1
|
Prigent S, Nguyen HN, Leconte L, Valades-Cruz CA, Hajj B, Salamero J, Kervrann C. SPITFIR(e): a supermaneuverable algorithm for fast denoising and deconvolution of 3D fluorescence microscopy images and videos. Sci Rep 2023; 13:1489. [PMID: 36707688 PMCID: PMC9883505 DOI: 10.1038/s41598-022-26178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/12/2022] [Indexed: 01/28/2023] Open
Abstract
Modern fluorescent microscopy imaging is still limited by the optical aberrations and the photon budget available in the specimen. A direct consequence is the necessity to develop flexible and "off-road" algorithms in order to recover structural details and improve spatial resolution, which is critical when restraining the illumination to low levels in order to limit photo-damages. Here, we report SPITFIR(e) a flexible method designed to accurately and quickly restore 2D-3D fluorescence microscopy images and videos (4D images). We designed a generic sparse-promoting regularizer to subtract undesirable out-of-focus background and we developed a primal-dual algorithm for fast optimization. SPITFIR(e) is a "swiss-knife" method for practitioners as it adapts to any microscopy techniques, to various sources of signal degradation (noise, blur), to variable image contents, as well as to low signal-to-noise ratios. Our method outperforms existing state-of-the-art algorithms, and is more flexible than supervised deep-learning methods requiring ground truth datasets. The performance, the flexibility, and the ability to push the spatiotemporal resolution limit of sub-diffracted fluorescence microscopy techniques are demonstrated on experimental datasets acquired with various microscopy techniques from 3D spinning-disk confocal up to lattice light sheet microscopy.
Collapse
Affiliation(s)
- Sylvain Prigent
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Hoai-Nam Nguyen
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Ludovic Leconte
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Cesar Augusto Valades-Cruz
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Bassam Hajj
- grid.465542.40000 0004 1759 735XLaboratoire Physico-Chimie, Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR168, 75005 Paris, France
| | - Jean Salamero
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Charles Kervrann
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| |
Collapse
|
2
|
Prigent S, Valades-Cruz CA, Leconte L, Maury L, Salamero J, Kervrann C. BioImageIT: Open-source framework for integration of image data management with analysis. Nat Methods 2022; 19:1328-1330. [PMID: 36207445 DOI: 10.1038/s41592-022-01642-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sylvain Prigent
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France
| | - Cesar Augusto Valades-Cruz
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France
| | - Ludovic Leconte
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France
| | - Léo Maury
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France
| | - Jean Salamero
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France. .,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France.
| | - Charles Kervrann
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France. .,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France.
| |
Collapse
|
3
|
Valades-Cruz CA, Leconte L, Fouche G, Blanc T, Van Hille N, Fournier K, Laurent T, Gallean B, Deslandes F, Hajj B, Faure E, Argelaguet F, Trubuil A, Isenberg T, Masson JB, Salamero J, Kervrann C. Challenges of intracellular visualization using virtual and augmented reality. Front Bioinform 2022; 2:997082. [PMID: 36304296 PMCID: PMC9580941 DOI: 10.3389/fbinf.2022.997082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Abstract
Microscopy image observation is commonly performed on 2D screens, which limits human capacities to grasp volumetric, complex, and discrete biological dynamics. With the massive production of multidimensional images (3D + time, multi-channels) and derived images (e.g., restored images, segmentation maps, and object tracks), scientists need appropriate visualization and navigation methods to better apprehend the amount of information in their content. New modes of visualization have emerged, including virtual reality (VR)/augmented reality (AR) approaches which should allow more accurate analysis and exploration of large time series of volumetric images, such as those produced by the latest 3D + time fluorescence microscopy. They include integrated algorithms that allow researchers to interactively explore complex spatiotemporal objects at the scale of single cells or multicellular systems, almost in a real time manner. In practice, however, immersion of the user within 3D + time microscopy data represents both a paradigm shift in human-image interaction and an acculturation challenge, for the concerned community. To promote a broader adoption of these approaches by biologists, further dialogue is needed between the bioimaging community and the VR&AR developers.
