1
|
O'Shaughnessy EC, Lam M, Ryken SE, Wiesner T, Lukasik K, Zuchero JB, Leterrier C, Adalsteinsson D, Gupton SL. pHusion - a robust and versatile toolset for automated detection and analysis of exocytosis. J Cell Sci 2024; 137:jcs261828. [PMID: 38690758 PMCID: PMC11190432 DOI: 10.1242/jcs.261828] [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: 11/23/2023] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
Exocytosis is a fundamental process used by eukaryotes to regulate the composition of the plasma membrane and facilitate cell-cell communication. To investigate exocytosis in neuronal morphogenesis, previously we developed computational tools with a graphical user interface to enable the automatic detection and analysis of exocytic events from fluorescence timelapse images. Although these tools were useful, we found the code was brittle and not easily adapted to different experimental conditions. Here, we developed and validated a robust and versatile toolkit, named pHusion, for the analysis of exocytosis, written in ImageTank, a graphical programming language that combines image visualization and numerical methods. We tested pHusion using a variety of imaging modalities and pH-sensitive fluorophores, diverse cell types and various exocytic markers, to generate a flexible and intuitive package. Using this system, we show that VAMP3-mediated exocytosis occurs 30-times more frequently in melanoma cells compared with primary oligodendrocytes, that VAMP2-mediated fusion events in mature rat hippocampal neurons are longer lasting than those in immature murine cortical neurons, and that exocytic events are clustered in space yet random in time in developing cortical neurons.
Collapse
Affiliation(s)
- Ellen C. O'Shaughnessy
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
| | - Mable Lam
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samantha E. Ryken
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
| | - Theresa Wiesner
- NeuroCyto, Aix Marseille Université, CNRS, INP UMR7051, Marseille 13385, France
| | - Kimberly Lukasik
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
| | - J. Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - David Adalsteinsson
- University of North Carolina at Chapel Hill, Department of Mathematics, Chapel Hill, NC 27599, USA
| | - Stephanie L. Gupton
- University of North Carolina at Chapel Hill, Department of Cell Biology and Physiology, Chapel Hill, NC 27599, USA
| |
Collapse
|
2
|
Mutalik SP, O'Shaughnessy EC, Ho CT, Gupton SL. TRIM9 controls growth cone responses to netrin through DCC and UNC5C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593135. [PMID: 38765979 PMCID: PMC11100671 DOI: 10.1101/2024.05.08.593135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The guidance cue netrin-1 promotes both growth cone attraction and growth cone repulsion. How netrin-1 elicits these diverse axonal responses, beyond engaging the attractive receptor DCC and repulsive receptors of the UNC5 family, remains elusive. Here we demonstrate that murine netrin-1 induces biphasic axonal responses in cortical neurons: attraction at lower concentrations and repulsion at higher concentrations using both a microfluidic-based netrin-1 gradient and bath application of netrin-1. TRIM9 is a brain-enriched E3 ubiquitin ligase previously shown to bind and cluster the attractive receptor DCC at the plasma membrane and regulate netrin-dependent attractive responses. However, whether TRIM9 also regulated repulsive responses to netrin-1 remained to be seen. In this study, we show that TRIM9 localizes and interacts with both the attractive netrin receptor DCC and the repulsive netrin receptor, UNC5C, and that deletion of murine Trim9 alters both attractive and repulsive responses to murine netrin-1. TRIM9 was required for netrin-1-dependent changes in surface levels of DCC and total levels of UNC5C in the growth cone during morphogenesis. We demonstrate that DCC at the membrane regulates growth cone area and show that TRIM9 negatively regulates FAK activity in the absence of netrin-1. We investigate membrane dynamics of the UNC5C receptor using pH-mScarlet fused to the extracellular domain of UNC5C. Minutes after netrin addition, levels of UNC5C at the plasma membrane drop in a TRIM9-independent fashion, however TRIM9 regulated the mobility of UNC5C in the plasma membrane in the absence of netrin-1. Together this work demonstrates that TRIM9 interacts with and regulates both DCC and UNC5C during attractive and repulsive axonal responses to netrin-1.
Collapse
|
3
|
Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 DOI: 10.1111/jmi.13270] [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: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
Collapse
Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| |
Collapse
|
4
|
Zhang JZ, Nguyen WH, Greenwood N, Rose JC, Ong SE, Maly DJ, Baker D. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nat Biotechnol 2024:10.1038/s41587-023-02107-w. [PMID: 38273065 DOI: 10.1038/s41587-023-02107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
The utility of genetically encoded biosensors for sensing the activity of signaling proteins has been hampered by a lack of strategies for matching sensor sensitivity to the physiological concentration range of the target. Here we used computational protein design to generate intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity (Ras-LOCKR-S)) and proximity labelers of the Ras signaling environment (LOCKR-based, Ras activity-dependent Proximity Labeler (Ras-LOCKR-PL)). These tools allow the detection of endogenous Ras activity and labeling of the surrounding environment at subcellular resolution. Using these sensors in human cancer cell lines, we identified Ras-interacting proteins in oncogenic EML4-Alk granules and found that Src-Associated in Mitosis 68-kDa (SAM68) protein specifically enhances Ras activity in the granules. The ability to subcellularly localize endogenous Ras activity should deepen our understanding of Ras function in health and disease and may suggest potential therapeutic strategies.
