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Shelby SA, Shaw TR, Veatch SL. Measuring the Co-Localization and Dynamics of Mobile Proteins in Live Cells Undergoing Signaling Responses. Methods Mol Biol 2023; 2654:1-23. [PMID: 37106172 PMCID: PMC10758997 DOI: 10.1007/978-1-0716-3135-5_1] [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] [Indexed: 04/29/2023]
Abstract
Single molecule imaging in live cells enables the study of protein interactions and dynamics as they participate in signaling processes. When combined with fluorophores that stochastically transition between fluorescent and reversible dark states, as in super-resolution localization imaging, labeled molecules can be visualized in single cells over time. This improvement in sampling enables the study of extended cellular responses at the resolution of single molecule localization. This chapter provides optimized experimental and analytical methods used to quantify protein interactions and dynamics within the membranes of adhered live cells. Importantly, the use of pair-correlation functions resolved in both space and time allows researchers to probe interactions between proteins on biologically relevant distance and timescales, even though fluorescence localization methods typically require long times to assemble well-sampled reconstructed images. We describe an application of this approach to measure protein interactions in B cell receptor signaling and include sample analysis code for post-processing of imaging data. These methods are quantitative, sensitive, and broadly applicable to a range of signaling systems.
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Affiliation(s)
- Sarah A Shelby
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Thomas R Shaw
- Program in Applied Physics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
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2
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Balagopalan L, Raychaudhuri K, Samelson LE. Microclusters as T Cell Signaling Hubs: Structure, Kinetics, and Regulation. Front Cell Dev Biol 2021; 8:608530. [PMID: 33575254 PMCID: PMC7870797 DOI: 10.3389/fcell.2020.608530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 11/16/2022] Open
Abstract
When T cell receptors (TCRs) engage with stimulatory ligands, one of the first microscopically visible events is the formation of microclusters at the site of T cell activation. Since the discovery of these structures almost 20 years ago, they have been studied extensively in live cells using confocal and total internal reflection fluorescence (TIRF) microscopy. However, due to limits in image resolution and acquisition speed, the spatial relationships of signaling components within microclusters, the kinetics of their assembly and disassembly, and the role of vesicular trafficking in microcluster formation and maintenance were not finely characterized. In this review, we will summarize how new microscopy techniques have revealed novel insights into the assembly of these structures. The sub-diffraction organization of microclusters as well as the finely dissected kinetics of recruitment and disassociation of molecules from microclusters will be discussed. The role of cell surface molecules in microcluster formation and the kinetics of molecular recruitment via intracellular vesicular trafficking to microclusters is described. Finally, the role of post-translational modifications such as ubiquitination in the downregulation of cell surface signaling molecules is also discussed. These results will be related to the role of these structures and processes in T cell activation.
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Affiliation(s)
- Lakshmi Balagopalan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kumarkrishna Raychaudhuri
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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3
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Murin CD. Considerations of Antibody Geometric Constraints on NK Cell Antibody Dependent Cellular Cytotoxicity. Front Immunol 2020; 11:1635. [PMID: 32849559 PMCID: PMC7406664 DOI: 10.3389/fimmu.2020.01635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
It has been well-established that antibody isotype, glycosylation, and epitope all play roles in the process of antibody dependent cellular cytotoxicity (ADCC). For natural killer (NK) cells, these phenotypes are linked to cellular activation through interaction with the IgG receptor FcγRIIIa, a single pass transmembrane receptor that participates in cytoplasmic signaling complexes. Therefore, it has been hypothesized that there may be underlying spatial and geometric principles that guide proper assembly of an activation complex within the NK cell immune synapse. Further, synergy of antibody phenotypic properties as well as allosteric changes upon antigen binding may also play an as-of-yet unknown role in ADCC. Understanding these facets, however, remains hampered by difficulties associated with studying immune synapse dynamics using classical approaches. In this review, I will discuss relevant NK cell biology related to ADCC, including the structural biology of Fc gamma receptors, and how the dynamics of the NK cell immune synapse are being studied using innovative microscopy techniques. I will provide examples from the literature demonstrating the effects of spatial and geometric constraints on the T cell receptor complex and how this relates to intracellular signaling and the molecular nature of lymphocyte activation complexes, including those of NK cells. Finally, I will examine how the integration of high-throughput and "omics" technologies will influence basic NK cell biology research moving forward. Overall, the goal of this review is to lay a basis for understanding the development of drugs and therapeutic antibodies aimed at augmenting appropriate NK cell ADCC activity in patients being treated for a wide range of illnesses.