Collapse
Affiliation(s)
- Cesar Augusto Valades-Cruz
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
| | - Ludovic Leconte
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
| | - Gwendal Fouche
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
- Inria, CNRS, IRISA, University Rennes, Rennes, France
| | - Thomas Blanc
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, Sorbonne Universites, CNRS UMR168, Paris, France
| | | | - Kevin Fournier
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
- Inria, CNRS, IRISA, University Rennes, Rennes, France
| | - Tao Laurent
- LIRMM, Université Montpellier, CNRS, Montpellier, France
| | | | | | - Bassam Hajj
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, Sorbonne Universites, CNRS UMR168, Paris, France
| | - Emmanuel Faure
- LIRMM, Université Montpellier, CNRS, Montpellier, France
| | | | - Alain Trubuil
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Jean-Baptiste Masson
- Decision and Bayesian Computation, Neuroscience and Computational Biology Departments, CNRS UMR 3571, Institut Pasteur, Université Paris Cité, Paris, France
| | - Jean Salamero
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
| | - Charles Kervrann
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
- *Correspondence: Charles Kervrann,
| |
Collapse
|
4
|
Prigent S, Valades-Cruz CA, Leconte L, Salamero J, Kervrann C. STracking: a free and open-source python library for particle tracking and analysis. Bioinformatics 2022; 38:3671-3673. [PMID: 35639941 DOI: 10.1093/bioinformatics/btac365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/05/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Analysis of intra and extra cellular dynamic like vesicles transport involves particle tracking algorithms. The design of a particle tracking pipeline is a routine but tedious task. Therefore, particle dynamics analysis is often performed by combining several pieces of software (filtering, detection, tracking…) requiring many manual operations, and thus leading to poorly reproducible results. Given the new segmentation tools based on deep learning, modularity and interoperability between software have become essential in particle tracking algorithms. A good synergy between a particle detector and a tracker is of paramount importance. In addition, a user-friendly interface to control the quality of estimated trajectories is necessary. To address these issues, we developed STracking, a python library that allows combining algorithms into standardized particle tracking pipelines. AVAILABILITY AND IMPLEMENTATION STracking is available as a python library using "pip install" and the source code is publicly available on GitHub (https://github.com/sylvainprigent/stracking). A graphical interface is available using two napari plugins: napari-stracking and napari-tracks-reader. These napari plugins can be installed via the napari plugins menu or using "pip install". The napari plugin source codes are available on GitHub (https://github.com/sylvainprigent/napari-tracks-reader, https://github.com/sylvainprigent/napari-stracking). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Sylvain Prigent
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, F-35042, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, F-75005, Paris, France
| | - Cesar Augusto Valades-Cruz
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, F-35042, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, F-75005, Paris, France
| | - Ludovic Leconte
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, F-35042, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, F-75005, Paris, France
| | - Jean Salamero
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, F-35042, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, F-75005, Paris, France
| | - Charles Kervrann
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, F-35042, Rennes, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, F-75005, Paris, France
| |
Collapse
|
5
|
Vargas-Hurtado D, Brault JB, Piolot T, Leconte L, Da Silva N, Pennetier C, Baffet A, Marthiens V, Basto R. Differences in Mitotic Spindle Architecture in Mammalian Neural Stem Cells Influence Mitotic Accuracy during Brain Development. Curr Biol 2019; 29:2993-3005.e9. [DOI: 10.1016/j.cub.2019.07.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/31/2019] [Accepted: 07/19/2019] [Indexed: 12/16/2022]
|
6
|
