1
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Kolmus K, Van Troys M, Van Wesemael K, Ampe C, Haegeman G, Tavernier J, Gerlo S. Correction: β-Agonists Selectively Modulate Proinflammatory Gene Expression in Skeletal Muscle Cells via Non-Canonical Nuclear Crosstalk Mechanisms. PLoS One 2023; 18:e0287938. [PMID: 37368923 DOI: 10.1371/journal.pone.0287938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0090649.].
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2
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Hu J, Serra‐Picamal X, Bakker G, Van Troys M, Winograd‐Katz S, Ege N, Gong X, Didan Y, Grosheva I, Polansky O, Bakkali K, Van Hamme E, van Erp M, Vullings M, Weiss F, Clucas J, Dowbaj AM, Sahai E, Ampe C, Geiger B, Friedl P, Bottai M, Strömblad S. Multisite assessment of reproducibility in high-content cell migration imaging data. Mol Syst Biol 2023; 19:e11490. [PMID: 37063090 PMCID: PMC10258559 DOI: 10.15252/msb.202211490] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
High-content image-based cell phenotyping provides fundamental insights into a broad variety of life science disciplines. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, with particular relevance for high-quality open-access data sharing and meta-analysis. However, the sources and degree of biological and technical variability, and thus the reproducibility and usefulness of meta-analysis of results from live-cell microscopy, have not been systematically investigated. Here, using high-content data describing features of cell migration and morphology, we determine the sources of variability across different scales, including between laboratories, persons, experiments, technical repeats, cells, and time points. Significant technical variability occurred between laboratories and, to lesser extent, between persons, providing low value to direct meta-analysis on the data from different laboratories. However, batch effect removal markedly improved the possibility to combine image-based datasets of perturbation experiments. Thus, reproducible quantitative high-content cell image analysis of perturbation effects and meta-analysis depend on standardized procedures combined with batch correction.
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Affiliation(s)
- Jianjiang Hu
- Department of Biosciences and NutritionKarolinska InstitutetStockholmSweden
| | | | - Gert‐Jan Bakker
- Department of Medical BioSciencesRadboud University Medical CenterNijmegenThe Netherlands
| | | | - Sabina Winograd‐Katz
- Department of Immunology and Regenerative BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Nil Ege
- The Francis Crick InstituteLondonUK
| | - Xiaowei Gong
- Department of Biosciences and NutritionKarolinska InstitutetStockholmSweden
| | - Yuliia Didan
- Department of Biosciences and NutritionKarolinska InstitutetStockholmSweden
| | - Inna Grosheva
- Department of Immunology and Regenerative BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Omer Polansky
- Department of Immunology and Regenerative BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Karima Bakkali
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | | | - Merijn van Erp
- Department of Medical BioSciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Manon Vullings
- Department of Medical BioSciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Felix Weiss
- Department of Medical BioSciencesRadboud University Medical CenterNijmegenThe Netherlands
| | | | | | | | - Christophe Ampe
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Benjamin Geiger
- Department of Immunology and Regenerative BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Peter Friedl
- Department of Medical BioSciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Matteo Bottai
- Division of Biostatistics, Institute of Environmental MedicineKarolinska InstitutetStockholmSweden
| | - Staffan Strömblad
- Department of Biosciences and NutritionKarolinska InstitutetStockholmSweden
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3
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Mendive‐Tapia L, Miret‐Casals L, Barth ND, Wang J, de Bray A, Beltramo M, Robert V, Ampe C, Hodson DJ, Madder A, Vendrell M. Acid-Resistant BODIPY Amino Acids for Peptide-Based Fluorescence Imaging of GPR54 Receptors in Pancreatic Islets. Angew Chem Int Ed Engl 2023; 62:e202302688. [PMID: 36917014 PMCID: PMC10947197 DOI: 10.1002/anie.202302688] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/15/2023]
Abstract
The G protein-coupled kisspeptin receptor (GPR54 or KISS1R) is an important mediator in reproduction, metabolism and cancer biology; however, there are limited fluorescent probes or antibodies for direct imaging of these receptors in cells and intact tissues, which can help to interrogate their multiple biological roles. Herein, we describe the rational design and characterization of a new acid-resistant BODIPY-based amino acid (Trp-BODIPY PLUS), and its implementation for solid-phase synthesis of fluorescent bioactive peptides. Trp-BODIPY PLUS retains the binding capabilities of both short linear and cyclic peptides and displays notable turn-on fluorescence emission upon target binding for wash-free imaging. Finally, we employed Trp-BODIPY PLUS to prepare some of the first fluorogenic kisspeptin-based probes and visualized the expression and localization of GPR54 receptors in human cells and in whole mouse pancreatic islets by fluorescence imaging.
