1
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Aboy-Pardal MC, Jimenez-Carretero D, Terrés-Domínguez S, Pavón DM, Sotodosos-Alonso L, Jiménez-Jiménez V, Sánchez-Cabo F, Del Pozo MA. A deep learning-based tool for the automated detection and analysis of caveolae in transmission electron microscopy images. Comput Struct Biotechnol J 2022; 21:224-237. [PMID: 36544477 PMCID: PMC9755247 DOI: 10.1016/j.csbj.2022.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Caveolae are nanoscopic and mechanosensitive invaginations of the plasma membrane, essential for adipocyte biology. Transmission electron microscopy (TEM) offers the highest resolution for caveolae visualization, but provides complicated images that are difficult to classify or segment using traditional automated algorithms such as threshold-based methods. As a result, the time-consuming tasks of localization and quantification of caveolae are currently performed manually. We used the Keras library in R to train a convolutional neural network with a total of 36,000 TEM image crops obtained from adipocytes previously annotated manually by an expert. The resulting model can differentiate caveolae from non-caveolae regions with a 97.44% accuracy. The predictions of this model are further processed to obtain caveolae central coordinate detection and cytoplasm boundary delimitation. The model correctly finds negligible caveolae predictions in images from caveolae depleted Cav1-/- adipocytes. In large reconstructions of adipocyte sections, model and human performances are comparable. We thus provide a new tool for accurate caveolae automated analysis that could speed up and assist in the characterization of the cellular mechanical response.
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Affiliation(s)
- María C.M. Aboy-Pardal
- Mechanoadaptation and Caveolae Biology lab, Cell and Developmental
Biology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029
Madrid, Spain
| | - Daniel Jimenez-Carretero
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares
(CNIC), 28029 Madrid, Spain
| | - Sara Terrés-Domínguez
- Mechanoadaptation and Caveolae Biology lab, Cell and Developmental
Biology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029
Madrid, Spain
| | - Dácil M. Pavón
- Mechanoadaptation and Caveolae Biology lab, Cell and Developmental
Biology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029
Madrid, Spain
| | - Laura Sotodosos-Alonso
- Mechanoadaptation and Caveolae Biology lab, Cell and Developmental
Biology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029
Madrid, Spain
| | - Víctor Jiménez-Jiménez
- Mechanoadaptation and Caveolae Biology lab, Cell and Developmental
Biology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029
Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares
(CNIC), 28029 Madrid, Spain
| | - Miguel A. Del Pozo
- Mechanoadaptation and Caveolae Biology lab, Cell and Developmental
Biology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029
Madrid, Spain
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2
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
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3
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Correlated STORM-homoFRET imaging reveals highly heterogeneous membrane receptor structures. J Biol Chem 2022; 298:102448. [PMID: 36063991 PMCID: PMC9539790 DOI: 10.1016/j.jbc.2022.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Mapping the self-organization and spatial distribution of membrane proteins is key to understanding their function. Developing methods that can provide insight into correlations between membrane protein co-localization and interactions is challenging. We report here on a correlated stochastic optical reconstruction microscopy (STORM)/homoFRET imaging approach for resolving the nanoscale distribution and oligomeric state of membrane proteins. Using live cell homoFRET imaging of carcinoembryonic antigen-related cellular adhesion molecule (CEACAM1), a cell-surface receptor known to exist in a complex equilibrium between monomer and dimer/oligomer states, we revealed highly heterogeneous diffraction-limited structures on the surface of HeLa cells. Furthermore, correlated super-resolved STORM imaging showed that these structures comprised a complex mixture and spatial distribution of self-associated CEACAM1 molecules. In conclusion, this correlated approach provides a compelling strategy for addressing challenging questions about the interplay between membrane protein concentration, distribution, interaction, clustering, and function.
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4
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Nishimura T, Suetsugu S. Super-resolution analysis of PACSIN2 and EHD2 at caveolae. PLoS One 2022; 17:e0271003. [PMID: 35834519 PMCID: PMC9282494 DOI: 10.1371/journal.pone.0271003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
Caveolae are plasma membrane invaginations that play important roles in both endocytosis and membrane tension buffering. Typical caveolae have invaginated structures with a high-density caveolin assembly. Membrane sculpting proteins, including PACSIN2 and EHD2, are involved in caveolar biogenesis. PACSIN2 is an F-BAR domain-containing protein with a membrane sculpting ability that is essential for caveolar shaping. EHD2 is also localized at caveolae and involved in their stability. However, the spatial relationship between PACSIN2, EHD2, and caveolin has not yet been investigated. We observed the single-molecule localizations of PACSIN2 and EHD2 relative to caveolin-1 in three-dimensional space. The single-molecule localizations were grouped by their proximity localizations into the geometric structures of blobs. In caveolin-1 blobs, PACSIN2, EHD2, and caveolin-1 had overlapped spatial localizations. Interestingly, the mean centroid of the PACSIN2 F-BAR domain at the caveolin-1 blobs was closer to the plasma membrane than those of EHD2 and caveolin-1, suggesting that PACSIN2 is involved in connecting caveolae to the plasma membrane. Most of the blobs with volumes typical of caveolae had PACSIN2 and EHD2, in contrast to those with smaller volumes. Therefore, PACSIN2 and EHD2 are apparently localized at typically sized caveolae.