Venzac B, Madoun R, Benarab T, Monnier S, Cayrac F, Myram S, Leconte L, Amblard F, Viovy JL, Descroix S, Coscoy S. Engineering small tubes with changes in diameter for the study of kidney cell organization. Biomicrofluidics 2018; 12:024114. [PMID: 29657657 PMCID: PMC5882411 DOI: 10.1063/1.5025027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/19/2018] [Indexed: 05/08/2023]
Abstract
Multicellular tubes are structures ubiquitously found during development and in adult organisms. Their topologies (diameter, direction or branching), together with their mechanical characteristics, play fundamental roles in organ function and in the emergence of pathologies. In tubes of micrometric range diameters, typically found in the vascular system, renal tubules or excretory ducts, cells are submitted to a strong curvature and confinement effects in addition to flow. Then, small tubes with change in diameter are submitted to a local gradient of shear stress and curvature, which may lead to complex mechanotransduction responses along tubes, and may be involved in the onset or propagation of cystic or obstructive pathologies. We describe here a simple method to build a microfluidic device that integrates cylindrical channels with changes in diameter that mimic in vivo tube geometries. This microfabrication approach is based on molding of etched tungsten wires, which can achieve on a flexible way any change in diameter in a polydimethylsiloxane (PDMS) microdevice. The interest of this biomimetic multitube system has been evidenced by reproducing renal tubules on chip. In particular, renal cell lines were successfully seeded and grown in PDMS circular tubes with a transition between 80 μm and 50 μm diameters. Thanks to this biomimetic platform, the effect of the tube curvature has been investigated especially regarding cell morphology and orientation. The effect of shear stress on confluent cells has also been assessed simultaneously in both parts of tubes. It is thus possible to study interconnected cell response to differential constraints which is of central importance when mimicking tubes present in the organism.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ludovic Leconte
- Institut Curie, PSL Research University, CNRS UMR 144, 75005 Paris, France
| | | | | | | | - Sylvie Coscoy
- Authors to whom correspondence should be addressed: and
| |
Collapse
|
7
|
Degrelle SA, Gerbaud P, Leconte L, Ferreira F, Pidoux G. Annexin-A5 organized in 2D-network at the plasmalemma eases human trophoblast fusion. Sci Rep 2017; 7:42173. [PMID: 28176826 PMCID: PMC5297248 DOI: 10.1038/srep42173] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/30/2016] [Indexed: 12/13/2022] Open
Abstract
Only a limited number of human cells can fuse to form a multinucleated syncytium. Cell fusion occurs as part of the differentiation of some cell types, including myotubes in muscle and osteoclasts in remodeling bone. In the differentiation of the human placenta, mononuclear cytotrophoblasts aggregate and fuse to form endocrinologically active, non-proliferative, multinucleated syncytia. These syncytia allow the exchange of nutrients and gases between the maternal and fetal circulation. Alteration of syncytial formation during pregnancy affects fetal growth and the outcome of the pregnancy. Here, we demonstrate the role of annexin A5 (AnxA5) in syncytial formation by cellular delivery of recombinant AnxA5 and RNA interference. By a variety of co-immunoprecipitation, immunolocalization and proximity experiments, we show that a pool of AnxA5 organizes at the inner-leaflet of the plasma membrane in the vicinity of a molecular complex that includes E-Cadherin, α-Catenin and β-Catenin, three proteins previously shown to form adherens junctions implicated in cell fusion. A combination of knockdown and reconstitution experiments with AnxA5, with or without the ability to self-assemble in 2D-arrays, demonstrate that this AnxA5 2D-network mediates E-Cadherin mobility in the plasmalemma that triggers human trophoblasts aggregation and thereby cell fusion.
Collapse
Affiliation(s)
- Severine A Degrelle
- INSERM, U767, Cell fusion, Paris, F-75006 France.,Université Paris Descartes, Paris, F-75006 France.,PremUp, Paris, F-75006 France
| | - Pascale Gerbaud
- INSERM, U767, Cell fusion, Paris, F-75006 France.,Université Paris Descartes, Paris, F-75006 France.,UMR-S1180, Inserm, Univ. Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Ludovic Leconte
- UMR144, Institut Curie/CNRS, Cell and Tissue Imaging Platform, Paris, France
| | - Fatima Ferreira
