying the influence of protein concentration and valency on phase separation in cells are also discussed. MLOs undergoing the LLPS process have diverse functions, including stimulation of some adaptive and reversible responses to alter the transcriptional or translational processes, regulation of the concentrations of biomolecules in living cells, and maintenance of cell morphogenesis. Finally, we highlight that the development of this field could pave the way for developing novel therapeutic strategies for the treatment of LLPS-related diseases based on the understanding of phase separation in the coming years.
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Affiliation(s)
- Weihan Li
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Chenwei Jiang
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Erhao Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, China.,Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
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34
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Di Credico A, Gaggi G, Izzicupo P, Bucci I, Di Baldassarre A. Resveratrol Enhances the Cytotoxic Activity of Lymphocytes from Menopausal Women. Antioxidants (Basel) 2021; 10:antiox10121914. [PMID: 34943018 PMCID: PMC8750017 DOI: 10.3390/antiox10121914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/24/2022] Open
Abstract
Nutraceuticals and functional foods are the main sources of antioxidants and have positive effects on health through regulation of the redox balance. Accordingly, they represent a useful nutritional source for the prevention of noncommunicable diseases (NCDs). Menopausal women have an increased risk of developing NCDs due to hormonal dysregulation and the ongoing aging process. Accordingly, a healthy lifestyle and good nutritional habits are of utmost importance in this population. Resveratrol (RSV) is a natural polyphenol, and it is used as a nutraceutical given its estrogenic, anti-inflammatory, and antioxidant properties. The aim of this study was to analyze the effects of RSV on the lymphocyte cytotoxicity in menopausal women. Lymphocytes from 13 healthy menopausal women (56.18 ± 4.24 years) were isolated, and then cocultured with hTERT-HME1, a breast cell line with a precancerous phenotype. The results showed that, when treated with RSV, lymphocytes significantly increased the TNF-α production (p < 0.001), the formation of immune synapses (p = 0.009), and the target cell lysis (p = 0.002). No effects were detected in the lymphocyte total antioxidant capacity. In conclusion, RSV might enhance the immune surveillance in menopausal women by increasing the cytotoxic activity of lymphocytes.
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Affiliation(s)
- Andrea Di Credico
- Department of Medicine and Aging Sciences, University “G. D’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (A.D.C.); (P.I.); (I.B.)
| | - Giulia Gaggi
- Beth Israel Deaconess Medical Center, Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA;
| | - Pascal Izzicupo
- Department of Medicine and Aging Sciences, University “G. D’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (A.D.C.); (P.I.); (I.B.)
| | - Ines Bucci
- Department of Medicine and Aging Sciences, University “G. D’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (A.D.C.); (P.I.); (I.B.)
| | - Angela Di Baldassarre
- Department of Medicine and Aging Sciences, University “G. D’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (A.D.C.); (P.I.); (I.B.)
- Correspondence: ; Tel.: +39-0871-3554545
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35
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Liu J, Li M, Li F, Ge Z, Li Q, Liu M, Shi J, Wang L, Zuo X, Fan C, Mao X. Reconstructing Soma-Soma Synapse-like Vesicular Exocytosis with DNA Origami. ACS CENTRAL SCIENCE 2021; 7:1400-1407. [PMID: 34471683 PMCID: PMC8393203 DOI: 10.1021/acscentsci.1c00645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Indexed: 05/23/2023]
Abstract
Cell-cell communications exhibit distinct physiological functions in immune responses and neurotransmitter signaling. Nevertheless, the ability to reconstruct a soma-soma synapse-like junction for probing intercellular communications remains difficult. In this work, we develop a DNA origami nanostructure-based method for establishing cell conjugation, which consequently facilitates the reconstruction of a soma-soma synapse-like junction. We demonstrate that intercellular communications including small molecule and membrane vesicle exchange between cells are maintained in the artificially designed synapse-like junction. By inserting the carbon fiber nanometric electrodes into the soma-soma synapse-like junction, we accomplish the real-time monitoring of individual vesicular exocytotic events and obtain the information on vesicular exocytosis kinetics via analyzing the parameters of current spikes. This strategy provides a versatile platform to study synaptic communications.