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Affiliation(s)
- Tamako Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shiro Suetsugu
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Data Science Center, Nara Institute of Science and Technology, Ikoma, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Japan
- * E-mail:
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5
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Xing H, Chin SM, Udumula VR, Krishnaiah M, Rodrigues de Almeida N, Huck-Iriart C, Picco AS, Lee SR, Zaldivar G, Jackson KA, Tagliazucchi M, Stupp SI, Conda-Sheridan M. Control of Peptide Amphiphile Supramolecular Nanostructures by Isosteric Replacements. Biomacromolecules 2021; 22:3274-3283. [PMID: 34291897 DOI: 10.1021/acs.biomac.1c00379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Supramolecular nanostructures with tunable properties can have applications in medicine, pharmacy, and biotechnology. In this work, we show that the self-assembly behavior of peptide amphiphiles (PAs) can be effectively tuned by replacing the carboxylic acids exposed to the aqueous media with isosteres, functionalities that share key physical or chemical properties with another chemical group. Transmission electron microscopy, atomic force microscopy, and small-angle X-ray scattering studies indicated that the nanostructure's morphologies are responsive to the ionization states of the side chains, which are related to their pKa values. Circular dichroism studies revealed the effect of the isosteres on the internal arrangement of the nanostructures. The interactions between diverse surfaces and the nanostructures and the effect of salt concentration and temperature were assessed to further understand the properties of these self-assembled systems. These results indicate that isosteric replacements allow the pH control of supramolecular morphology by manipulating the pKa of the charged groups located on the nanostructure's surface. Theoretical studies were performed to understand the morphological transitions that the nanostructures underwent in response to pH changes, suggesting that the transitions result from alterations in the Coulomb forces between PA molecules. This work provides a strategy for designing biomaterials that can maintain or change behaviors based on the pH differences found within cells and tissues.
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Affiliation(s)
- Huihua Xing
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68105, United States
| | - Stacey M Chin
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Venkata Reddy Udumula
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68105, United States
| | - Maddeboina Krishnaiah
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68105, United States
| | | | - Cristián Huck-Iriart
- Laboratorio de Cristalografía Aplicada, Escuela de Ciencia y Tecnología, Universidad Nacional de General San Martín, B1650 San Martín, Buenos Aires, Argentina
| | - Agustín S Picco
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA) - Universidad Nacional de La Plata (UNLP) - CONICET, 1900, La Plata, Argentina
| | - Sieun Ruth Lee
- Department of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gervasio Zaldivar
- INQUIMAE-CONICET and DQIAQF, Universidad de Buenos Aires, Facultad de Ciencias, Ciudad Universitaria, C1428 Ciudad de Buenos Aires, Argentina
| | - Kelsey A Jackson
- College of Arts and Sciences, Creighton University, Omaha, Nebraska 68178, United States
| | - Mario Tagliazucchi
- INQUIMAE-CONICET and DQIAQF, Universidad de Buenos Aires, Facultad de Ciencias, Ciudad Universitaria, C1428 Ciudad de Buenos Aires, Argentina
| | - Samuel I Stupp
- Department of Materials Science & Engineering, Chemistry, Biomedical Engineering, Medicine, and Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Martin Conda-Sheridan
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68105, United States
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6
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Sullivan C, Soos BL, Millard PJ, Kim CH, King BL. Modeling Virus-Induced Inflammation in Zebrafish: A Balance Between Infection Control and Excessive Inflammation. Front Immunol 2021; 12:636623. [PMID: 34025644 PMCID: PMC8138431 DOI: 10.3389/fimmu.2021.636623] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
The inflammatory response to viral infection in humans is a dynamic process with complex cell interactions that are governed by the immune system and influenced by both host and viral factors. Due to this complexity, the relative contributions of the virus and host factors are best studied in vivo using animal models. In this review, we describe how the zebrafish (Danio rerio) has been used as a powerful model to study host-virus interactions and inflammation by combining robust forward and reverse genetic tools with in vivo imaging of transparent embryos and larvae. The innate immune system has an essential role in the initial inflammatory response to viral infection. Focused studies of the innate immune response to viral infection are possible using the zebrafish model as there is a 4-6 week timeframe during development where they have a functional innate immune system dominated by neutrophils and macrophages. During this timeframe, zebrafish lack a functional adaptive immune system, so it is possible to study the innate immune response in isolation. Sequencing of the zebrafish genome has revealed significant genetic conservation with the human genome, and multiple studies have revealed both functional conservation of genes, including those critical to host cell infection and host cell inflammatory response. In addition to studying several fish viruses, zebrafish infection models have been developed for several human viruses, including influenza A, noroviruses, chikungunya, Zika, dengue, herpes simplex virus type 1, Sindbis, and hepatitis C virus. The development of these diverse viral infection models, coupled with the inherent strengths of the zebrafish model, particularly as it relates to our understanding of macrophage and neutrophil biology, offers opportunities for far more intensive studies aimed at understanding conserved host responses to viral infection. In this context, we review aspects relating to the evolution of innate immunity, including the evolution of viral pattern recognition receptors, interferons and interferon receptors, and non-coding RNAs.