- INSERM, U767, Cell fusion, Paris, F-75006 France.,Université Paris Descartes, Paris, F-75006 France
| | - Guillaume Pidoux
- INSERM, U767, Cell fusion, Paris, F-75006 France.,Université Paris Descartes, Paris, F-75006 France.,PremUp, Paris, F-75006 France.,UMR-S1180, Inserm, Univ. Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| |
Collapse
|
8
|
Bourdon F, Lecoeur M, Leconte L, Ultré V, Kouach M, Odou P, Vaccher C, Foulon C. Evaluation of Pentravan ® , Pentravan ® Plus, Phytobase ® , Lipovan ® and Pluronic Lecithin Organogel for the transdermal administration of antiemetic drugs to treat chemotherapy-induced nausea and vomiting at the hospital. Int J Pharm 2016; 515:774-787. [DOI: 10.1016/j.ijpharm.2016.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/28/2016] [Accepted: 11/03/2016] [Indexed: 12/11/2022]
|
9
|
Velot L, Molina A, Rodrigues-Ferreira S, Nehlig A, Bouchet BP, Morel M, Leconte L, Serre L, Arnal I, Braguer D, Savina A, Honore S, Nahmias C. Negative regulation of EB1 turnover at microtubule plus ends by interaction with microtubule-associated protein ATIP3. Oncotarget 2016; 6:43557-70. [PMID: 26498358 PMCID: PMC4791250 DOI: 10.18632/oncotarget.6196] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/14/2015] [Indexed: 01/15/2023] Open
Abstract
The regulation of microtubule dynamics is critical to ensure essential cell functions. End binding protein 1 (EB1) is a master regulator of microtubule dynamics that autonomously binds an extended GTP/GDP-Pi structure at growing microtubule ends and recruits regulatory proteins at this location. However, negative regulation of EB1 association with growing microtubule ends remains poorly understood. We show here that microtubule-associated tumor suppressor ATIP3 interacts with EB1 through direct binding of a non-canonical proline-rich motif. Results indicate that ATIP3 does not localize at growing microtubule ends and that in situ ATIP3-EB1 molecular complexes are mostly detected in the cytosol. We present evidence that a minimal EB1-interacting sequence of ATIP3 is both necessary and sufficient to prevent EB1 accumulation at growing microtubule ends in living cells and that EB1-interaction is involved in reducing cell polarity. By fluorescence recovery of EB1-GFP after photobleaching, we show that ATIP3 silencing accelerates EB1 turnover at microtubule ends with no modification of EB1 diffusion in the cytosol. We propose a novel mechanism by which ATIP3-EB1 interaction indirectly reduces the kinetics of EB1 exchange on its recognition site, thereby accounting for negative regulation of microtubule dynamic instability. Our findings provide a unique example of decreased EB1 turnover at growing microtubule ends by cytosolic interaction with a tumor suppressor.
Collapse
Affiliation(s)
- Lauriane Velot
- Inserm U981, Institut Gustave Roussy Department of Molecular Medicine, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,CNRS UMR8104, Institut Cochin, Paris, France
| | - Angie Molina
- Inserm U981, Institut Gustave Roussy Department of Molecular Medicine, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,CNRS UMR8104, Institut Cochin, Paris, France
| | - Sylvie Rodrigues-Ferreira
- Inserm U981, Institut Gustave Roussy Department of Molecular Medicine, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,CNRS UMR8104, Institut Cochin, Paris, France
| | - Anne Nehlig
- Inserm U981, Institut Gustave Roussy Department of Molecular Medicine, Villejuif, France.,Université Paris-Saclay, Villejuif, France
| | - Benjamin Pierre Bouchet
- Cell Biology, Faculty of Science, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | | | - Ludovic Leconte
- Cell and Tissue Imaging Core Facilty, PICT-IBiSA, CNRS UMR144 Institut Curie, Centre de Recherche, Paris, France
| | - Laurence Serre
- Inserm U836, Grenoble Institut des Neurosciences, Grenoble, France
| | - Isabelle Arnal
- Inserm U836, Grenoble Institut des Neurosciences, Grenoble, France
| | - Diane Braguer
- Aix Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France.,APHM, Hôpital Timone, Marseille, France
| | - Ariel Savina
- Scientific Partnerships Roche SAS, Boulogne Billancourt, France
| | - Stéphane Honore
- Aix Marseille Université, Inserm, CRO2 UMR_S 911, Marseille, France.,APHM, Hôpital Timone, Marseille, France
| | - Clara Nahmias
- Inserm U981, Institut Gustave Roussy Department of Molecular Medicine, Villejuif, France.,Université Paris-Saclay, Villejuif, France.,CNRS UMR8104, Institut Cochin, Paris, France