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Affiliation(s)
- Jiangbo Liu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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36
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Chen Z, Oh D, Biswas KH, Zaidel-Bar R, Groves JT. Probing the effect of clustering on EphA2 receptor signaling efficiency by subcellular control of ligand-receptor mobility. eLife 2021; 10:67379. [PMID: 34414885 PMCID: PMC8397371 DOI: 10.7554/elife.67379] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022] Open
Abstract
Clustering of ligand:receptor complexes on the cell membrane is widely presumed to have functional consequences for subsequent signal transduction. However, it is experimentally challenging to selectively manipulate receptor clustering without altering other biochemical aspects of the cellular system. Here, we develop a microfabrication strategy to produce substrates displaying mobile and immobile ligands that are separated by roughly 1 µm, and thus experience an identical cytoplasmic signaling state, enabling precision comparison of downstream signaling reactions. Applying this approach to characterize the ephrinA1:EphA2 signaling system reveals that EphA2 clustering enhances both receptor phosphorylation and downstream signaling activity. Single-molecule imaging clearly resolves increased molecular binding dwell times at EphA2 clusters for both Grb2:SOS and NCK:N-WASP signaling modules. This type of intracellular comparison enables a substantially higher degree of quantitative analysis than is possible when comparisons must be made between different cells and essentially eliminates the effects of cellular response to ligand manipulation.
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Affiliation(s)
- Zhongwen Chen
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China.,Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Dongmyung Oh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, United States.,Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Kabir Hassan Biswas
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
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37
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Kocher C, Agozzino L, Dill K. Nanoscale Catalyst Chemotaxis Can Drive the Assembly of Functional Pathways. J Phys Chem B 2021; 125:8781-8786. [PMID: 34324352 PMCID: PMC8366527 DOI: 10.1021/acs.jpcb.1c04498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent experiments demonstrate molecular chemotaxis or altered diffusion rates of enzymes in the presence of their own substrates. We show here an important implication, namely, that if a nanoscale catalyst A produces a small-molecule ligand product L which is the substrate of another catalyst B, the two catalysts will attract each other. We explore this nonequilibrium producer recruitment force (ProRec) in a reaction-diffusion model. The predicted cat-cat association will be the strongest when A is a fast producer of L and B is a tight binder to it. ProRec is a force that could drive a mechanism (the catpath mechanism) by which catalysts could become spatially localized into functional pathways, such as in the biochemical networks in cells, which can achieve complex goals.
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Affiliation(s)
- Charles Kocher
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States.,Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Luca Agozzino
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Ken Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States.,Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States.,Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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38
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Bernabé-Rubio M, Bosch-Fortea M, Alonso MA, Bernardino de la Serna J. Multi-dimensional and spatiotemporal correlative imaging at the plasma membrane of live cells to determine the continuum nano-to-micro scale lipid adaptation and collective motion. Methods 2021; 193:136-147. [PMID: 34126167 DOI: 10.1016/j.ymeth.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/25/2022] Open
Abstract
The primary cilium is a specialized plasma membrane protrusion with important receptors for signalling pathways. In polarized epithelial cells, the primary cilium assembles after the midbody remnant (MBR) encounters the centrosome at the apical surface. The membrane surrounding the MBR, namely remnant-associated membrane patch (RAMP), once situated next to the centrosome, releases some of its lipid components to form a centrosome-associated membrane patch (CAMP) from which the ciliary membrane stems. The RAMP undergoes a spatiotemporal membrane refinement during the formation of the CAMP, which becomes highly enriched in condensed membranes with low lateral mobility. To better understand this process, we have developed a correlative imaging approach that yields quantitative information about the lipid lateral packing, its mobility and collective assembly at the plasma membrane at different spatial scales over time. Our work paves the way towards a quantitative understanding of the spatiotemporal lipid collective assembly at the plasma membrane as a functional determinant in cell biology and its direct correlation with the membrane physicochemical state. These findings allowed us to gain a deeper insight into the mechanisms behind the biogenesis of the ciliary membrane of polarized epithelial cells.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
| | - Minerva Bosch-Fortea
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Miguel A Alonso
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell OX11 0QX, UK; National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK; NIHR Imperial Biomedical Research Centre, London SW7 2AZ, UK.