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Affiliation(s)
- Charles D. Murin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, United States
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4
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Raghunathan K, Kenworthy AK. Dynamic pattern generation in cell membranes: Current insights into membrane organization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2018-2031. [PMID: 29752898 DOI: 10.1016/j.bbamem.2018.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 12/18/2022]
Abstract
It has been two decades since the lipid raft hypothesis was first presented. Even today, whether these nanoscale cholesterol-rich domains are present in cell membranes is not completely resolved. However, especially in the last few years, a rich body of literature has demonstrated both the presence and the importance of non-random distribution of biomolecules on the membrane, which is the focus of this review. These new developments have pushed the experimental limits of detection and have brought us closer to observing lipid domains in the plasma membrane of live cells. Characterization of biomolecules associated with lipid rafts has revealed a deep connection between biological regulation and function and membrane compositional heterogeneities. Finally, tantalizing new developments in the field have demonstrated that lipid domains might not just be associated with the plasma membrane of eukaryotes but could potentially be a ubiquitous membrane-organizing principle in several other biological systems. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.
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Affiliation(s)
- Krishnan Raghunathan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, PA 15224, USA.
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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5
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Barr VA, Yi J, Samelson LE. Super-resolution Analysis of TCR-Dependent Signaling: Single-Molecule Localization Microscopy. Methods Mol Biol 2017; 1584:183-206. [PMID: 28255704 PMCID: PMC6676910 DOI: 10.1007/978-1-4939-6881-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-molecule localization microscopy (SMLM) comprises methods that produce super-resolution images from molecular locations of single molecules. These techniques mathematically determine the center of a diffraction-limited spot produced by a fluorescent molecule, which represents the most likely location of the molecule. Only a small cohort of well-separated molecules is visualized in a single image, and then many images are obtained from a single sample. The localizations from all the images are combined to produce a super-resolution picture of the sample. Here we describe the application of two methods, photoactivation localization microscopy (PALM) and direct stochastic optical reconstruction microscopy (dSTORM), to the study of signaling microclusters in T cells.
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Affiliation(s)
- Valarie A Barr
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Jason Yi
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA.
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6
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Barr VA, Sherman E, Yi J, Akpan I, Rouquette-Jazdanian AK, Samelson LE. Development of nanoscale structure in LAT-based signaling complexes. J Cell Sci 2016; 129:4548-4562. [PMID: 27875277 PMCID: PMC5201021 DOI: 10.1242/jcs.194886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/04/2016] [Indexed: 12/30/2022] Open
Abstract
The adapter molecule linker for activation of T cells (LAT) plays a crucial role in forming signaling complexes induced by stimulation of the T cell receptor (TCR). These multi-molecular complexes are dynamic structures that activate highly regulated signaling pathways. Previously, we have demonstrated nanoscale structure in LAT-based complexes where the adapter SLP-76 (also known as LCP2) localizes to the periphery of LAT clusters. In this study, we show that initially LAT and SLP-76 are randomly dispersed throughout the clusters that form upon TCR engagement. The segregation of LAT and SLP-76 develops near the end of the spreading process. The local concentration of LAT also increases at the same time. Both changes require TCR activation and an intact actin cytoskeleton. These results demonstrate that the nanoscale organization of LAT-based signaling complexes is dynamic and indicates that different kinds of LAT-based complexes appear at different times during T cell activation.