| |
Collapse
|
10
|
Chen DS, Feltquate DM, Smothers F, Hoos A, Langermann S, Marshall S, May R, Fleming M, Hodi FS, Senderowicz A, Wiman KG, de Dosso S, Fiedler W, Gianni L, Cresta S, Schulze-Bergkamen HB, Gurrieri L, Salzberg M, Dietrich B, Danielczyk A, Baumeister H, Goletz S, Sessa C, Strumberg D, Schultheis B, Santel A, Gebhardt F, Meyer-Sabellek W, Keil O, Giese K, Kaufmann J, Maio M, Choy G, Covre A, Parisi G, Nicolay H, Fratta E, Fonsatti E, Sigalotti L, Coral S, Taverna P, Azab M, Deutsch E, Lepechoux C, Pignon JP, Tao YT, Rivera S, Bourgier BC, Angokai M, Bahleda R, Slimane K, Angevin E, Besse BB, Soria JC, Dragnev K, Beumer JH, Anyang B, Ma T, Galimberti F, Erkmen CP, Nugent W, Rigas J, Abraham K, Johnstone D, Memoli V, Dmitrovsky E, Voest EE, Siu L, Janku F, Soria JC, Tsimberidou A, Kurzrock R, Tabernero J, Rodon J, Berger R, Onn A, Batist G, Bresson C, Lazar V, Molenaar JJ, Koster J, Ebus M, Zwijnenburg DA, van Sluis P, Lamers F, Schild L, van der Ploeg I, Caron HN, Versteeg R, Pouyssegur J, Marchiq I, Chiche J, Roux D, Le Floch R, Critchlow SE, Wooster RF, Agresta S, Yen KE, Janne PA, Plummer ER, Trinchieri G, Ellis L, Chan SL, Yeo W, Chan AT, Mouliere F, El Messaoudi S, Gongora C, Lamy PJ, del Rio M, Lopez-Crapez E, Gillet B, Mathonnet M, Pezet D, Ychou M, Thierry AR, Ribrag V, Vainchenker W, Constantinescu S, Keilhack H, Umelo IA, Noeparast A, Chen G, Renard M, Geers C, Vansteenkiste J, Teugels E, de Greve J, Rixe O, Qi X, Chu Z, Celerier J, Leconte L, Minet N, Pakradouni J, Kaur B, Cuttitta F, Wagner AJ, Zhang YX, Sicinska E, Czaplinski JT, Remillard SP, Demetri GD, Weng S, Debussche L, Agoni L, Reddy EP, Guha C, Silence K, Thibault A, de Haard H, Dreier T, Ulrichts P, Moshir M, Gabriels S, Luo J, Carter C, Rajan A, Khozin S, Thomas A, Lopez-Chavez A, Brzezniak C, Doyle L, Keen C, Manu M, Raffeld M, Giaccone G, Lutzker S, Melief JM, Eckhardt SG, Trusolino L, Migliardi G, Zanella ER, Cottino F, Galimi F, Sassi F, Marsoni S, Comoglio PM, Bertotti A, Hidalgo M, Weroha SJ, Haluska P, Becker MA, Harrington SC, Goodman KM, Gonzalez SE, al Hilli M, Butler KA, Kalli KR, Oberg AL, Huijbers IJ, Bin Ali R, Pritchard C, Cozijnsen M, Proost N, Song JY, Krimpenfort P, Michalak E, Jonkers J, Berns A, Banerji U, Stewart A, Thavasu P, Banerjee S, Kaye SB. Lectures. Ann Oncol 2013. [DOI: 10.1093/annonc/mdt042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
11
|
Rixe O, Qi X, Chu Z, Celerier J, Leconte L, Minet N, Pakradouni J, Kaur B, Cuttitta F. Nov C-TER: A Novel VEGF-Independent Anti-Angiogenic Agent with a Promising Preclinical Anti-Tumor Efficacy. Ann Oncol 2013. [DOI: 10.1093/annonc/mdt042.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
12
|
Plouhinec JL, Leconte L, Sauka-Spengler T, Bovolenta P, Mazan S, Saule S. Comparative analysis of gnathostome Otx gene expression patterns in the developing eye: implications for the functional evolution of the multigene family. Dev Biol 2005; 278:560-75. [PMID: 15680370 DOI: 10.1016/j.ydbio.2004.11.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Revised: 11/12/2004] [Accepted: 11/12/2004] [Indexed: 10/26/2022]
Abstract
We have performed a detailed analysis of the expression pattern of the three gnathostome Otx classes in order to gain new insights into their functional evolution. Expression patterns were examined in the developing eye of a chondrichthyan, the dogfish, and an amniote, the chick, and compared with the capacity of paralogous proteins to induce a pigmented phenotype in cultured retina cells in cooperation with the bHLH-leucine zipper protein Mitf. This analysis indicates that each Otx class is characterized by highly specific and conserved expression features in the presumptive RPE, where Otx1 and Otx2, but not Otx5, are transcribed at optic vesicle stages, in the differentiating neural retina, where Otx2 and Otx5 show a conserved dynamic expression pattern, and in the forming ciliary process, a major site of Otx1 expression. Furthermore, the paralogous proteins of the dogfish and the mouse do not display any significant difference in their capacity to induce a pigmented phenotype, suggesting a functional equivalency in the specification and differentiation of the RPE. These data indicate that specific functions selectively involving each Otx orthology class were fixed prior to the gnathostome radiation and highlight the prominent role of regulatory changes in the functional diversification of the multigene family.