Collapse
Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - William H Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Greenwood
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Rose
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
5
|
O'Shaughnessy EC, Lam M, Ryken SE, Wiesner T, Lukasik K, Zuchero BJ, Leterrier C, Adalsteinsson D, Gupton SL. pHusion: A robust and versatile toolset for automated detection and analysis of exocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550499. [PMID: 37546865 PMCID: PMC10402102 DOI: 10.1101/2023.07.25.550499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Exocytosis is a fundamental process used by eukaryotic cells to regulate the composition of the plasma membrane and facilitate cell-cell communication. To investigate the role exocytosis plays in neuronal morphogenesis, previously we developed computational tools with a graphical user interface (GUI) to enable the automatic detection and analysis of exocytic events (ADAE GUI) from fluorescence timelapse images. Though these tools have proven useful, we found that the code was brittle and not easily adapted to different experimental conditions. Here, we have developed and validated a robust and versatile toolkit, named pHusion, for the analysis of exocytosis written in ImageTank, a graphical programming language that combines image visualization and numerical methods. We tested this method using a variety of imaging modalities and pH-sensitive fluorophores, diverse cell types, and various exocytic markers to generate a flexible and intuitive package. Using pHusion, we show that VAMP3-mediated exocytosis occurs 30-times more frequently in melanoma cells compared with primary oligodendrocytes, that VAMP2-mediated fusion events in mature rat hippocampal neurons are longer lasting than those in immature murine cortical neurons, and that exocytic events are clustered in space yet random in time in developing cortical neurons. Summary Statement Exocytosis is an essential process by which cells change shape, alter membrane composition, and communicate with other cells. Though all eukaryotic cells carry out exocytosis, the regulation of vesicle fusion, the cargo of vesicles, and the role exocytosis plays in cell fate differ greatly across cell types. Here, we developed a flexible and robust set of tools to enable automatic identification and analysis of exocytic events across a wide range of cell types, vesicle types, and imaging conditions.
Collapse
|
6
|
Mazloom-Farsibaf H, Zou Q, Hsieh R, Danuser G, Driscoll MK. Cellular harmonics for the morphology-invariant analysis of molecular organization at the cell surface. NATURE COMPUTATIONAL SCIENCE 2023; 3:777-788. [PMID: 38177778 PMCID: PMC10840993 DOI: 10.1038/s43588-023-00512-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/08/2023] [Indexed: 01/06/2024]
Abstract
The spatiotemporal organization of membrane-associated molecules is central to the regulation of cellular signals. Powerful new microscopy techniques enable the three-dimensional visualization of localization and activation of these molecules; however, the quantitative interpretation and comparison of molecular organization on the three-dimensional cell surface remains challenging because cells themselves vary greatly in morphology. Here we introduce u-signal3D, a framework to assess the spatial scales of molecular organization at the cell surface in a cell-morphology-invariant manner. We validated the framework by analyzing synthetic signaling patterns painted onto observed cell morphologies, as well as measured distributions of cytoskeletal and signaling molecules. To demonstrate the framework's versatility, we further compared the spatial organization of cell surface signals both within, and between, cell populations, and powered an upstream machine-learning-based analysis of signaling motifs.
Collapse
Affiliation(s)
- Hanieh Mazloom-Farsibaf
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rebecca Hsieh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Meghan K Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
7
|
Ballard-Kordeliski A, Lee RH, O'Shaughnessy EC, Kim PY, Jones S, Mackman N, Flick MJ, Paul DS, Adalsteinsson D, Bergmeier W. 4D intravital imaging studies identify platelets as the predominant cellular procoagulant surface in a mouse model of hemostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554449. [PMID: 37662350 PMCID: PMC10473702 DOI: 10.1101/2023.08.25.554449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Interplay between platelets, coagulation/fibrinolytic factors, and endothelial cells (ECs) is necessary for effective hemostatic plug formation. This study describes a novel four-dimensional (4D) imaging platform to visualize and quantify hemostatic plug components with high spatiotemporal resolution. Fibrin accumulation following laser-induced endothelial ablation was observed at the EC-platelet plug interface, controlled by the antagonistic balance between fibrin generation and breakdown. Phosphatidylserine (PS) was first detected in close physical proximity to the fibrin ring, followed by exposure across the endothelium. Impaired PS exposure in cyclophilinD -/- mice resulted in a significant reduction in fibrin accumulation. Adoptive transfer and inhibitor studies demonstrated a key role for platelets, but not ECs, in fibrin generation during hemostatic plug formation. Inhibition of fibrinolysis with tranexamic acid (TXA) led to increased fibrin accumulation in WT mice, but not in cyclophilinD -/- mice or WT mice treated with antiplatelet drugs. These studies implicate platelets as the functionally dominant procoagulant surface during hemostatic plug formation. In addition, they suggest that impaired fibrin formation due to reduced platelet procoagulant activity is not reversed by TXA treatment.
Collapse
|
8
|
Boulton S, Crupi MJF, Singh S, Carter-Timofte ME, Azad T, Organ BC, He X, Gill R, Neault S, Jamieson T, Dave J, Kurmasheva N, Austin B, Petryk J, Singaravelu R, Huang BZ, Franco N, Babu K, Parks RJ, Ilkow CS, Olagnier D, Bell JC. Inhibition of Exchange Proteins Directly Activated by cAMP (EPAC) as a Strategy for Broad-Spectrum Antiviral Development. J Biol Chem 2023; 299:104749. [PMID: 37100284 PMCID: PMC10124099 DOI: 10.1016/j.jbc.2023.104749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
The recent SARS-CoV-2 and mpox outbreaks have highlighted the need to expand our arsenal of broad-spectrum antiviral agents for future pandemic preparedness. Host-directed antivirals are an important tool to accomplish this as they typically offer protection against a broader range of viruses than direct-acting antivirals and have a lower susceptibility to viral mutations that cause drug resistance. In this study, we investigate the Exchange Protein Activated by cAMP (EPAC) as a target for broad-spectrum antiviral therapy. We find that the EPAC-selective inhibitor, ESI-09 provides robust protection against a variety of viruses, including SARS-CoV-2 and Vaccinia (VACV) - an orthopoxvirus from the same family as mpox. We show, using a series of immunofluorescence experiments, that ESI-09 remodels the actin cytoskeleton through Rac1/Cdc42 GTPases and the Arp2/3 complex, impairing internalization of viruses that use clathrin-mediated endocytosis (e.g. VSV) or micropinocytosis (e.g. VACV). Additionally, we find that ESI-09 disrupts syncytia formation and inhibits cell-to-cell transmission of viruses such as measles and VACV. When administered to immune-deficient mice in an intranasal challenge model, ESI-09 protects mice from lethal doses of VACV and prevents formation of pox lesions. Altogether, our finding show that EPAC antagonists such as ESI-09 are promising candidates for broad-spectrum antiviral therapy that can aid in the fight against ongoing and future viral outbreaks.