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Affiliation(s)
- Con Sullivan
- College of Arts and Sciences, University of Maine at Augusta, Bangor, ME, United States
| | - Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States
| | - Paul J Millard
- Department of Environmental and Sustainable Engineering, University at Albany, Albany, NY, United States
| | - Carol H Kim
- Department of Biomedical Sciences, University at Albany, Albany, NY, United States.,Department of Biological Sciences, University at Albany, Albany, NY, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
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7
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Zanin N, Viaris de Lesegno C, Lamaze C, Blouin CM. Interferon Receptor Trafficking and Signaling: Journey to the Cross Roads. Front Immunol 2021; 11:615603. [PMID: 33552080 PMCID: PMC7855707 DOI: 10.3389/fimmu.2020.615603] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
Like most plasma membrane proteins, type I interferon (IFN) receptor (IFNAR) traffics from the outer surface to the inner compartments of the cell. Long considered as a passive means to simply control subunits availability at the plasma membrane, an array of new evidence establishes IFNAR endocytosis as an active contributor to the regulation of signal transduction triggered by IFN binding to IFNAR. During its complex journey initiated at the plasma membrane, the internalized IFNAR complex, i.e. IFNAR1 and IFNAR2 subunits, will experience post-translational modifications and recruit specific effectors. These finely tuned interactions will determine not only IFNAR subunits destiny (lysosomal degradation vs. plasma membrane recycling) but also the control of IFN-induced signal transduction. Finally, the IFNAR system perfectly illustrates the paradigm of the crosstalk between membrane trafficking and intracellular signaling. Investigating the complexity of IFN receptor intracellular routes is therefore necessary to reveal new insight into the role of IFNAR membrane dynamics in type I IFNs signaling selectivity and biological activity.
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Affiliation(s)
- Natacha Zanin
- NDORMS, The Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Christine Viaris de Lesegno
- Institut Curie-Centre de Recherche, PSL Research University, Membrane Dynamics and Mechanics of Intracellular Signalling Laboratory, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
| | - Christophe Lamaze
- Institut Curie-Centre de Recherche, PSL Research University, Membrane Dynamics and Mechanics of Intracellular Signalling Laboratory, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
| | - Cedric M Blouin
- Institut Curie-Centre de Recherche, PSL Research University, Membrane Dynamics and Mechanics of Intracellular Signalling Laboratory, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3666, Paris, France
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8
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Dudãu M, Codrici E, Tanase C, Gherghiceanu M, Enciu AM, Hinescu ME. Caveolae as Potential Hijackable Gates in Cell Communication. Front Cell Dev Biol 2020; 8:581732. [PMID: 33195223 PMCID: PMC7652756 DOI: 10.3389/fcell.2020.581732] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Caveolae are membrane microdomains described in many cell types involved in endocytocis, transcytosis, cell signaling, mechanotransduction, and aging. They are found at the interface with the extracellular environment and are structured by caveolin and cavin proteins. Caveolae and caveolins mediate transduction of chemical messages via signaling pathways, as well as non-chemical messages, such as stretching or shear stress. Various pathogens or signals can hijack these gates, leading to infectious, oncogenic and even caveolin-related diseases named caveolinopathies. By contrast, preclinical and clinical research have fallen behind in their attempts to hijack caveolae and caveolins for therapeutic purposes. Caveolae involvement in human disease is not yet fully explored or understood and, of all their scaffold proteins, only caveolin-1 is being considered in clinical trials as a possible biomarker of disease. This review briefly summarizes current knowledge about caveolae cell signaling and raises the hypothesis whether these microdomains could serve as hijackable “gatekeepers” or “gateways” in cell communication. Furthermore, because cell signaling is one of the most dynamic domains in translating data from basic to clinical research, we pay special attention to translation of caveolae, caveolin, and cavin research into clinical practice.