Collapse
Affiliation(s)
- J L Plouhinec
- Equipe Développement et Evolution des Vertébrés, UPRES-A 8080, Université Paris-Sud, Bat. 441 91405 Orsay Cedex, France
| | | | | | | | | | | |
Collapse
|
13
|
Planque N, Leconte L, Coquelle FM, Benkhelifa S, Martin P, Felder-Schmittbuhl MP, Saule S. Interaction of Maf transcription factors with Pax-6 results in synergistic activation of the glucagon promoter. J Biol Chem 2001; 276:35751-60. [PMID: 11457839 DOI: 10.1074/jbc.m104523200] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the endocrine pancreas, alpha-cell-specific expression of the glucagon gene is mediated by DNA-binding proteins that interact with the G1 proximal promoter element. Among these proteins, the paired domain transcription factor Pax-6 has been shown to bind to G1 and to transactivate glucagon gene expression. Close to the Pax-6-binding site, we observed the presence of a binding site for a basic leucine zipper transcription factor of the Maf family. In the present study, we demonstrate the presence of Maf family members in the endocrine pancreas that bind to G1 and transactivate glucagon promoter expression. In transient transfection experiments, we found that the transactivating effect on the glucagon promoter was greatly enhanced by the simultaneous expression of Maf transcription factors and Pax-6. This enhancement on glucagon transactivation could be correlated with the ability of these proteins to interact together but does not require binding of Maf proteins to the G1 element. Furthermore, we found that Maf enhanced the Pax-6 DNA binding capacity. Our data indicate that Maf transcription factors may contribute to glucagon gene expression in the pancreas.
Collapse
Affiliation(s)
- N Planque
- CNRS-UMR 146, Institut Curie-Section de Recherche, Bât 110, Centre Universitaire, 91405 Orsay, France
| | | | | | | | | | | | | |
Collapse
|
14
|
Planque N, Leconte L, Coquelle FM, Martin P, Saule S. Specific Pax-6/Microphthalmia Transcription Factor Interactions Involve Their DNA-binding Domains and Inhibit Transcriptional Properties of Both Proteins. J Biol Chem 2001; 276:29330-7. [PMID: 11350962 DOI: 10.1074/jbc.m101812200] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pax-6 and microphthalmia transcription factor (Mitf) are required for proper eye development. Pax-6, expressed in both the neuroretina and pigmented retina, has two DNA-binding domains: the paired domain and the homeodomain. Mice homozygous for Pax-6 mutations are anophthalmic. Mitf, a basic helix-loop-helix leucine zipper (b-HLH-LZ) transcription factor associated with the onset and maintenance of pigmentation, identifies the retinal pigmented epithelium during eye development. Loss of Mitf function results in the formation of an ectopic neuroretina at the expense of the dorsal retinal pigmented epithelium. In the present study, we investigated the interaction between Pax-6 and Mitf. In transient transfection-expression experiments, we found that transactivating effects of Pax-6 and Mitf on their respective target promoters were strongly inhibited by co-transfection of both transcription factors. This repression was due to direct protein/protein interactions involving both Pax-6 DNA-binding domains and the Mitf b-HLH-LZ domain. These results suggest that Pax-6/Mitf interactions may be critical for retinal pigmented epithelium development.