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39
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Dine E, Reed EH, Toettcher JE. Positive feedback between the T cell kinase Zap70 and its substrate LAT acts as a clustering-dependent signaling switch. Cell Rep 2021; 35:109280. [PMID: 34161759 PMCID: PMC8292983 DOI: 10.1016/j.celrep.2021.109280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/24/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
Protein clustering is pervasive in cell signaling, yet how signaling from higher-order assemblies differs from simpler forms of molecular organization is still poorly understood. We present an optogenetic approach to switch between oligomers and heterodimers with a single point mutation. We apply this system to study signaling from the kinase Zap70 and its substrate linker for activation of T cells (LAT), proteins that normally form membrane-localized condensates during T cell activation. We find that fibroblasts expressing synthetic Zap70:LAT clusters activate downstream signaling, whereas one-to-one heterodimers do not. We provide evidence that clusters harbor a positive feedback loop among Zap70, LAT, and Src-family kinases that binds phosphorylated LAT and further activates Zap70. Finally, we extend our optogenetic approach to the native T cell signaling context, where light-induced LAT clustering is sufficient to drive a calcium response. Our study reveals a specific signaling function for protein clusters and identifies a biochemical circuit that robustly senses protein oligomerization state. Dine et al. study how different modes of molecular organization contribute to cell signaling using the kinase Zap70 and its substrate LAT as a model system. Optogenetic manipulation reveals that LAT:Zap70 clusters—but not dimers—trigger potent signaling via localized positive feedback among LAT, Zap70, and Src-family kinases.
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Affiliation(s)
- Elliot Dine
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ellen H Reed
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; IRCC International Research Collaboration Center, National Institutes of Natural Sciences, 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; IRCC International Research Collaboration Center, National Institutes of Natural Sciences, 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan.
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40
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Bhingardive V, Kossover A, Iraqi M, Khand B, Le Saux G, Porgador A, Schvartzman M. Antibody-Functionalized Nanowires: A Tuner for the Activation of T Cells. NANO LETTERS 2021; 21:4241-4248. [PMID: 33989498 DOI: 10.1021/acs.nanolett.1c00245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
T cells sense both chemical cues delivered by antigen molecules and physical cues delivered by the environmental elasticity and topography; yet, it is still largely unclear how these cues cumulatively regulate the immune activity of T cells. Here, we engineered a nanoscale platform for ex vivo stimulation of T cells based on antigen-functionalized nanowires. The nanowire topography and elasticity, as well as the immobilized antigens, deliver the physical and chemical cues, respectively, enabling the systematic study of the integrated effect of these cues on a T cell's immune response. We found that T cells sense both the topography and bending modulus of the nanowires and modulate their signaling, degranulation, and cytotoxicity with the variation in these physical features. Our study provides an important insight into the physical mechanism of T cell activation and paves the way to novel nanomaterials for the controlled ex vivo activation of T cells in immunotherapy.
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41
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Zeng L, Palaia I, Šarić A, Su X. PLCγ1 promotes phase separation of T cell signaling components. J Cell Biol 2021; 220:212040. [PMID: 33929486 PMCID: PMC8094118 DOI: 10.1083/jcb.202009154] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/21/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction.
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Affiliation(s)
- Longhui Zeng
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Ivan Palaia
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK.,Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK.,Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Xiaolei Su
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Yale Cancer Center, Yale University, New Haven, CT
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42
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Moretti M, La Rocca R, Perrone Donnorso M, Torre B, Canale C, Malerba M, Das G, Sottile R, Garofalo C, Achour A, Kärre K, Carbone E, Di Fabrizio E. Clustering of Major Histocompatibility Complex-Class I Molecules in Healthy and Cancer Colon Cells Revealed from Their Nanomechanical Properties. ACS NANO 2021; 15:7500-7512. [PMID: 33749234 DOI: 10.1021/acsnano.1c00897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The activation of the T cell mediated immune response relies on the fine interaction between the T cell receptor on the immune cell and the antigen-presenting major histocompatibility complex (MHC) molecules on the membrane surface of antigen-presenting cells. Both the distribution and quantity of MHC/peptide complexes and their adequate morphological presentation affect the activation of the immune cells. In several types of cancer the immune response is down-regulated due to the low expression of MHC-class I (MHC-I) molecules on the cell's surface, and in addition, the mechanical properties of the membrane seem to play a role. Herein, we investigate the distribution of MHC-I molecules and the related nanoscale mechanical environment on the cell surface of two cell lines derived from colon adenocarcinoma and a healthy epithelial colon reference cell line. Atomic force microscopy (AFM) force spectroscopy analysis using an antibody-tagged pyramidal probe specific for MHC-I molecules and a formula that relates the elasticity of the cell to the energy of adhesion revealed the different population distributions of MHC-I molecules in healthy cells compared to cancer cells. We found that MHC-I molecules are significantly less expressed in cancer cells. Moreover, the local elastic modulus is significantly reduced in cancer cells. We speculate that these results might be related to the proven ability of cancer cells to evade the immune system, not only by reducing MHC-I cell surface expression but also by modifying the local mechanical properties affecting the overall morphology of MHC-I synapse presentation to immune cells.