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Affiliation(s)
- Maria Dudãu
- Biochemistry-Proteomics Laboratory, Victor Babes National Institute of Pathology, Bucharest, Romania.,Cell Biology and Histology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Elena Codrici
- Biochemistry-Proteomics Laboratory, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Cristiana Tanase
- Biochemistry-Proteomics Laboratory, Victor Babes National Institute of Pathology, Bucharest, Romania.,Clinical Biochemistry Department, Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Mihaela Gherghiceanu
- Biochemistry-Proteomics Laboratory, Victor Babes National Institute of Pathology, Bucharest, Romania.,Cell Biology and Histology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Ana-Maria Enciu
- Biochemistry-Proteomics Laboratory, Victor Babes National Institute of Pathology, Bucharest, Romania.,Cell Biology and Histology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Mihail E Hinescu
- Biochemistry-Proteomics Laboratory, Victor Babes National Institute of Pathology, Bucharest, Romania.,Cell Biology and Histology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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9
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Tyrpak DR, Wang Y, Avila H, Guo H, Fu R, Truong AT, Park M, Okamoto CT, Hamm-Alvarez SF, MacKay JA. Caveolin elastin-like polypeptide fusions mediate temperature-dependent assembly of caveolar microdomains. ACS Biomater Sci Eng 2020; 6:198-204. [PMID: 32542186 DOI: 10.1021/acsbiomaterials.9b01331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Caveolae are membrane organelles formed by submicron invaginations in the plasma membrane, and are involved in mechanosensing, cell signaling, and endocytosis. Although implicated broadly in physiology and pathophysiology, better tools are required to elucidate the precise role of caveolar processes through selective activation and inactivation of their trafficking. Our group recently reported that thermally-responsive elastin-like polypeptides (ELPs) can trigger formation of 'genetically engineered protein microdomains (GEPMs)' functionalized with either Clathrin-light chain or the epidermal growth factor receptor. This manuscript is the first report of this strategy to modulate caveolin-1 (CAV1). By attaching different ELP sequences to CAV1, mild heating can be used to self-assemble CAV1-ELP microdomains inside of cells. The temperature of self-assembly can be controlled by tuning the ELP sequence. The formation of CAV1-ELP microdomains internalizes Cholera Toxin Subunit B, a commonly used marker of caveolae mediated endocytosis. CAV1-ELPs also colocalize with Cavin 1, an essential component of functional caveolae biogenesis. With the emerging significance of caveolae in health and disease and the lack of specific probes to rapidly and reversibly affect caveolar function, CAV1-ELP microdomains are a new tool to rapidly probe caveolae associated processes in endocytosis, cell signaling, and mechanosensing.
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Affiliation(s)
- David R Tyrpak
- University of Southern California Viterbi School of Engineering, Biomedical Engineering. 1042 Downey Way, Los Angeles, CA, USA 90089
| | - Yue Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089
| | - Hugo Avila
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089
| | - Hao Guo
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089
| | - Runzhong Fu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089
| | - Anh T Truong
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089
| | - Mincheol Park
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089
| | - Curtis T Okamoto
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089
| | - Sarah F Hamm-Alvarez
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089.,Keck School of Medicine of the University of Southern California, Department of Ophthalmology, Roski Eye Institute. 1450 San Pablo St, Los Angeles, CA, USA 90033
| | - John Andrew MacKay
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy of the University of Southern California, 1985 Zonal Ave, Los Angeles, CA, USA 90089.,Keck School of Medicine of the University of Southern California, Department of Ophthalmology, Roski Eye Institute. 1450 San Pablo St, Los Angeles, CA, USA 90033.,University of Southern California Viterbi School of Engineering, Biomedical Engineering. 1042 Downey Way, Los Angeles, CA, USA 90089
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10
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Khater IM, Aroca-Ouellette ST, Meng F, Nabi IR, Hamarneh G. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. PLoS One 2019; 14:e0211659. [PMID: 31449531 PMCID: PMC6709882 DOI: 10.1371/journal.pone.0211659] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
Caveolae are plasma membrane invaginations whose formation requires caveolin-1 (Cav1), the adaptor protein polymerase I, and the transcript release factor (PTRF or CAVIN1). Caveolae have an important role in cell functioning, signaling, and disease. In the absence of CAVIN1/PTRF, Cav1 forms non-caveolar membrane domains called scaffolds. In this work, we train machine learning models to automatically distinguish between caveolae and scaffolds from single molecule localization microscopy (SMLM) data. We apply machine learning algorithms to discriminate biological structures from SMLM data. Our work is the first that is leveraging machine learning approaches (including deep learning models) to automatically identifying biological structures from SMLM data. In particular, we develop and compare three binary classification methods to identify whether or not a given 3D cluster of Cav1 proteins is a caveolae. The first uses a random forest classifier applied to 28 hand-crafted/designed features, the second uses a convolutional neural net (CNN) applied to a projection of the point clouds onto three planes, and the third uses a PointNet model, a recent development that can directly take point clouds as its input. We validate our methods on a dataset of super-resolution microscopy images of PC3 prostate cancer cells labeled for Cav1. Specifically, we have images from two cell populations: 10 PC3 and 10 CAVIN1/PTRF-transfected PC3 cells (PC3-PTRF cells) that form caveolae. We obtained a balanced set of 1714 different cellular structures. Our results show that both the random forest on hand-designed features and the deep learning approach achieve high accuracy in distinguishing the intrinsic features of the caveolae and non-caveolae biological structures. More specifically, both random forest and deep CNN classifiers achieve classification accuracy reaching 94% on our test set, while the PointNet model only reached 83% accuracy. We also discuss the pros and cons of the different approaches.