Collapse
Affiliation(s)
- N Planque
- CNRS UMR 146, Institut Curie Section Recherche, Centre Universitaire Bâtiment 110, 91405 Orsay Cedex, France
| | | | | | | | | |
Collapse
|
15
|
Leconte L, Barnstable CJ. Impairment of rod cGMP-gated channel alpha-subunit expression leads to photoreceptor and bipolar cell degeneration. Invest Ophthalmol Vis Sci 2000; 41:917-26. [PMID: 10711714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
PURPOSE To determine whether alterations in rod cGMP-gated channel function mediate retinal degeneration, a transgenic approach in which the alpha subunit of the rod cGMP-gated channel is reduced by the expression of an antisense RNA was used. METHODS A 890-bp fragment of the 5' mouse rod cGMP-gated channel cDNA was cloned in the antisense orientation under the control of the strong bacterial cytomegalovirus promoter. This antisense construct was used to generate transgenic mice in which the expression of the antisense transgene was measured by reverse transcription-polymerase chain reaction. Histologic, immunocytochemical, and TdT-dUTP terminal nick-end labeling (TUNEL) analyses were performed on control and transgenic retina sections to determine the effects of antisense expression on specific cell types. RESULTS The antisense RNA was able to inhibit the translation of the rod channel protein in an in vitro assay. Three transgenic mouse lines expressing the antisense construct were obtained. Molecular analyses showed that the antisense is expressed in the eye of each transgenic mouse line, where it reduces rod cGMP-gated channel RNA expression. Histologic and immunocytochemical data showed that transgenic retinas have a reduced number of photoreceptors and bipolar cells. TUNEL staining confirmed that photoreceptor and bipolar cells degenerate along an apoptotic pathway. CONCLUSIONS Impairment of rod cGMP-gated channel alpha subunit expression leads to photoreceptor and bipolar cell degeneration. These transgenic mice are the first model of retinal degeneration caused by an alteration in the expression of the rod cGMP-gated channel. This model system can be used to test therapies designed to slow or stalled retinal degenerations.
Collapse
Affiliation(s)
- L Leconte
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut 06520-8061, USA
| | | |
Collapse
|
16
|
Wei JY, Roy DS, Leconte L, Barnstable CJ. Molecular and pharmacological analysis of cyclic nucleotide-gated channel function in the central nervous system. Prog Neurobiol 1998; 56:37-64. [PMID: 9723130 DOI: 10.1016/s0301-0082(98)00029-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most functional studies of cyclic nucleotide-gated (CNG) channels have been confined to photoreceptors and olfactory epithelium, in which CNG channels are abundant and easy to study. The widespread distribution of CNG channels in tissues throughout the body has only recently been recognized and the functions of this channel family in many of these tissues remain largely unknown. The molecular biological and pharmacological properties of the CNG channel family are summarized in order to put in context studies aimed at probing CNG channel functions in these tissues using pharmacological and genetic methods. Compounds have now been identified that are useful in distinguishing CNG channel activated pathways from cAMP/cGMP dependent-protein kinases or other pathways. The ways in which these interact with CNG channels are understood and this knowledge is leading to the identification of more potent and more specific CNG channel subtype-specific agonists or antagonists. Recent molecular and genetic analyses have identified novel roles of CNG channels in neuronal development and plasticity in both invertebrates and vertebrates. Targeting CNG channels via specific drugs and genetic manipulation (such as knockout mice) will permit better understanding of the role of CNG channels in both basic and higher orders of brain function.
Collapse
Affiliation(s)
- J Y Wei
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | | | | |
Collapse
|
17
|
Abstract
The Ret 1 element, located at -136 to -110 in the rat opsin promoter, binds developmentally regulated retinal nuclear proteins. A similar sequence is found up-stream of opsin genes, from humans to Drosophila, as well as many other photoreceptor-specific genes. The function of the Ret 1 element was tested both in vitro and in two sets of transgenic mice. A mutated Ret 1 element did not bind retinal nuclear proteins in vitro. The same mutations in an otherwise normal 1.9-kb rat opsin promoter failed to drive expression of a lacZ reporter gene in nine of 12 lines. In the three other lines, expression in photoreceptors was very faint. Four tandem copies of the Ret 1 element maintained the Ret 1 binding specificity in vitro and were able to direct expression of a lacZ transgene in photoreceptors of all nine mouse lines obtained. In two lines, expression was also detected in the ganglion cell layer and the ciliary epithelium. In three lines, a characteristic pattern of expression was found in the nervous system in addition to the normal retinal expression. These results indicate that Ret 1 can and is necessary to drive gene expression in rod photoreceptors. Furthermore, our results suggest that Ret 1-like elements may also be important in the developing nervous system.