Collapse
Affiliation(s)
- Stephen Boulton
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
| | - Mathieu J F Crupi
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Siddharth Singh
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | | | - Taha Azad
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada; Faculty of Medicine and Health Sciences, Department of microbiology and infectious diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; Centre de Recherche du CHUS, Sherbrooke, QC J1H 5N4, Canada
| | - Bailey C Organ
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Xiaohong He
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Rida Gill
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Serge Neault
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Taylor Jamieson
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Jaahnavi Dave
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Naziia Kurmasheva
- Aarhus University, Department of Biomedicine, Aarhus C, 8000, Denmark
| | - Bradley Austin
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Julia Petryk
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Ragunath Singaravelu
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada; Public Health Agency of Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Ben Zhen Huang
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Noah Franco
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Kaaviya Babu
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Robin J Parks
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada; Department of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Carolina S Ilkow
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - David Olagnier
- Aarhus University, Department of Biomedicine, Aarhus C, 8000, Denmark
| | - John C Bell
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada; Department of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
| |
Collapse
|
9
|
Zhou FY, Weems A, Gihana GM, Chen B, Chang BJ, Driscoll M, Danuser G. Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536640. [PMID: 37131779 PMCID: PMC10153113 DOI: 10.1101/2023.04.12.536640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have limited quantitative understanding of the processes implicated in the regulation of molecular signals at the whole cell scale. In particular, complex and transient cell surface morphologies challenge the complete sampling of cell geometry, membrane-associated molecular concentration and activity and the computing of meaningful parameters such as the cofluctuation between morphology and signals. Here, we introduce u-Unwrap3D, a framework to remap arbitrarily complex 3D cell surfaces and membrane-associated signals into equivalent lower dimensional representations. The mappings are bidirectional, allowing the application of image processing operations in the data representation best suited for the task and to subsequently present the results in any of the other representations, including the original 3D cell surface. Leveraging this surface-guided computing paradigm, we track segmented surface motifs in 2D to quantify the recruitment of Septin polymers by blebbing events; we quantify actin enrichment in peripheral ruffles; and we measure the speed of ruffle movement along topographically complex cell surfaces. Thus, u-Unwrap3D provides access to spatiotemporal analyses of cell biological parameters on unconstrained 3D surface geometries and signals.
Collapse
Affiliation(s)
- Felix Y. Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Weems
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gabriel M. Gihana
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bingying Chen
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meghan Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
10
|
Zhou FY, Weems A, Gihana GM, Chen B, Chang BJ, Driscoll M, Danuser G. Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D. ARXIV 2023:arXiv:2304.06176v1. [PMID: 37090235 PMCID: PMC10120750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have limited quantitative understanding of the processes implicated in the regulation of molecular signals at the whole cell scale. In particular, complex and transient cell surface morphologies challenge the complete sampling of cell geometry, membrane-associated molecular concentration and activity and the computing of meaningful parameters such as the cofluctuation between morphology and signals. Here, we introduce u-Unwrap3D, a framework to remap arbitrarily complex 3D cell surfaces and membrane-associated signals into equivalent lower dimensional representations. The mappings are bidirectional, allowing the application of image processing operations in the data representation best suited for the task and to subsequently present the results in any of the other representations, including the original 3D cell surface. Leveraging this surface-guided computing paradigm, we track segmented surface motifs in 2D to quantify the recruitment of Septin polymers by blebbing events; we quantify actin enrichment in peripheral ruffles; and we measure the speed of ruffle movement along topographically complex cell surfaces. Thus, u-Unwrap3D provides access to spatiotemporal analyses of cell biological parameters on unconstrained 3D surface geometries and signals.
Collapse
Affiliation(s)
- Felix Y. Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Weems
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gabriel M. Gihana
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bingying Chen
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meghan Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
11
|
Fares J, Davis ZB, Rechberger JS, Toll SA, Schwartz JD, Daniels DJ, Miller JS, Khatua S. Advances in NK cell therapy for brain tumors. NPJ Precis Oncol 2023; 7:17. [PMID: 36792722 PMCID: PMC9932101 DOI: 10.1038/s41698-023-00356-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Despite advances in treatment regimens that comprise surgery, chemotherapy, and radiation, outcome of many brain tumors remains dismal, more so when they recur. The proximity of brain tumors to delicate neural structures often precludes complete surgical resection. Toxicity and long-term side effects of systemic therapy remain a concern. Novel therapies are warranted. The field of NK cell-based cancer therapy has grown exponentially and currently constitutes a major area of immunotherapy innovation. This provides a new avenue for the treatment of cancerous lesions in the brain. In this review, we explore the mechanisms by which the brain tumor microenvironment suppresses NK cell mediated tumor control, and the methods being used to create NK cell products that subvert immune suppression. We discuss the pre-clinical studies evaluating NK cell-based immunotherapies that target several neuro-malignancies and highlight advances in molecular imaging of NK cells that allow monitoring of NK cell-based therapeutics. We review current and ongoing NK cell based clinical trials in neuro-oncology.