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Affiliation(s)
- Ismail M. Khater
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- * E-mail:
| | - Stephane T. Aroca-Ouellette
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Fanrui Meng
- Department of Cellular and Physiological Sciences, LSI Imaging, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, LSI Imaging, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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11
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Wijesooriya CS, Nyamekye CKA, Smith EA. Optical Imaging of the Nanoscale Structure and Dynamics of Biological Membranes. Anal Chem 2018; 91:425-440. [DOI: 10.1021/acs.analchem.8b04755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Charles K. A. Nyamekye
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Emily A. Smith
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
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12
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Udayantha HMV, Bathige SDNK, Priyathilaka TT, Lee S, Kim MJ, Lee J. Identification and characterization of molluscan caveolin-1 ortholog from Haliotis discus discus: Possible involvement in embryogenesis and host defense mechanism against pathogenic stress. Gene Expr Patterns 2017; 27:85-92. [PMID: 29128397 DOI: 10.1016/j.gep.2017.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 06/13/2017] [Accepted: 11/06/2017] [Indexed: 02/05/2023]
Abstract
Caveolins are principal membrane proteins of caveolae that play a central role in signal transduction, substrate transport, and membrane trafficking in various cell types. Numerous studies have reported the crucial role of caveolin-1 (CAV1) in response to invading microbes; yet, very little is known about molluscan CAV1. In this study, we identified and characterized CAV1 ortholog from the disk abalone, Haliotis discus discus (HdCAV1). The cDNA sequence of HdCAV1 is 826 bp long and encodes a 127-amino acid polypeptide. Characteristic caveolin superfamily domain (Glu3 - Lys126) and two possible transmembrane domains (Cys48 - Tyr67 and Ile103 - Phe120) were identified in the HdCAV1 protein. Homology analysis revealed that HdCAV1 shared higher identity (>47%) with molluscans, but lower identity with other species. Phylogenetic tree constructed by the neighbor-joining (NJ) method revealed a distinct evolutionary pathway for molluscans. Transcriptional analysis by SYBR Green qPCR showed the highest expression of HdCAV1 mRNA in late veliger stage, as compared to that in other embryonic developmental stages of disk abalone. In adult animals, gill tissue showed highest HdCAV1 transcript levels under normal physiological condition. Stimulations with two bacteria (Vibrio parahaemolyticus and Listeria monocytogenes), viral hemorrhagic septicemia virus, and two pathogen-associated molecular patterns (LPS and poly I:C) significantly modulated the expression of HdCAV1 transcripts. Collectively, these data suggest that CAV1 plays an important role in embryogenesis and host immune defense in disk abalone.
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Affiliation(s)
- H M V Udayantha
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - S D N K Bathige
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Sri Lanka Institute of Nanotechnology (SLINTEC), Nanotechnology and Science Park, Mahenwatta, Pitipana, Homagama, Sri Lanka
| | - Thanthrige Thiunuwan Priyathilaka
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea
| | - Sukkyoung Lee
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea
| | - Myoung-Jin Kim
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea.
| | - Jehee Lee
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea.
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13
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Stone MB, Shelby SA, Veatch SL. Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane. Chem Rev 2017; 117:7457-7477. [PMID: 28211677 PMCID: PMC5471115 DOI: 10.1021/acs.chemrev.6b00716] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments. These microscopy techniques have been used to examine the organization and dynamics of plasma membrane components, providing insight into the fundamental interactions that determine membrane functions. Here, we broadly introduce the structure and organization of the mammalian plasma membrane and review recent applications of super-resolution microscopy to the study of membranes. We then highlight some inherent challenges faced when using super-resolution microscopy to study membranes, and we discuss recent technical advancements that promise further improvements to super-resolution microscopy and its application to the plasma membrane.
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Affiliation(s)
- Matthew B Stone
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah A Shelby
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah L Veatch
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
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14
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Ludwig A, Nguyen TH, Leong D, Ravi LI, Tan BH, Sandin S, Sugrue RJ. Caveolae provide a specialized membrane environment for respiratory syncytial virus assembly. J Cell Sci 2017; 130:1037-1050. [PMID: 28154158 PMCID: PMC5358342 DOI: 10.1242/jcs.198853] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/26/2017] [Indexed: 12/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is an enveloped virus that assembles into filamentous virus particles on the surface of infected cells. Morphogenesis of RSV is dependent upon cholesterol-rich (lipid raft) membrane microdomains, but the specific role of individual raft molecules in RSV assembly is not well defined. Here, we show that RSV morphogenesis occurs within caveolar membranes and that both caveolin-1 and cavin-1 (also known as PTRF), the two major structural and functional components of caveolae, are actively recruited to and incorporated into the RSV envelope. The recruitment of caveolae occurred just prior to the initiation of RSV filament assembly, and was dependent upon an intact actin network as well as a direct physical interaction between caveolin-1 and the viral G protein. Moreover, cavin-1 protein levels were significantly increased in RSV-infected cells, leading to a virus-induced change in the stoichiometry and biophysical properties of the caveolar coat complex. Our data indicate that RSV exploits caveolae for its assembly, and we propose that the incorporation of caveolae into the virus contributes to defining the biological properties of the RSV envelope.