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Affiliation(s)
- Valarie A Barr
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
| | - Jason Yi
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Itoro Akpan
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
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7
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Megens RT, Bianchini M, Schmitt MM, Weber C. Optical Imaging Innovations for Atherosclerosis Research. Arterioscler Thromb Vasc Biol 2015; 35:1339-46. [DOI: 10.1161/atvbaha.115.304875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/09/2015] [Indexed: 11/16/2022]
Abstract
Cardiovascular disease is the leading cause of death and morbidity worldwide. Improving vascular prevention and therapy based on a refined mechanistic pervasion of atherosclerosis as the underlying pathology could limit the effect of vascular disease in aging societies. During the past decades, microscopy has contributed greatly to a better understanding of vascular physiology and pathology by allowing imaging of living specimen with subcellular resolution and high specificity. An important advance has been accomplished through the application of multiphoton microscopy in the vascular domain, a technological development that enabled multidimensional and dynamic imaging deep into the cellular architecture of intact tissue under physiological conditions. To identify and validate new targets for treating atherosclerosis, novel imaging strategies with nanoscale resolution will be essential to visualize molecular processes in intracellular and extracellular compartments. This review will discuss the current use of 2-photon microscopy and will provide an overview and outlook on options for introducing nanoscopic optical imaging modalities in atherosclerosis research.
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Affiliation(s)
- Remco T.A. Megens
- From the Institute for Prevention of Cardiovascular Diseases (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany (R.T.A.M., M.B., M.M.N.S., C.W.); Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands (R.T.A.M., C.W.); and DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (C.W.)
| | - Mariaelvy Bianchini
- From the Institute for Prevention of Cardiovascular Diseases (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany (R.T.A.M., M.B., M.M.N.S., C.W.); Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands (R.T.A.M., C.W.); and DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (C.W.)
| | - Martin M.N. Schmitt
- From the Institute for Prevention of Cardiovascular Diseases (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany (R.T.A.M., M.B., M.M.N.S., C.W.); Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands (R.T.A.M., C.W.); and DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (C.W.)
| | - Christian Weber
- From the Institute for Prevention of Cardiovascular Diseases (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany (R.T.A.M., M.B., M.M.N.S., C.W.); Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands (R.T.A.M., C.W.); and DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (C.W.)
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8
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Curthoys NM, Parent M, Mlodzianoski M, Nelson AJ, Lilieholm J, Butler MB, Valles M, Hess ST. Dances with Membranes: Breakthroughs from Super-resolution Imaging. CURRENT TOPICS IN MEMBRANES 2015; 75:59-123. [PMID: 26015281 PMCID: PMC5584789 DOI: 10.1016/bs.ctm.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biological membrane organization mediates numerous cellular functions and has also been connected with an immense number of human diseases. However, until recently, experimental methodologies have been unable to directly visualize the nanoscale details of biological membranes, particularly in intact living cells. Numerous models explaining membrane organization have been proposed, but testing those models has required indirect methods; the desire to directly image proteins and lipids in living cell membranes is a strong motivation for the advancement of technology. The development of super-resolution microscopy has provided powerful tools for quantification of membrane organization at the level of individual proteins and lipids, and many of these tools are compatible with living cells. Previously inaccessible questions are now being addressed, and the field of membrane biology is developing rapidly. This chapter discusses how the development of super-resolution microscopy has led to fundamental advances in the field of biological membrane organization. We summarize the history and some models explaining how proteins are organized in cell membranes, and give an overview of various super-resolution techniques and methods of quantifying super-resolution data. We discuss the application of super-resolution techniques to membrane biology in general, and also with specific reference to the fields of actin and actin-binding proteins, virus infection, mitochondria, immune cell biology, and phosphoinositide signaling. Finally, we present our hopes and expectations for the future of super-resolution microscopy in the field of membrane biology.