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Affiliation(s)
- Manola Moretti
- Single Molecule Imaging by Light Enhanced Spectroscopies Lab, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Rosanna La Rocca
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Bruno Torre
- Single Molecule Imaging by Light Enhanced Spectroscopies Lab, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Claudio Canale
- Department of Physics, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Mario Malerba
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Gobind Das
- Department of Physics, Khalifa University, P. O. Box 127788 Abu Dhabi, United Arab Emirates
| | - Rosa Sottile
- Katharine Hsu Lab, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Cinzia Garofalo
- Department for Experimental and Clinical Medicine, University of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, 17176 Solna, Stockholm, Sweden
| | - Klas Kärre
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Biomedicum Solnavägen 9, 17165 Solna, Stockholm, Sweden
| | - Ennio Carbone
- Dipartimento Medicina di Precisione, Università della Campania, via L. De Crecchio, 7, 80138 Naples, Italy
| | - Enzo Di Fabrizio
- Department of Applied Physics, Polytechnic University of Turin, Corso Duca degli Abruzzi, 24, 10129 Torino, Italy
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43
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Acquisition of optimal TFH cell function is defined by specific molecular, positional, and TCR dynamic signatures. Proc Natl Acad Sci U S A 2021; 118:2016855118. [PMID: 33903232 DOI: 10.1073/pnas.2016855118] [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: 12/12/2022] Open
Abstract
The development of follicular helper CD4 T (TFH) cells is a dynamic process resulting in a heterogenous pool of TFH subsets. However, the cellular and molecular determinants of this heterogeneity and the possible mechanistic links between them is not clear. We found that human TFH differentiation is associated with significant changes in phenotypic, chemokine, functional, metabolic and transcriptional profile. Furthermore, this differentiation was associated with distinct positioning to follicular proliferating B cells. Single-cell T cell receptor (TCR) clonotype analysis indicated the transitioning toward PD-1hiCD57hi phenotype. Furthermore, the differentiation of TFH cells was associated with significant reduction in TCR level and drastic changes in immunological synapse formation. TFH synapse lacks a tight cSMAC (central supra molecular activation Cluster) but displays the TCR in peripheral microclusters, which are potentially advantageous in the ability of germinal center (GC) B cells to receive necessary help. Our data reveal significant aspects of human TFH heterogeneity and suggest that the PD-1hiCD57hi TFH cells, in particular, are endowed with distinctive programming and spatial positioning for optimal GC B cell help.
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Yu X, Zhang L, Shen J, Zhai Y, Jiang Q, Yi M, Deng X, Ruan Z, Fang R, Chen Z, Ning X, Jiang Z. The STING phase-separator suppresses innate immune signalling. Nat Cell Biol 2021; 23:330-340. [PMID: 33833429 DOI: 10.1038/s41556-021-00659-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023]
Abstract
Biomolecular condensates (biocondensates) formed via liquid-liquid phase-separation of soluble proteins have been studied extensively. However, neither the phase-separation of endoplasmic reticulum (ER) transmembrane protein nor a biocondensate with organized membranous structures has been reported. Here, we have discovered a spherical ER membranous biocondensate with puzzle-like structures caused by condensation of the ER-resident stimulator of interferon genes (STING) in DNA virus-infected or 2'3'-cGAMP (cyclic GMP-AMP)-treated cells, which required STING transmembrane domains, an intrinsically disordered region (IDR) and a dimerization domain. Intracellular 2'3'-cGAMP concentrations determined STING translocation or condensation. STING biocondensates constrained STING and TBK1 (TANK binding protein 1) to prevent innate immunity from overactivation, presumably acting like a 'STING-TBK1-cGAMP sponge'. Cells expressing STING-E336G/E337G showed notably enhanced innate immune responses due to impaired STING condensation after viral infection at later stages. Microtubule inhibitors impeded the STING condensate gel-like transition and augmented type I-interferon production in DNA virus-infected cells. This membranous biocondensate was therefore named the STING phase-separator.