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Affiliation(s)
- Alexander Ludwig
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Tra Huong Nguyen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Daniel Leong
- Detection and Diagnostics Laboratory, DSO National Laboratories, 27 Medical Drive, Singapore 117510
| | - Laxmi Iyer Ravi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Boon Huan Tan
- Detection and Diagnostics Laboratory, DSO National Laboratories, 27 Medical Drive, Singapore 117510
| | - Sara Sandin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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15
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Modelling viral infections using zebrafish: Innate immune response and antiviral research. Antiviral Res 2017; 139:59-68. [DOI: 10.1016/j.antiviral.2016.12.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022]
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16
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Yang L, Scarlata S. Super-resolution Visualization of Caveola Deformation in Response to Osmotic Stress. J Biol Chem 2017; 292:3779-3788. [PMID: 28096469 DOI: 10.1074/jbc.m116.768499] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/16/2017] [Indexed: 11/06/2022] Open
Abstract
Caveolae are protein-dense plasma membrane domains structurally composed of caveolin-1 or -3 along with other proteins. Our previous studies have shown that caveolae enhance calcium signals generated through the Gαq/phospholipase Cβ signaling pathway and that subjecting cells to hypo-osmotic stress reverses this enhancement. In this study, we have used super-resolution fluorescence microscopy supplemented by fluorescence correlation studies to determine the structural factors that underlie this behavior. We find similar and significant population of Gαq and one of its receptors, bradykinin type 2 receptor (B2R), as well as a significant population of Gαi and its coupled β2-adrenergic receptor (βAR), are localized to caveola domains. Although mild osmotic stress deforms caveolae and alters interactions between the caveolae and these proteins, the general structure and the localization of caveola components remain largely unchanged. This deformation eliminates the ability of caveolae to stabilize calcium signals mediated through Gαq-B2R, but does not affect cAMP signals mediated through Gαi and βAR. Structurally, we find that mild osmotic stress corresponding roughly to a pressure of 3.82 newtons/m2 increases the domain diameter by ∼30% and increases the fluorescence intensity in the center of the domain mouth suggesting a flattening of the invagination. Approximate calculations show that caveolae in muscle tissue have the strength to handle the stress of muscle movement.
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Affiliation(s)
- Lu Yang
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Suzanne Scarlata
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
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17
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Gabor KA, Fessler MB. Roles of the Mevalonate Pathway and Cholesterol Trafficking in Pulmonary Host Defense. Curr Mol Pharmacol 2017; 10:27-45. [PMID: 26758950 PMCID: PMC6026538 DOI: 10.2174/1874467209666160112123603] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 08/01/2015] [Accepted: 12/23/2015] [Indexed: 01/17/2023]
Abstract
The mevalonic acid synthesis pathway, cholesterol, and lipoproteins play fundamental roles in lung physiology and the innate immune response. Recent literature investigating roles for cholesterol synthesis and trafficking in host defense against respiratory infection was critically reviewed. The innate immune response and the cholesterol biosynthesis/trafficking network regulate one another, with important implications for pathogen invasion and host defense in the lung. The activation of pathogen recognition receptors and downstream cellular host defense functions are critically sensitive to cellular cholesterol. Conversely, microorganisms can co-opt the sterol/lipoprotein network in order to facilitate replication and evade immunity. Emerging literature suggests the potential for harnessing these insights towards therapeutic development. Given that >50% of adults in the U.S. have serum cholesterol abnormalities and pneumonia remains a leading cause of death, the potential impact of cholesterol on pulmonary host defense is of tremendous public health significance and warrants further mechanistic and translational investigation.
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Affiliation(s)
| | - Michael B Fessler
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, P.O. Box 12233, Maildrop D2-01, Research Triangle Park, NC 27709, United States
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18
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Green TJ, Speck P, Geng L, Raftos D, Beard MR, Helbig KJ. Oyster viperin retains direct antiviral activity and its transcription occurs via a signalling pathway involving a heat-stable haemolymph protein. J Gen Virol 2016; 96:3587-3597. [PMID: 26407968 DOI: 10.1099/jgv.0.000300] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Little is known about the response of non-model invertebrates, such as oysters, to virus infection. The vertebrate innate immune system detects virus-derived nucleic acids to trigger the type I IFN pathway, leading to the transcription of hundreds of IFN-stimulated genes (ISGs) that exert antiviral functions. Invertebrates were thought to lack the IFN pathway based on the absence of IFN or ISGs encoded in model invertebrate genomes. However, the oyster genome encodes many ISGs, including the well-described antiviral protein viperin. In this study, we characterized oyster viperin and showed that it localizes to caveolin-1 and inhibits dengue virus replication in a heterologous model. In a second set of experiments, we have provided evidence that the haemolymph from poly(I : C)-injected oysters contains a heat-stable, protease-susceptible factor that induces haemocyte transcription of viperin mRNA in conjunction with upregulation of IFN regulatory factor. Collectively, these results support the concept that oysters have antiviral systems that are homologous to the vertebrate IFN pathway.