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Affiliation(s)
- Nikki M. Curthoys
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Matthew Parent
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | | | - Andrew J. Nelson
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Jennifer Lilieholm
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Michael B. Butler
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Matthew Valles
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
| | - Samuel T. Hess
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
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9
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Shelby SA, Holowka D, Baird B, Veatch SL. Distinct stages of stimulated FcεRI receptor clustering and immobilization are identified through superresolution imaging. Biophys J 2014; 105:2343-54. [PMID: 24268146 DOI: 10.1016/j.bpj.2013.09.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/05/2013] [Accepted: 09/09/2013] [Indexed: 12/25/2022] Open
Abstract
Recent advances in fluorescence localization microscopy have made it possible to image chemically fixed and living cells at 20 nm lateral resolution. We apply this methodology to simultaneously record receptor organization and dynamics on the ventral surface of live RBL-2H3 mast cells undergoing antigen-mediated signaling. Cross-linking of IgE bound to FcεRI by multivalent antigen initiates mast cell activation, which leads to inflammatory responses physiologically. We quantify receptor organization and dynamics as cells are stimulated at room temperature (22°C). Within 2 min of antigen addition, receptor diffusion coefficients decrease by an order of magnitude, and single-particle trajectories are confined. Within 5 min of antigen addition, receptors organize into clusters containing ∼100 receptors with average radii of ∼70 nm. By comparing simultaneous measurements of clustering and mobility, we determine that there are two distinct stages of receptor clustering. In the first stage, which precedes stimulated Ca(2+) mobilization, receptors slow dramatically but are not tightly clustered. In the second stage, receptors are tightly packed and confined. We find that stimulation-dependent changes in both receptor clustering and mobility can be reversed by displacing multivalent antigen with monovalent ligands, and that these changes can be modulated through enrichment or reduction in cellular cholesterol levels.
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Affiliation(s)
- Sarah A Shelby
- Department of Chemistry and Chemical Biology, and Field of Biophysics, Cornell University, Ithaca, NY
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10
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Koval M, Molina SA, Burt JM. Mix and match: investigating heteromeric and heterotypic gap junction channels in model systems and native tissues. FEBS Lett 2014; 588:1193-204. [PMID: 24561196 DOI: 10.1016/j.febslet.2014.02.025] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 02/12/2014] [Accepted: 02/13/2014] [Indexed: 12/12/2022]
Abstract
This review is based in part on a roundtable discussion session: "Physiological roles for heterotypic/heteromeric channels" at the 2013 International Gap Junction Conference (IGJC 2013) in Charleston, South Carolina. It is well recognized that multiple connexins can specifically co-assemble to form mixed gap junction channels with unique properties as a means to regulate intercellular communication. Compatibility determinants for both heteromeric and heterotypic gap junction channel formation have been identified and associated with specific connexin amino acid motifs. Hetero-oligomerization is also a regulated process; differences in connexin quality control and monomer stability are likely to play integral roles to control interactions between compatible connexins. Gap junctions in oligodendrocyte:astrocyte communication and in the cardiovascular system have emerged as key systems where heterotypic and heteromeric channels have unique physiologic roles. There are several methodologies to study heteromeric and heterotypic channels that are best applied to either heterologous expression systems, native tissues or both. There remains a need to use and develop different experimental approaches in order to understand the prevalence and roles for mixed gap junction channels in human physiology.
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Affiliation(s)
- Michael Koval
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, United States; Department of Cell Biology, Emory University, Atlanta, GA, United States.