Collapse
Affiliation(s)
- X Yu
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut 06520-8061, USA
| | | | | | | |
Collapse
|
18
|
Leconte L, Santha M, Fort C, Poujeol C, Portier MM, Simonneau M. Cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences in transgenic mouse embryos. Brain Res Dev Brain Res 1996; 92:1-9. [PMID: 8861716 DOI: 10.1016/0165-3806(95)00182-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Peripherin is a neuron-specific type III intermediate filament protein expressed in well-defined populations of neurons projecting towards peripheral targets. To investigate the molecular mechanisms by which a gene is expressed in a specific subset of neurons, we used a transgenic approach in order to define peripherin gene sequences that are necessary for cell-type specific expression. Transgenic mice carrying different various genomic regions of the mouse peripherin gene fused to the Escherichia coli lacZ reporter gene were generated. We used three different peripherin/lacZ constructs containing either 5.8 kb upstream sequences, or both 5.8 kb upstream and 1.1 kb intragenic sequences, or 1.1 kb intragenic sequences associated with an heterologous promoter. Analysis of lacZ gene expression in transgenic mouse embryos showed that cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences. Analysis of transgenic mouse lines expressing the construct containing both upstream and intragenic sequences showed that this transgene contains all regulatory elements essential for both spatial and temporal expression of the mouse peripherin gene during embryogenesis. Furthermore, lacZ+ positive cells isolated from these transgenic lines by fluorescence-activated cell sorting (FACS) can be stained with a peripherin antibody, demonstrating that the transgene containing both upstream and intragenic sequences is expressed in peripherin neurons. These mouse peripherin upstream and intragenic sequences can now be used to identify cis-acting regulatory elements and transcription factors involved in peripherin gene regulation.
Collapse
Affiliation(s)
- L Leconte
- Laboratoire de Neurobiologie Cellulaire et Moleculaire, France
| | | | | | | | | | | |
Collapse
|
19
|
Leconte L, Semonin O, Zvara A, Boisseau S, Poujeol C, Julien JP, Simonneau M. Both upstream and intragenic sequences of the human neurofilament light gene direct expression of lacZ in neurons of transgenic mouse embryos. J Mol Neurosci 1994; 5:273-95. [PMID: 7577369 DOI: 10.1007/bf02736727] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Initial expression of the neurofilament light gene coincides with the appearance of postmitotic neurons. To investigate the molecular mechanisms involved in neuron-specific gene expression during embryogenesis, we generated transgenic mice carrying various regions of the human neurofilament light gene (hNF-L) fused to the lacZ reporter gene. We found that 2.3 or 0.3 kb of the hNF-L promoter region directs expression of lacZ in neurons of transgenic embryos. Addition of 1.8 kb hNF-L intragenic sequences (IS) enlarges the neuronal pattern of transgene expression. The 2.3-kb hNF-L promote lacZ-IS construct contains all regulatory elements essential for both spatial and temporal expression of the hNF-L gene during embryogenesis and in the adult. The use of a heterologous promoter demonstrated that the 1.8-kb hNF-L intragenic sequences are sufficient to direct the expression of lacZ in a NF-L-specific manner both temporally and spatially during development and in the adult. We conclude that these hNF-L intragenic sequences contain cis-acting DNA regulatory elements that specify neuronal expression. Taken together, these results show that the neurofilament light gene contains separate upstream and intragenic elements, each of which directs lacZ expression in embryonic neurons.
Collapse
Affiliation(s)
- L Leconte
- Laboratoire de Neurobiologie Cellulaire et Moléculaire, CNRS, Gif-sur-Yvette, France
| | | | | | | | | | | | | |
Collapse
|