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Affiliation(s)
- Xiaoyu Yu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Liyuan Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jingxiang Shen
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Yanfang Zhai
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qifei Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Mengran Yi
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaobing Deng
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Ziran Ruan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Run Fang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhaolong Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Xiaohan Ning
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhengfan Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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45
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Bhingardive V, Le Saux G, Edri A, Porgador A, Schvartzman M. Nanowire Based Guidance of the Morphology and Cytotoxic Activity of Natural Killer Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007347. [PMID: 33719212 DOI: 10.1002/smll.202007347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/13/2021] [Indexed: 06/12/2023]
Abstract
The cytotoxic activity of natural killer (NK) cells is regulated by many chemical and physical cues, whose integration mechanism is still obscure. Here, a multifunctional platform is engineered for NK cell stimulation, to study the effect of the signal integration and spatial heterogeneity on NK cell function. The platform is based on nanowires, whose mechanical compliance and site-selective tip functionalization with antigens produce the physical and chemical stimuli, respectively. The nanowires are confined to micron-sized islands, which induce a splitting of the NK cells into two subpopulations with distinct morphologies and immune responses: NK cells atop the nanowire islands display symmetrical spreading and enhanced activation, whereas cells lying in the straits between the islands develop elongated profiles and show lower activation levels. The demonstrated tunability of NK cell cytotoxicity provides an important insight into the mechanism of their immune function and introduces a novel technological route for the ex vivo shaping of cytotoxic lymphocytes in immunotherapy.
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Affiliation(s)
- Viraj Bhingardive
- Department of Materials Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, The Shraga Segal Department of Microbiology, Immunology, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Guillaume Le Saux
- Department of Materials Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, The Shraga Segal Department of Microbiology, Immunology, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Avishay Edri
- Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Angel Porgador
- Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Mark Schvartzman
- Department of Materials Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, The Shraga Segal Department of Microbiology, Immunology, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
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46
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Sánchez MF, Els-Heindl S, Beck-Sickinger AG, Wieneke R, Tampé R. Photoinduced receptor confinement drives ligand-independent GPCR signaling. Science 2021; 371:science.abb7657. [PMID: 33632896 DOI: 10.1126/science.abb7657] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022]
Abstract
Cell-cell communication relies on the assembly of receptor-ligand complexes at the plasma membrane. The spatiotemporal receptor organization has a pivotal role in evoking cellular responses. We studied the clustering of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) and established a photoinstructive matrix with ultrasmall lock-and-key interaction pairs to control lateral membrane organization of hormone neuropeptide Y2 receptors in living cells by light. Within seconds, receptor clustering was modulated in size, location, and density. After in situ confinement, changes in cellular morphology, motility, and calcium signaling revealed ligand-independent receptor activation. This approach may enhance the exploration of mechanisms in cell signaling and mechanotransduction.
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Affiliation(s)
- M Florencia Sánchez
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sylvia Els-Heindl
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, 04109 Leipzig, Germany
| | | | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
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47
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Li M, Yu Y. Innate immune receptor clustering and its role in immune regulation. J Cell Sci 2021; 134:134/4/jcs249318. [PMID: 33597156 DOI: 10.1242/jcs.249318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The discovery of receptor clustering in the activation of adaptive immune cells has revolutionized our understanding of the physical basis of immune signal transduction. In contrast to the extensive studies of adaptive immune cells, particularly T cells, there is a lesser, but emerging, recognition that the formation of receptor clusters is also a key regulatory mechanism in host-pathogen interactions. Many kinds of innate immune receptors have been found to assemble into nano- or micro-sized domains on the surfaces of cells. The clusters formed between diverse categories of innate immune receptors function as a multi-component apparatus for pathogen detection and immune response regulation. Here, we highlight these pioneering efforts and the outstanding questions that remain to be answered regarding this largely under-explored research topic. We provide a critical analysis of the current literature on the clustering of innate immune receptors. Our emphasis is on studies that draw connections between the phenomenon of receptor clustering and its functional role in innate immune regulation.