Collapse
Affiliation(s)
- Jawad Fares
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Northwestern Medicine Malnati Brain Tumor Institute, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Zachary B Davis
- Department of Medicine, Division of Hematology, Oncology and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Julian S Rechberger
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, 55905, USA
| | - Stephanie A Toll
- Department of Pediatrics, Division of Hematology/Oncology, Children's Hospital of Michigan, Detroit, MI, 48201, USA
| | - Jonathan D Schwartz
- Department of Pediatric Hematology/Oncology, Section of Neuro-Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - David J Daniels
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, 55905, USA
| | - Jeffrey S Miller
- Department of Medicine, Division of Hematology, Oncology and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55454, USA.
| | - Soumen Khatua
- Department of Pediatric Hematology/Oncology, Section of Neuro-Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| |
Collapse
|
12
|
Roden C, Dai Y, Giannetti C, Seim I, Lee M, Sealfon R, McLaughlin G, Boerneke M, Iserman C, Wey S, Ekena J, Troyanskaya O, Weeks K, You L, Chilkoti A, Gladfelter A. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res 2022; 50:8168-8192. [PMID: 35871289 PMCID: PMC9371935 DOI: 10.1093/nar/gkac596] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 12/11/2022] Open
Abstract
Nucleocapsid protein (N-protein) is required for multiple steps in betacoronaviruses replication. SARS-CoV-2-N-protein condenses with specific viral RNAs at particular temperatures making it a powerful model for deciphering RNA sequence specificity in condensates. We identify two separate and distinct double-stranded, RNA motifs (dsRNA stickers) that promote N-protein condensation. These dsRNA stickers are separately recognized by N-protein's two RNA binding domains (RBDs). RBD1 prefers structured RNA with sequences like the transcription-regulatory sequence (TRS). RBD2 prefers long stretches of dsRNA, independent of sequence. Thus, the two N-protein RBDs interact with distinct dsRNA stickers, and these interactions impart specific droplet physical properties that could support varied viral functions. Specifically, we find that addition of dsRNA lowers the condensation temperature dependent on RBD2 interactions and tunes translational repression. In contrast RBD1 sites are sequences critical for sub-genomic (sg) RNA generation and promote gRNA compression. The density of RBD1 binding motifs in proximity to TRS-L/B sequences is associated with levels of sub-genomic RNA generation. The switch to packaging is likely mediated by RBD1 interactions which generate particles that recapitulate the packaging unit of the virion. Thus, SARS-CoV-2 can achieve biochemical complexity, performing multiple functions in the same cytoplasm, with minimal protein components based on utilizing multiple distinct RNA motifs that control N-protein interactions.
Collapse
Affiliation(s)
- Christine A Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Catherine A Giannetti
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Ian Seim
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Rachel Sealfon
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Grace A McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark A Boerneke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Christiane Iserman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel A Wey
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Joanne L Ekena
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| |
Collapse
|
13
|
Both G protein-coupled and immunoreceptor tyrosine-based activation motif receptors mediate venous thrombosis in mice. Blood 2022; 139:3194-3203. [PMID: 35358299 PMCID: PMC9136879 DOI: 10.1182/blood.2022015787] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/27/2022] [Indexed: 01/26/2023] Open
Abstract
Platelets are critical in hemostasis and a major contributor to arterial thrombosis (AT). (Pre)clinical studies suggest platelets also contribute to venous thrombosis (VT), but the mechanisms are largely unknown. We hypothesized that in VT, platelets use signaling machinery distinct from AT. Here we aimed to characterize the contributions of platelet G protein-coupled (GPCR) and immunoreceptor tyrosine-based activation motif (ITAM) receptor signaling to VT. Wild-type (WT) and transgenic mice were treated with inhibitors to selectively inhibit platelet-signaling pathways: ITAM-CLEC2 (Clec2mKO), glycoprotein VI (JAQ1 antibody), and Bruton's tyrosine kinase (ibrutinib); GPCR-cyclooxygenase 1 (aspirin); and P2Y12 (clopidogrel). VT was induced by inferior vena cava stenosis. Thrombin generation in platelet-rich plasma and whole-blood clot formation were studied ex vivo. Intravital microscopy was used to study platelet-leukocyte interactions after flow restriction. Thrombus weights were reduced in WT mice treated with high-dose aspirin + clopidogrel (dual antiplatelet therapy [DAPT]) but not in mice treated with either inhibitor alone or low-dose DAPT. Similarly, thrombus weights were reduced in mice with impaired ITAM signaling (Clec2mKO + JAQ1; WT + ibrutinib) but not in Clec2mKO or WT + JAQ1 mice. Both aspirin and clopidogrel, but not ibrutinib, protected mice from FeCl3-induced AT. Thrombin generation and clot formation were normal in blood from high-dose DAPT- or ibrutinib-treated mice; however, platelet adhesion and platelet-neutrophil aggregate formation at the vein wall were reduced in mice treated with high-dose DAPT or ibrutinib. In summary, VT initiation requires platelet activation via GPCRs and ITAM receptors. Strong inhibition of either signaling pathway reduces VT in mice.
Collapse
|
14
|
Winter M, Cohen AR. LEVERSC: Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images. FRONTIERS IN BIOINFORMATICS 2022; 2:740078. [PMID: 36304277 PMCID: PMC9580858 DOI: 10.3389/fbinf.2022.740078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
We describe a new open-source program called LEVERSC to address the challenges of visualizing the multi-channel 3-D images prevalent in biological microscopy. LEVERSC uses a custom WebGL hardware-accelerated raycasting engine unique in its combination of rendering quality and performance, particularly for multi-channel data. Key features include platform independence, quantitative visualization through interactive voxel localization, and reproducible dynamic visualization via the scripting interface. LEVERSC is fully scriptable and interactive, and works with MATLAB, Python and Java/ImageJ.