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Affiliation(s)
- Timothy J Green
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.,Department of Biological Sciences and Sydney Institute of Marine Science, Macquarie University, NSW 2109, Australia
| | - Peter Speck
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Lu Geng
- School of Biological Sciences, University of Adelaide, SA 5001, Australia
| | - David Raftos
- Department of Biological Sciences and Sydney Institute of Marine Science, Macquarie University, NSW 2109, Australia
| | - Michael R Beard
- School of Biological Sciences, University of Adelaide, SA 5001, Australia
| | - Karla J Helbig
- School of Biological Sciences, University of Adelaide, SA 5001, Australia
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19
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Cao J, Navis A, Cox BD, Dickson AL, Gemberling M, Karra R, Bagnat M, Poss KD. Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration. Development 2015; 143:232-43. [PMID: 26657776 DOI: 10.1242/dev.130534] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/24/2015] [Indexed: 01/07/2023]
Abstract
In contrast to mammals, adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of cardiomyocytes spared from damage. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source, and has received recent attention as a target in cardiac repair strategies. Although it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential, the extent of cellular heterogeneity within epicardial tissue is largely unexplored. Here, we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan-epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan-epicardial and epicardial markers by alternative expression assays. Additionally, we explored the function of the scaffolding protein and main component of caveolae, caveolin 1 (cav1), which was present in each epicardial subset. In BAC transgenic zebrafish, cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover, cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy, but displayed profound defects in injury-induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers, genetic tools, and mechanisms of heart regeneration.
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Affiliation(s)
- Jingli Cao
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Adam Navis
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ben D Cox
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Amy L Dickson
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Matthew Gemberling
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ravi Karra
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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20
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Gabor KA, Charette JR, Pietraszewski MJ, Wingfield DJ, Shim JS, Millard PJ, Kim CH. A DN-mda5 transgenic zebrafish model demonstrates that Mda5 plays an important role in snakehead rhabdovirus resistance. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 51:298-304. [PMID: 25634485 PMCID: PMC4442029 DOI: 10.1016/j.dci.2015.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/17/2015] [Accepted: 01/21/2015] [Indexed: 05/14/2023]
Abstract
Melanoma Differentiation-Associated protein 5 (MDA5) is a member of the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) family, which is a cytosolic pattern recognition receptor that detects viral nucleic acids. Here we show an Mda5-dependent response to rhabdovirus infection in vivo using a dominant-negative mda5 transgenic zebrafish. Dominant-negative mda5 zebrafish embryos displayed an impaired antiviral immune response compared to wild-type counterparts that can be rescued by recombinant full-length Mda5. To our knowledge, we have generated the first dominant-negative mda5 transgenic zebrafish and demonstrated a critical role for Mda5 in the antiviral response to rhabdovirus.
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Affiliation(s)
- K A Gabor
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA; Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - J R Charette
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - M J Pietraszewski
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - D J Wingfield
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - J S Shim
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
| | - P J Millard
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA; Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - C H Kim
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA; Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA.
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21
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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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22
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Nanoscale imaging of caveolin-1 membrane domains in vivo. PLoS One 2015; 10:e0117225. [PMID: 25646724 PMCID: PMC4315472 DOI: 10.1371/journal.pone.0117225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 12/20/2014] [Indexed: 11/26/2022] Open
Abstract
Light microscopy enables noninvasive imaging of fluorescent species in biological specimens, but resolution is generally limited by diffraction to ~200–250 nm. Many biological processes occur on smaller length scales, highlighting the importance of techniques that can image below the diffraction limit and provide valuable single-molecule information. In recent years, imaging techniques have been developed which can achieve resolution below the diffraction limit. Utilizing one such technique, fluorescence photoactivation localization microscopy (FPALM), we demonstrated its ability to construct super-resolution images from single molecules in a living zebrafish embryo, expanding the realm of previous super-resolution imaging to a living vertebrate organism. We imaged caveolin-1 in vivo, in living zebrafish embryos. Our results demonstrate the successful image acquisition of super-resolution images in a living vertebrate organism, opening several opportunities to answer more dynamic biological questions in vivo at the previously inaccessible nanoscale.
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23
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Vacaru AM, Unlu G, Spitzner M, Mione M, Knapik EW, Sadler KC. In vivo cell biology in zebrafish - providing insights into vertebrate development and disease. J Cell Sci 2014; 127:485-95. [PMID: 24481493 DOI: 10.1242/jcs.140194] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Over the past decades, studies using zebrafish have significantly advanced our understanding of the cellular basis for development and human diseases. Zebrafish have rapidly developing transparent embryos that allow comprehensive imaging of embryogenesis combined with powerful genetic approaches. However, forward genetic screens in zebrafish have generated unanticipated findings that are mirrored by human genetic studies: disruption of genes implicated in basic cellular processes, such as protein secretion or cytoskeletal dynamics, causes discrete developmental or disease phenotypes. This is surprising because many processes that were assumed to be fundamental to the function and survival of all cell types appear instead to be regulated by cell-specific mechanisms. Such discoveries are facilitated by experiments in whole animals, where zebrafish provides an ideal model for visualization and manipulation of organelles and cellular processes in a live vertebrate. Here, we review well-characterized mutants and newly developed tools that underscore this notion. We focus on the secretory pathway and microtubule-based trafficking as illustrative examples of how studying cell biology in vivo using zebrafish has broadened our understanding of the role fundamental cellular processes play in embryogenesis and disease.