| | - Samuel A Molina
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Janis M Burt
- Department of Physiology, University of Arizona, Tucson, AZ, United States
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11
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Récamier V, Izeddin I, Bosanac L, Dahan M, Proux F, Darzacq X. Single cell correlation fractal dimension of chromatin: a framework to interpret 3D single molecule super-resolution. Nucleus 2014; 5:75-84. [PMID: 24637833 PMCID: PMC4028358 DOI: 10.4161/nucl.28227] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin is a major nuclear component, and it is an active matter of debate to understand its different levels of spatial organization, as well as its implication in gene regulation. Measurements of nuclear chromatin compaction were recently used to understand how DNA is folded inside the nucleus and to detect cellular dysfunctions such as cancer. Super-resolution imaging opens new possibilities to measure chromatin organization in situ. Here, we performed a direct measure of chromatin compaction at the single cell level. We used histone H2B, one of the 4 core histone proteins forming the nucleosome, as a chromatin density marker. Using photoactivation localization microscopy (PALM) and adaptive optics, we measured the three-dimensional distribution of H2B with nanometric resolution. We computed the distribution of distances between every two points of the chromatin structure, namely the Ripley K(r) distribution. We found that the K(r) distribution of H2B followed a power law, leading to a precise measurement of the correlation fractal dimension of chromatin of 2.7. Moreover, using photoactivable GFP fused to H2B, we observed dynamic evolution of chromatin sub-regions compaction. As a result, the correlation fractal dimension of chromatin reported here can be interpreted as a dynamically maintained non-equilibrium state.
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Affiliation(s)
- Vincent Récamier
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Paris Descartes University; Paris, France
| | - Ignacio Izeddin
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
| | - Lana Bosanac
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France; Molecular and Cellular Biology Department; University of California; Berkeley, CA USA
| | - Maxime Dahan
- Laboratoire Physico-Chimie Curie; Institut Curie; CNRS UMR168; Université Pierre et Marie Curie-Paris; Paris, France
| | - Florence Proux
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
| | - Xavier Darzacq
- Functional Imaging of Transcription; Ecole Normale Supérieur; Institut de Biologie de l'ENS (IBENS); Inserm U1024; CNRS UMR 8197; Paris, France
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12
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Duan C, Adam V, Byrdin M, Bourgeois D. Structural basis of photoswitching in fluorescent proteins. Methods Mol Biol 2014; 1148:177-202. [PMID: 24718802 DOI: 10.1007/978-1-4939-0470-9_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fluorescent proteins have revolutionized life sciences because they allow noninvasive and highly specific labeling of biological samples. The subset of "phototransformable" fluorescent proteins recently attracted a widespread interest, as their fluorescence state can be modified upon excitation at defined wavelengths. The fluorescence emission of Reversibly Switchable Fluorescent Proteins (RSFPs), in particular, can be repeatedly switched on and off. RSFPs enable many new exciting modalities in fluorescence microscopy and biotechnology, including protein tracking, photochromic Förster Resonance Energy Transfer, super-resolution microscopy, optogenetics, and ultra-high-density optical data storage. Photoswitching in RSFPs typically results from chromophore cis-trans isomerization accompanied by a protonation change, but other switching schemes based on, e.g., chromophore hydration/dehydration have also been discovered. In this chapter, we review the main structural features at the basis of photoswitching in RSFPs.
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Affiliation(s)
- Chenxi Duan
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France
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13
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Super-resolution microscopy of the immunological synapse. Curr Opin Immunol 2013; 25:307-12. [PMID: 23746999 DOI: 10.1016/j.coi.2013.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 12/18/2022]
Abstract
Deciphering the spatial organisation of signalling proteins is the key to understanding the mechanisms underlying immune cell activation. Every advance in imaging technology has led to major breakthroughs in unravelling how receptor and signalling proteins are distributed within the plasma membrane and how membrane signalling is integrated with endosomes and vesicular trafficking. Recently, super-resolution fluorescence microscopy has been applied to immunological synapses, gaining new insights into the nanoscale organisation of signalling processes. Here, we review the advantages and potential of super-resolution microscopy for elucidating the regulation of many aspects of immune signalling.