Collapse
|
15
|
Varadarajan SN, Mathew KA, Chandrasekharan A, Lupitha SS, Lekshmi A, Mini M, Darvin P, Santhoshkumar TR. Real-time visualization and quantitation of cell death and cell cycle progression in 2D and 3D cultures utilizing genetically encoded probes. J Cell Biochem 2022; 123:782-797. [PMID: 35106828 DOI: 10.1002/jcb.30222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022]
Abstract
Cancer cells grown as 3D-structures are better models for mimicking in vivo conditions than the 2D-culture systems employable in drug discovery applications. Cell cycle and cell death are important determinants for preclinical drug screening and tumor growth studies in laboratory conditions. Though several 3D-models and live-cell compatible approaches are available, a method for simultaneous real-time detection of cell cycle and cell death is required. Here we demonstrate a high-throughput adaptable method using genetically encoded fluorescent probes for the real-time quantitative detection of cell death and cell cycle. The cell-cycle indicator cdt1-Kusabira orange (KO) is stably integrated into cancer cells and further transfected with the Fluorescence Resonance Energy Transfer-based ECFP-DEVD-EYFP caspase activation sensor. The nuclear cdt1-KO expression serves as the readout for cell-cycle, and caspase activation is visualized by ECFP/EYFP ratiometric imaging. The image-based platform allowed imaging of growing spheres for prolonged periods in 3D-culture with excellent single-cell resolution through confocal microscopy. High-throughput screening (HTS) adaptation was achieved by targeting the caspase-sensor at the nucleus, which enabled the quantitation of cell death in 3D-models. The HTS using limited compound libraries, identified two lead compounds that induced caspase-activation both in 2D and 3D-cultures. This is the first report of an approach for noninvasive stain-free quantitative imaging of cell death and cell cycle with potential drug discovery applications.
Collapse
Affiliation(s)
| | - Krupa Ann Mathew
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Aneesh Chandrasekharan
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | - Asha Lekshmi
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Minsa Mini
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Pramod Darvin
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - T R Santhoshkumar
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| |
Collapse
|
16
|
He Y, Adalsteinsson D, Walker B, Lawrimore J, Forest MG, Bloom K. Simulating Dynamic Chromosome Compaction: Methods for Bridging In Silico to In Vivo. Methods Mol Biol 2022; 2415:211-220. [PMID: 34972957 PMCID: PMC9289795 DOI: 10.1007/978-1-0716-1904-9_16] [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: 01/03/2023]
Abstract
The application of polymer models to chromosome structure and dynamics is a powerful approach for dissecting functional properties of the chromosome. The models are based on well-established bead-spring models of polymers and are distinct from molecular dynamics studies used in structural biology. In this work, we outline a polymer dynamics model that simulates budding yeast chromatin fibers in a viscous environment inside the nucleus using DataTank as a user interface for the C++ simulation. We highlight features for creating the nucleolus, a dynamic region of chromatin with protein-mediated, transient chromosomal cross-links, providing a predictive, stochastic polymer-physics model for versatile analyses of chromosome spatiotemporal organization. DataTank provides real-time visualization and data analytics methods during simulation. The simulation pipeline provides insights into the entangled chromosome milieu in the nucleus and creates simulated chromosome data, both structural and dynamic, that can be directly compared to experimental observations of live cells in interphase and mitosis.
Collapse
Affiliation(s)
- Yunyan He
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin Walker
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M. Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
17
|
Plexin-B2 orchestrates collective stem cell dynamics via actomyosin contractility, cytoskeletal tension and adhesion. Nat Commun 2021; 12:6019. [PMID: 34650052 PMCID: PMC8517024 DOI: 10.1038/s41467-021-26296-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 09/29/2021] [Indexed: 11/08/2022] Open
Abstract
During morphogenesis, molecular mechanisms that orchestrate biomechanical dynamics across cells remain unclear. Here, we show a role of guidance receptor Plexin-B2 in organizing actomyosin network and adhesion complexes during multicellular development of human embryonic stem cells and neuroprogenitor cells. Plexin-B2 manipulations affect actomyosin contractility, leading to changes in cell stiffness and cytoskeletal tension, as well as cell-cell and cell-matrix adhesion. We have delineated the functional domains of Plexin-B2, RAP1/2 effectors, and the signaling association with ERK1/2, calcium activation, and YAP mechanosensor, thus providing a mechanistic link between Plexin-B2-mediated cytoskeletal tension and stem cell physiology. Plexin-B2-deficient stem cells exhibit premature lineage commitment, and a balanced level of Plexin-B2 activity is critical for maintaining cytoarchitectural integrity of the developing neuroepithelium, as modeled in cerebral organoids. Our studies thus establish a significant function of Plexin-B2 in orchestrating cytoskeletal tension and cell-cell/cell-matrix adhesion, therefore solidifying the importance of collective cell mechanics in governing stem cell physiology and tissue morphogenesis.