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Affiliation(s)
- Ana M Vacaru
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
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24
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Gabor KA, Goody MF, Mowel WK, Breitbach ME, Gratacap RL, Witten PE, Kim CH. Influenza A virus infection in zebrafish recapitulates mammalian infection and sensitivity to anti-influenza drug treatment. Dis Model Mech 2014; 7:1227-37. [PMID: 25190709 PMCID: PMC4213727 DOI: 10.1242/dmm.014746] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Seasonal influenza virus infections cause annual epidemics and sporadic pandemics. These present a global health concern, resulting in substantial morbidity, mortality and economic burdens. Prevention and treatment of influenza illness is difficult due to the high mutation rate of the virus, the emergence of new virus strains and increasing antiviral resistance. Animal models of influenza infection are crucial to our gaining a better understanding of the pathogenesis of and host response to influenza infection, and for screening antiviral compounds. However, the current animal models used for influenza research are not amenable to visualization of host-pathogen interactions or high-throughput drug screening. The zebrafish is widely recognized as a valuable model system for infectious disease research and therapeutic drug testing. Here, we describe a zebrafish model for human influenza A virus (IAV) infection and show that zebrafish embryos are susceptible to challenge with both influenza A strains APR8 and X-31 (Aichi). Influenza-infected zebrafish show an increase in viral burden and mortality over time. The expression of innate antiviral genes, the gross pathology and the histopathology in infected zebrafish recapitulate clinical symptoms of influenza infections in humans. This is the first time that zebrafish embryos have been infected with a fluorescent IAV in order to visualize infection in a live vertebrate host, revealing a pattern of vascular endothelial infection. Treatment of infected zebrafish with a known anti-influenza compound, Zanamivir, reduced mortality and the expression of a fluorescent viral gene product, demonstrating the validity of this model to screen for potential antiviral drugs. The zebrafish model system has provided invaluable insights into host-pathogen interactions for a range of infectious diseases. Here, we demonstrate a novel use of this species for IAV research. This model has great potential to advance our understanding of influenza infection and the associated host innate immune response.
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Affiliation(s)
- Kristin A Gabor
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA. Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Michelle F Goody
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Walter K Mowel
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Meghan E Breitbach
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Remi L Gratacap
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - P Eckhard Witten
- Department of Biology, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Carol H Kim
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA. Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA.
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25
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Lin H, Lin D, Xiong XS, Dai XX, Lin T. Downregulation of caveolin-1 in chronic rhinosinusitis with and without nasal polyps. Eur Arch Otorhinolaryngol 2014; 272:613-8. [DOI: 10.1007/s00405-014-3146-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 06/10/2014] [Indexed: 01/21/2023]
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Notelaers K, Rocha S, Paesen R, Swinnen N, Vangindertael J, Meier JC, Rigo JM, Ameloot M, Hofkens J. Membrane distribution of the glycine receptor α3 studied by optical super-resolution microscopy. Histochem Cell Biol 2014; 142:79-90. [PMID: 24553792 DOI: 10.1007/s00418-014-1197-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2014] [Indexed: 11/24/2022]
Abstract
In this study, the effect of glycine receptor (GlyR) α3 alternative RNA splicing on the distribution of receptors in the membrane of human embryonic kidney 293 cells is investigated using optical super-resolution microscopy. Direct stochastic optical reconstruction microscopy is used to image both α3K and α3L splice variants individually and together using single- and dual-color imaging. Pair correlation analysis is used to extract quantitative measures from the resulting images. Autocorrelation analysis of the individually expressed variants reveals clustering of both variants, yet with differing properties. The cluster size is increased for α3L compared to α3K (mean radius 92 ± 4 and 56 ± 3 nm, respectively), yet an even bigger difference is found in the cluster density (9,870 ± 1,433 and 1,747 ± 200 μm(-2), respectively). Furthermore, cross-correlation analysis revealed that upon co-expression, clusters colocalize on the same spatial scales as for individually expressed receptors (mean co-cluster radius 94 ± 6 nm). These results demonstrate that RNA splicing determines GlyR α3 membrane distribution, which has consequences for neuronal GlyR physiology and function.
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Affiliation(s)
- Kristof Notelaers
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, Agoralaan Gebouw C, 3590, Diepenbeek, Belgium
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Huang LL, Xie HY. Progress on the labeling and single-particle tracking technologies of viruses. Analyst 2014; 139:3336-46. [DOI: 10.1039/c4an00038b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review recent advances in virus labeling and the emerging fluorescence imaging technologies used in the imaging and tracking of viruses.
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Affiliation(s)
- Li-Li Huang
- School of Life Science
- Beijing Institute of Technology
- Beijing 100081, China
| | - Hai-Yan Xie
- School of Life Science
- Beijing Institute of Technology
- Beijing 100081, China
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