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14
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Fluorescence nanoscopy. Methods and applications. J Chem Biol 2013; 6:97-120. [PMID: 24432127 DOI: 10.1007/s12154-013-0096-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/05/2013] [Indexed: 12/30/2022] Open
Abstract
Fluorescence nanoscopy refers to the experimental techniques and analytical methods used for fluorescence imaging at a resolution higher than conventional, diffraction-limited, microscopy. This review explains the concepts behind fluorescence nanoscopy and focuses on the latest and promising developments in acquisition techniques, labelling strategies to obtain highly detailed super-resolved images and in the quantitative methods to extract meaningful information from them.
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15
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T cell antigen receptor activation and actin cytoskeleton remodeling. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:546-56. [PMID: 23680625 DOI: 10.1016/j.bbamem.2013.05.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/02/2013] [Indexed: 12/20/2022]
Abstract
T cells constitute a crucial arm of the adaptive immune system and their optimal function is required for a healthy immune response. After the initial step of T cell-receptor (TCR) triggering by antigenic peptide complexes on antigen presenting cell (APC), the T cell exhibits extensive cytoskeletal remodeling. This cytoskeletal remodeling leads to the formation of an "immunological synapse" [1] characterized by regulated clustering, segregation and movement of receptors at the interface. Synapse formation regulates T cell activation and response to antigenic peptides and proceeds via feedback between actin cytoskeleton and TCR signaling. Actin polymerization participates in various events during the synapse formation, maturation, and eventually its disassembly. There is increasing knowledge about the actin effectors that couple TCR activation to actin rearrangements [2,3], and how defects in these effectors translate into impairment of T cell activation. In this review we aim to summarize and integrate parts of what is currently known about this feedback process. In addition, in light of recent advancements in our understanding of TCR triggering and translocation at the synapse, we speculate on the organizational and functional diversity of microfilament architecture in the T cell. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé.
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16
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Sherman E, Barr VA, Samelson LE. Resolving multi-molecular protein interactions by photoactivated localization microscopy. Methods 2013; 59:261-9. [PMID: 23266704 PMCID: PMC3608816 DOI: 10.1016/j.ymeth.2012.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/30/2012] [Accepted: 12/14/2012] [Indexed: 11/19/2022] Open
Abstract
Multi-molecular protein complexes are critical to many cellular functions, including signaling, DNA transcription and enzymatic reactions. In spite of their importance, current research techniques such as biochemistry and diffraction-limited microscopy cannot resolve the heterogeneity and nanoscale organization of protein complexes in intact cells. Here we describe a technique that enables the study of multi-molecular protein complexes at the single molecule level in intact cells. The technique uses photoactivated localization microscopy (PALM) to resolve individual proteins with a resolution down to 20nm in intact cells, and second-order statistics to study the spatial interactions of the proteins. We demonstrate the feasibility of this technique by studying signaling complexes that form in activated T cells. We first use single color PALM imaging and univariate second-order statistics to resolve the clustering of Linker for Activation of T cells (LAT) at the plasma membrane (PM) of the cells. We then use two color PALM and bivariate second-order statistics to resolve the interaction of LAT with key interacting proteins. We discuss potential caveats in studying molecular clustering and the robustness of the technique to study bimolecular interactions. Our proposed technique, combined with older techniques, could help shed new light on the nature of multimolecular protein complexes and their significance to cell function.
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Affiliation(s)
- Eilon Sherman
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA.
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Sengupta P, Van Engelenburg S, Lippincott-Schwartz J. Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 2013; 23:1092-102. [PMID: 23237943 DOI: 10.1016/j.devcel.2012.09.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease.
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Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Curado S, Kumari S, Dustin ML. "Cell biology meets physiology: functional organization of vertebrate plasma membranes"--the immunological synapse. CURRENT TOPICS IN MEMBRANES 2013; 72:313-46. [PMID: 24210434 PMCID: PMC4878826 DOI: 10.1016/b978-0-12-417027-8.00009-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The immunological synapse (IS) is an excellent example of cell-cell communication, where signals are exchanged between two cells, resulting in a well-structured line of defense during adaptive immune response. This process has been the focus of several studies that aimed at understanding its formation and subsequent events and has led to the realization that it relies on a well-orchestrated molecular program that only occurs when specific requirements are met. The development of more precise and controllable T cell activation systems has led to new insights including the role of mechanotransduction in the process of formation of the IS and T cell activation. Continuous advances in our understanding of the IS formation, particularly in the context of T cell activation and differentiation, as well the development of new T cell activation systems are being applied to the establishment and improvement of immune therapeutical approaches.