Collapse
|
18
|
Hobson CM, Aaron JS, Heddleston JM, Chew TL. Visualizing the Invisible: Advanced Optical Microscopy as a Tool to Measure Biomechanical Forces. Front Cell Dev Biol 2021; 9:706126. [PMID: 34552926 PMCID: PMC8450411 DOI: 10.3389/fcell.2021.706126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/09/2021] [Indexed: 01/28/2023] Open
Abstract
The importance of mechanical force in biology is evident across diverse length scales, ranging from tissue morphogenesis during embryo development to mechanotransduction across single adhesion proteins at the cell surface. Consequently, many force measurement techniques rely on optical microscopy to measure forces being applied by cells on their environment, to visualize specimen deformations due to external forces, or even to directly apply a physical perturbation to the sample via photoablation or optogenetic tools. Recent developments in advanced microscopy offer improved approaches to enhance spatiotemporal resolution, imaging depth, and sample viability. These advances can be coupled with already existing force measurement methods to improve sensitivity, duration and speed, amongst other parameters. However, gaining access to advanced microscopy instrumentation and the expertise necessary to extract meaningful insights from these techniques is an unavoidable hurdle. In this Live Cell Imaging special issue Review, we survey common microscopy-based force measurement techniques and examine how they can be bolstered by emerging microscopy methods. We further explore challenges related to the accompanying data analysis in biomechanical studies and discuss the various resources available to tackle the global issue of technology dissemination, an important avenue for biologists to gain access to pre-commercial instruments that can be leveraged for biomechanical studies.
Collapse
Affiliation(s)
- Chad M. Hobson
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - Jesse S. Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - John M. Heddleston
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, United States
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| |
Collapse
|
19
|
Lattice Light-Sheet Microscopy Multi-dimensional Analyses (LaMDA) of T-Cell Receptor Dynamics Predict T-Cell Signaling States. Cell Syst 2021; 10:433-444.e5. [PMID: 32437685 DOI: 10.1016/j.cels.2020.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/29/2020] [Accepted: 04/21/2020] [Indexed: 12/19/2022]
Abstract
Lattice light-sheet microscopy provides large amounts of high-dimensional, high-spatiotemporal resolution imaging data of cell surface receptors across the 3D surface of live cells, but user-friendly analysis pipelines are lacking. Here, we introduce lattice light-sheet microscopy multi-dimensional analyses (LaMDA), an end-to-end pipeline comprised of publicly available software packages that combines machine learning, dimensionality reduction, and diffusion maps to analyze surface receptor dynamics and classify cellular signaling states without the need for complex biochemical measurements or other prior information. We use LaMDA to analyze images of T-cell receptor (TCR) microclusters on the surface of live primary T cells under resting and stimulated conditions. We observe global spatial and temporal changes of TCRs across the 3D cell surface, accurately differentiate stimulated cells from unstimulated cells, precisely predict attenuated T-cell signaling after CD4 and CD28 receptor blockades, and reliably discriminate between structurally similar TCR ligands. All instructions needed to implement LaMDA are included in this paper.
Collapse
|
20
|
Freeman S, Grinstein S. Promoters and Antagonists of Phagocytosis: A Plastic and Tunable Response. Annu Rev Cell Dev Biol 2021; 37:89-114. [PMID: 34152790 DOI: 10.1146/annurev-cellbio-120219-055903] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent observations indicate that, rather than being an all-or-none response, phagocytosis is finely tuned by a host of developmental and environmental factors. The expression of key phagocytic determinants is regulated via transcriptional and epigenetic means that confer memory on the process. Membrane traffic, the cytoskeleton, and inside-out signaling control the activation of phagocytic receptors and their ability to access their targets. An exquisite extra layer of complexity is introduced by the coexistence of distinct "eat-me" and "don't-eat-me" signals on targets and of corresponding "eat" and "don't-eat" receptors on the phagocyte surface. Moreover, assorted physical barriers constitute "don't-come-close-to-me" hurdles that obstruct the engagement of ligands by receptors. The expression, mobility, and accessibility of all these determinants can be modulated, conferring extreme plasticity on phagocytosis and providing attractive targets for therapeutic intervention in cancer, atherosclerosis, and dementia. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Spencer Freeman
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada; , .,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sergio Grinstein
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada; , .,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
21
|
Roden CA, Dai Y, Seim I, Lee M, Sealfon R, McLaughlin GA, Boerneke MA, Iserman C, Wey SA, Ekena JL, Troyanskaya OG, Weeks KM, You L, Chilkoti A, Gladfelter AS. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34159327 DOI: 10.1101/2021.06.14.448452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Betacoronavirus SARS-CoV-2 infections caused the global Covid-19 pandemic. The nucleocapsid protein (N-protein) is required for multiple steps in the betacoronavirus replication cycle. SARS-CoV-2-N-protein is known to undergo liquid-liquid phase separation (LLPS) with specific RNAs at particular temperatures to form condensates. We show that N-protein recognizes at least two separate and distinct RNA motifs, both of which require double-stranded RNA (dsRNA) for LLPS. These motifs are separately recognized by N-protein's two RNA binding domains (RBDs). Addition of dsRNA accelerates and modifies N-protein LLPS in vitro and in cells and controls the temperature condensates form. The abundance of dsRNA tunes N-protein-mediated translational repression and may confer a switch from translation to genome packaging. Thus, N-protein's two RBDs interact with separate dsRNA motifs, and these interactions impart distinct droplet properties that can support multiple viral functions. These experiments demonstrate a paradigm of how RNA structure can control the properties of biomolecular condensates.