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Affiliation(s)
- Miao Li
- Department of Chemistry, Indiana University, Bloomington, IN 47401, USA
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, IN 47401, USA
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48
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Mordechay L, Le Saux G, Edri A, Hadad U, Porgador A, Schvartzman M. Mechanical Regulation of the Cytotoxic Activity of Natural Killer Cells. ACS Biomater Sci Eng 2020; 7:122-132. [DOI: 10.1021/acsbiomaterials.0c01121] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Lital Mordechay
- Department of Materials Engineering, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Guillaume Le Saux
- Department of Materials Engineering, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Avishay Edri
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Uzi Hadad
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Angel Porgador
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Mark Schvartzman
- Department of Materials Engineering, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
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49
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Li M, Wang H, Li W, Xu XG, Yu Y. Macrophage activation on "phagocytic synapse" arrays: Spacing of nanoclustered ligands directs TLR1/2 signaling with an intrinsic limit. SCIENCE ADVANCES 2020; 6:eabc8482. [PMID: 33268354 PMCID: PMC7821875 DOI: 10.1126/sciadv.abc8482] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/19/2020] [Indexed: 05/02/2023]
Abstract
The activation of Toll-like receptor heterodimer 1/2 (TLR1/2) by microbial components plays a critical role in host immune responses against pathogens. TLR1/2 signaling is sensitive to the chemical structure of ligands, but its dependence on the spatial distribution of ligands on microbial surfaces remains unexplored. Here, we reveal the quantitative relationship between TLR1/2-triggered immune responses and the spacing of ligand clusters by designing an artificial "phagocytic synapse" nanoarray platform to mimic the cell-microbe interface. The ligand spacing dictates the proximity of receptor clusters on the cell surface and consequently the pro-inflammatory responses of macrophages. However, cell responses reach their maximum at small ligand spacings when the receptor nanoclusters become adjacent to one another. Our study demonstrates the feasibility of using spatially patterned ligands to modulate innate immunity. It shows that the receptor clusters of TLR1/2 act as a driver in integrating the spatial cues of ligands into cell-level activation events.
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Affiliation(s)
- Miao Li
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Haomin Wang
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Wenqian Li
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
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50
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Tran TM, Ma Z, Triebl A, Nath S, Cheng Y, Gong BQ, Han X, Wang J, Li JF, Wenk MR, Torta F, Mayor S, Yang L, Miao Y. The bacterial quorum sensing signal DSF hijacks Arabidopsis thaliana sterol biosynthesis to suppress plant innate immunity. Life Sci Alliance 2020; 3:e202000720. [PMID: 32788227 PMCID: PMC7425213 DOI: 10.26508/lsa.202000720] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/26/2020] [Accepted: 07/30/2020] [Indexed: 01/04/2023] Open
Abstract
Quorum sensing (QS) is a recognized phenomenon that is crucial for regulating population-related behaviors in bacteria. However, the direct specific effect of QS molecules on host biology is largely understudied. In this work, we show that the QS molecule DSF (cis-11-methyl-dodecenoic acid) produced by Xanthomonas campestris pv. campestris can suppress pathogen-associated molecular pattern-triggered immunity (PTI) in Arabidopsis thaliana, mediated by flagellin-induced activation of flagellin receptor FLS2. The DSF-mediated attenuation of innate immunity results from the alteration of FLS2 nanoclusters and endocytic internalization of plasma membrane FLS2. DSF altered the lipid profile of Arabidopsis, with a particular increase in the phytosterol species, which impairs the general endocytosis pathway mediated by clathrin and FLS2 nano-clustering on the plasma membrane. The DSF effect on receptor dynamics and host immune responses could be entirely reversed by sterol removal. Together, our results highlighted the importance of sterol homeostasis to plasma membrane organization and demonstrate a novel mechanism by which pathogenic bacteria use their communicating molecule to manipulate pathogen-associated molecular pattern-triggered host immunity.
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Affiliation(s)
- Tuan Minh Tran
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander Triebl
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sangeeta Nath
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore, India
| | - Yingying Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ben-Qiang Gong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiao Han
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Junqi Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jian-Feng Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Markus R Wenk
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Satyajit Mayor
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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