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Affiliation(s)
- Silvia Curado
- Skirball Institute of Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA and Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, Headington, Oxfordshire, OX3 7FY, UK
| | - Sudha Kumari
- Skirball Institute of Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA and Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, Headington, Oxfordshire, OX3 7FY, UK
| | - Michael L. Dustin
- Skirball Institute of Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA and Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, Headington, Oxfordshire, OX3 7FY, UK
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Sherman E, Barr V, Samelson LE. Super-resolution characterization of TCR-dependent signaling clusters. Immunol Rev 2013; 251:21-35. [PMID: 23278738 PMCID: PMC3539238 DOI: 10.1111/imr.12010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Multi-molecular signaling complexes drive the earliest events of immune cell activation via immunoreceptors with unexplained specificity and speed. Fluorescence microscopy has shown that these complexes form microclusters at the plasma membrane of activated T cells upon engagement of their antigen receptors (TCRs). Although crucial for cell function, much remains to be learned about the molecular content, fine structure, formation mechanisms, and function of these microclusters. Recent advancements in super-resolution microscopy have enabled the study of signaling microclusters at the single molecule level with resolution down to approximately 20 nm. These techniques have now helped to characterize the size distributions of signaling clusters at the plasma membrane of intact cells and to shed light on the formation mechanisms that govern their assembly. Surprisingly, dynamic and functional nanostructures have been identified within the signaling clusters. We expect that these novel methodologies, combined with older techniques, will shed new light on the nature of signaling clusters and their critical role in T-cell activation.
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Affiliation(s)
- Eilon Sherman
- Laboratory of Cellular and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892-4256, USA.
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Coltharp C, Kessler RP, Xiao J. Accurate construction of photoactivated localization microscopy (PALM) images for quantitative measurements. PLoS One 2012; 7:e51725. [PMID: 23251611 PMCID: PMC3520911 DOI: 10.1371/journal.pone.0051725] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 11/05/2012] [Indexed: 11/25/2022] Open
Abstract
Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems.
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Affiliation(s)
- Carla Coltharp
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Rene P. Kessler
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jie Xiao
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Sengupta P, Lippincott-Schwartz J. Quantitative analysis of photoactivated localization microscopy (PALM) datasets using pair-correlation analysis. Bioessays 2012; 34:396-405. [PMID: 22447653 PMCID: PMC3659788 DOI: 10.1002/bies.201200022] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pointillistic based super-resolution techniques, such as photoactivated localization microscopy (PALM), involve multiple cycles of sequential activation, imaging, and precise localization of single fluorescent molecules. A super-resolution image, having nanoscopic structural information, is then constructed by compiling all the image sequences. Because the final image resolution is determined by the localization precision of detected single molecules and their density, accurate image reconstruction requires imaging of biological structures labeled with fluorescent molecules at high density. In such image datasets, stochastic variations in photon emission and intervening dark states lead to uncertainties in identification of single molecules. This, in turn, prevents the proper utilization of the wealth of information on molecular distribution and quantity. A recent strategy for overcoming this problem is pair-correlation analysis applied to PALM. Using rigorous statistical algorithms to estimate the number of detected proteins, this approach allows the spatial organization of molecules to be quantitatively described.
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Affiliation(s)
- Prabuddha Sengupta
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MA, USA.
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Annibale P, Scarselli M, Greco M, Radenovic A. Identification of the factors affecting co-localization precision for quantitative multicolor localization microscopy. ACTA ACUST UNITED AC 2012. [DOI: 10.1186/2192-2853-1-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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