Collapse
|
22
|
Abstract
For probing small distances in living cells, methods of super-resolution microscopy and molecular sensing are reported. A main requirement is low light exposure to maintain cell viability and to avoid photobleaching of relevant fluorophores. From this point of view, Structured Illumination Microscopy (SIM), Axial Tomography, Total Internal Reflection Fluorescence Microscopy (TIRFM) and often a combination of these methods are used. To show the high potential of these techniques, measurements on cell-substrate topology as well as on intracellular translocation of the glucose transporter GLUT4 are described. In addition, molecular parameters can be deduced from spectral data, fluorescence lifetimes or non-radiative energy transfer (FRET) between a donor and an acceptor molecule. As an example, FRET between the epidermal growth factor receptor (EGFR) and the growth factor receptor-bound protein 2 (Grb2) is described. Since this interaction, as well as further processes of cellular signaling (e.g., translocation of GLUT4) are sensitive to stimulation by pharmaceutical agents, methods (e.g., TIRFM) are transferred from a fluorescence microscope to a multi-well reader system for simultaneous detection of large cell populations.
Collapse
|
23
|
Mehta S, Zhang J. Biochemical Activity Architectures Visualized-Using Genetically Encoded Fluorescent Biosensors to Map the Spatial Boundaries of Signaling Compartments. Acc Chem Res 2021; 54:2409-2420. [PMID: 33949851 DOI: 10.1021/acs.accounts.1c00056] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All biological processes arise through the coordinated actions of biochemical pathways. How such functional diversity is achieved by a finite cast of molecular players remains a central mystery in biology. Spatial compartmentation-the idea that biochemical activities are organized around discrete spatial domains within cells-was first proposed nearly 40 years ago and has become firmly rooted in our understanding of how biochemical pathways are regulated to ensure specificity. However, directly interrogating spatial compartmentation and its mechanistic origins has only really become possible in the last 20 or so years, following technological advances such as the development of genetically encoded fluorescent biosensors. These powerful molecular tools permit a direct, real-time visualization of dynamic biochemical processes in native biological contexts, and they are essential for probing the spatial regulation of biochemical activities. In this Account, we review our lab's efforts in developing and using biosensors to map the spatial compartmentation of intracellular signaling pathways and illuminate key mechanisms that establish the boundaries of an intricate biochemical activity architecture. We first discuss the role of regulatory fences, wherein the dynamic activation and deactivation of diffusible messengers produce diverse signaling compartments. For example, we used biosensors for the Ca2+ effector calmodulin and its downstream target calcineurin to reveal a spatial gradient of calmodulin that controls the temporal dynamics of calcineurin signaling. Our studies using cyclic adenosine monophosphate (cAMP) biosensors have similarly elucidated fenced cAMP domains generated by competing production and degradation pathways, ranging in size from cell-spanning gradients to nanoscale hotspots. Second, we describe the role played by intracellular membranes in creating unique signaling platforms with distinctive pathway regulation, as revealed through studies using subcellularly targeted fluorescent biosensors. Using biosensors to visualize subcellular extracellular response kinase (ERK) pathway activity, for example, led us to discover a local signaling circuit that mediates distinct plasma membrane ERK dynamics versus global ERK signaling. Similarly, our work developing biosensors to monitor the subcellular mechanistic target of rapamycin complex 1 (mTORC1) signaling allowed us to not only clarify the presence of mTORC1 activity in the nucleus but also identify a novel mechanism governing the activation of mTORC1 in this location. Finally, we detail how molecular assemblies enable the precise spatial tuning of biochemical activity, through investigations enabled by cutting-edge advances in biosensor design. We recently identified liquid-liquid phase separation as a major factor in cAMP compartmentation aided by a new strategy for targeting biosensors to endogenously expressed proteins via genome editing, for instance, and have also been able to directly visualize nanometer-scale protein kinase signalosomes using an entirely new class of biosensors specifically developed for the dynamic super-resolution imaging of live-cell biochemical activities. Our work provides key insights into the molecular logic of spatially regulated signaling and lays the foundation for a broader exploration of biochemical activity architectures across multiple spatial scales.
Collapse
Affiliation(s)
- Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Jin Zhang
- Departments of Pharmacology, Bioengineering, and Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
24
|
Mimori-Kiyosue Y. Imaging mitotic processes in three dimensions with lattice light-sheet microscopy. Chromosome Res 2021; 29:37-50. [PMID: 33694045 PMCID: PMC8058003 DOI: 10.1007/s10577-021-09656-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
There are few technologies that can capture mitotic processes occurring in three-dimensional space with the desired spatiotemporal resolution. Due to such technical limitations, our understanding of mitosis, which has been studied since the early 1880s, is still incomplete with regard to mitotic processes and their regulatory mechanisms at a molecular level. A recently developed high-resolution type of light-sheet microscopy, lattice light-sheet microscopy (LLSM), has achieved unprecedented spatiotemporal resolution scans of intracellular spaces at the whole-cell level. This technology enables experiments that were not possible before (e.g., tracking of growth of every spindle microtubule end and discrimination of individual chromosomes in living cells), thus providing a new avenue for the analysis of mitotic processes. Herein, principles of LLSM technology are introduced, as well as experimental techniques that became possible with LLSM. In addition, issues remaining to be solved for use of this technology in mitosis research, big image data problems, are presented to help guide mitosis research into a new era.
Collapse
Affiliation(s)
- Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
| |
Collapse
|
25
|
Iserman C, Roden CA, Boerneke MA, Sealfon RSG, McLaughlin GA, Jungreis I, Fritch EJ, Hou YJ, Ekena J, Weidmann CA, Theesfeld CL, Kellis M, Troyanskaya OG, Baric RS, Sheahan TP, Weeks KM, Gladfelter AS. Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid. Mol Cell 2020; 80:1078-1091.e6. [PMID: 33290746 PMCID: PMC7691212 DOI: 10.1016/j.molcel.2020.11.041] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/28/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
We report that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with viral RNA. N-protein condenses with specific RNA genomic elements under physiological buffer conditions and condensation is enhanced at human body temperatures (33°C and 37°C) and reduced at room temperature (22°C). RNA sequence and structure in specific genomic regions regulate N-protein condensation while other genomic regions promote condensate dissolution, potentially preventing aggregation of the large genome. At low concentrations, N-protein preferentially crosslinks to specific regions characterized by single-stranded RNA flanked by structured elements and these features specify the location, number, and strength of N-protein binding sites (valency). Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is RNA sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules, and therefore presents a screenable process for identifying antiviral compounds effective against SARS-CoV-2.
Collapse
Affiliation(s)
- Christiane Iserman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christine A Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark A Boerneke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Grace A McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ethan J Fritch
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joanne Ekena
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
26
|
Keyes J, Ganesan A, Molinar-Inglis O, Hamidzadeh A, Zhang J, Ling M, Trejo J, Levchenko A, Zhang J. Signaling diversity enabled by Rap1-regulated plasma membrane ERK with distinct temporal dynamics. eLife 2020; 9:57410. [PMID: 32452765 PMCID: PMC7289600 DOI: 10.7554/elife.57410] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022] Open
Abstract
A variety of different signals induce specific responses through a common, extracellular-signal regulated kinase (ERK)-dependent cascade. It has been suggested that signaling specificity can be achieved through precise temporal regulation of ERK activity. Given the wide distrubtion of ERK susbtrates across different subcellular compartments, it is important to understand how ERK activity is temporally regulated at specific subcellular locations. To address this question, we have expanded the toolbox of Förster Resonance Energy Transfer (FRET)-based ERK biosensors by creating a series of improved biosensors targeted to various subcellular regions via sequence specific motifs to measure spatiotemporal changes in ERK activity. Using these sensors, we showed that EGF induces sustained ERK activity near the plasma membrane in sharp contrast to the transient activity observed in the cytoplasm and nucleus. Furthermore, EGF-induced plasma membrane ERK activity involves Rap1, a noncanonical activator, and controls cell morphology and EGF-induced membrane protrusion dynamics. Our work strongly supports that spatial and temporal regulation of ERK activity is integrated to control signaling specificity from a single extracellular signal to multiple cellular processes.
Collapse
Affiliation(s)
- Jeremiah Keyes
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Ambhighainath Ganesan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Olivia Molinar-Inglis
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Archer Hamidzadeh
- Department of Biomedical Engineering and Yale Systems Biology Institute, Yale University, New Haven, United States
| | - Jinfan Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Megan Ling
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, United States
| | - JoAnn Trejo
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Andre Levchenko
- Department of Biomedical Engineering and Yale Systems Biology Institute, Yale University, New Haven, United States
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, United States.,Department of Bioengineering, University of California San Diego, La Jolla, United States
| |
Collapse
|
27
|
Wen L, Fan Z, Mikulski Z, Ley K. Imaging of the immune system - towards a subcellular and molecular understanding. J Cell Sci 2020; 133:133/5/jcs234922. [PMID: 32139598 DOI: 10.1242/jcs.234922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immune responses involve many types of leukocytes that traffic to the site of injury, recognize the insult and respond appropriately. Imaging of the immune system involves a set of methods and analytical tools that are used to visualize immune responses at the cellular and molecular level as they occur in real time. We will review recent and emerging technological advances in optical imaging, and their application to understanding the molecular and cellular responses of neutrophils, macrophages and lymphocytes. Optical live-cell imaging provides deep mechanistic insights at the molecular, cellular, tissue and organism levels. Live-cell imaging can capture quantitative information in real time at subcellular resolution with minimal phototoxicity and repeatedly in the same living cells or in accessible tissues of the living organism. Advanced FRET probes allow tracking signaling events in live cells. Light-sheet microscopy allows for deeper tissue penetration in optically clear samples, enriching our understanding of the higher-level organization of the immune response. Super-resolution microscopy offers insights into compartmentalized signaling at a resolution beyond the diffraction limit, approaching single-molecule resolution. This Review provides a current perspective on live-cell imaging in vitro and in vivo with a focus on the assessment of the immune system.
Collapse
Affiliation(s)
- Lai Wen
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Zhichao Fan
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Zbigniew Mikulski
- Microscopy Core Facility, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Klaus Ley
- Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA .,Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|
28
|
Integration of Rap1 and Calcium Signaling. Int J Mol Sci 2020; 21:ijms21051616. [PMID: 32120817 PMCID: PMC7084553 DOI: 10.3390/ijms21051616] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
Ca2+ is a universal intracellular signal. The modulation of cytoplasmic Ca2+ concentration regulates a plethora of cellular processes, such as: synaptic plasticity, neuronal survival, chemotaxis of immune cells, platelet aggregation, vasodilation, and cardiac excitation–contraction coupling. Rap1 GTPases are ubiquitously expressed binary switches that alternate between active and inactive states and are regulated by diverse families of guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Active Rap1 couples extracellular stimulation with intracellular signaling through secondary messengers—cyclic adenosine monophosphate (cAMP), Ca2+, and diacylglycerol (DAG). Much evidence indicates that Rap1 signaling intersects with Ca2+ signaling pathways to control the important cellular functions of platelet activation or neuronal plasticity. Rap1 acts as an effector of Ca2+ signaling when activated by mechanisms involving Ca2+ and DAG-activated (CalDAG-) GEFs. Conversely, activated by other GEFs, such as cAMP-dependent GEF Epac, Rap1 controls cytoplasmic Ca2+ levels. It does so by regulating the activity of Ca2+ signaling proteins such as sarcoendoplasmic reticulum Ca2+-ATPase (SERCA). In this review, we focus on the physiological significance of the links between Rap1 and Ca2+ signaling and emphasize the molecular interactions that may offer new targets for the therapy of Alzheimer’s disease, hypertension, and atherosclerosis, among other diseases.
Collapse
|