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Affiliation(s)
| | - Laia Miret‐Casals
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Jinling Wang
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Anne de Bray
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Massimiliano Beltramo
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Vincent Robert
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Christophe Ampe
- Department of Biomolecular MedicineFaculty of Medicine and Health SciencesGhent University9052GhentBelgium
| | - David J. Hodson
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Annemieke Madder
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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4
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Mendive‐Tapia L, Miret‐Casals L, Barth ND, Wang J, de Bray A, Beltramo M, Robert V, Ampe C, Hodson DJ, Madder A, Vendrell M. Acid-Resistant BODIPY Amino Acids for Peptide-Based Fluorescence Imaging of GPR54 Receptors in Pancreatic Islets. Angew Chem Weinheim Bergstr Ger 2023; 135:e202302688. [PMID: 38516305 PMCID: PMC10952496 DOI: 10.1002/ange.202302688] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Indexed: 03/17/2023]
Abstract
The G protein-coupled kisspeptin receptor (GPR54 or KISS1R) is an important mediator in reproduction, metabolism and cancer biology; however, there are limited fluorescent probes or antibodies for direct imaging of these receptors in cells and intact tissues, which can help to interrogate their multiple biological roles. Herein, we describe the rational design and characterization of a new acid-resistant BODIPY-based amino acid (Trp-BODIPY PLUS), and its implementation for solid-phase synthesis of fluorescent bioactive peptides. Trp-BODIPY PLUS retains the binding capabilities of both short linear and cyclic peptides and displays notable turn-on fluorescence emission upon target binding for wash-free imaging. Finally, we employed Trp-BODIPY PLUS to prepare some of the first fluorogenic kisspeptin-based probes and visualized the expression and localization of GPR54 receptors in human cells and in whole mouse pancreatic islets by fluorescence imaging.
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Affiliation(s)
| | - Laia Miret‐Casals
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Jinling Wang
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Anne de Bray
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Massimiliano Beltramo
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Vincent Robert
- Equipe Neuroendocrinologie Moleculaire de la ReproductionPhysiologie de la Reproduction et des ComportementsCentre INRA Val de Loire37380NouzillyFrance
| | - Christophe Ampe
- Department of Biomolecular MedicineFaculty of Medicine and Health SciencesGhent University9052GhentBelgium
| | - David J. Hodson
- Oxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Radcliffe Department of MedicineUniversity of OxfordOX3 7LEOxfordUK
| | - Annemieke Madder
- Department of Organic and Macromolecular ChemistryFaculty of SciencesGhent University9000GhentBelgium
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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5
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Kleinberger I, Sanders E, Staes K, Van Troys M, Hirano S, Hochepied T, Lemeire K, Martens L, Ampe C, van Roy F. Innovative mouse models for the tumor suppressor activity of Protocadherin-10 isoforms. BMC Cancer 2022; 22:451. [PMID: 35468745 PMCID: PMC9040349 DOI: 10.1186/s12885-022-09381-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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/02/2022] [Indexed: 11/12/2022] Open
Abstract
Background Nonclustered mouse protocadherin genes (Pcdh) encode proteins with a typical single ectodomain and a cytoplasmic domain with conserved motifs completely different from those of classic cadherins. Alternative splice isoforms differ in the size of these cytoplasmic domains. In view of the compelling evidence for gene silencing of protocadherins in human tumors, we started investigations on Pcdh functions in mouse cancer models. Methods For Pcdh10, we generated two mouse lines: one with floxed exon 1, leading to complete Pcdh10 ablation upon Cre action, and one with floxed exons 2 and 3, leading to ablation of only the long isoforms of Pcdh10. In a mouse medulloblastoma model, we used GFAP-Cre action to locally ablate Pcdh10 in combination with Trp53 and Rb1 ablation. From auricular tumors, that also arose, we obtained tumor-derived cell lines, which were analyzed for malignancy in vitro and in vivo. By lentiviral transduction, we re-expressed Pcdh10 cDNAs. RNA-Seq analyses were performed on these cell families. Results Surprisingly, not only medulloblastomas were generated in our model but also tumors of tagged auricles (pinnae). For both tumor types, ablation of either all or only long isoforms of Pcdh10 aggravated the disease. We argued that the perichondrial stem cell compartment is at the origin of the pinnal tumors. Immunohistochemical analysis of these tumors revealed different subtypes. We obtained several pinnal-tumor derived (PTD) cell lines and analyzed these for anchorage-independent growth, invasion into collagen matrices, tumorigenicity in athymic mice. Re-expression of either the short or a long isoform of Pcdh10 in two PTD lines counteracted malignancy in all assays. RNA-Seq analyses of these two PTD lines and their respective Pcdh10-rescued cell lines allowed to identify many interesting differentially expressed genes, which were largely different in the two cell families. Conclusions A new mouse model was generated allowing for the first time to examine the remarkable tumor suppression activity of protocadherin-10 in vivo. Despite lacking several conserved motifs, the short isoform of Pcdh10 was fully active as tumor suppressor. Our model contributes to scrutinizing the complex molecular mechanisms of tumor initiation and progression upon PCDH10 silencing in many human cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09381-y.
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Affiliation(s)
- Irene Kleinberger
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Ellen Sanders
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Katrien Staes
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Marleen Van Troys
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052, Ghent, Belgium
| | - Shinji Hirano
- Department of Cell Biology, Kansai Medical University, Hirakata City, Osaka, 573-1010, Japan
| | - Tino Hochepied
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Kelly Lemeire
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Liesbet Martens
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Christophe Ampe
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052, Ghent, Belgium
| | - Frans van Roy
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium. .,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), 9052, Ghent, Belgium.
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6
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Miret-Casals L, Vannecke W, Hoogewijs K, Arauz-Garofalo G, Gay M, Díaz-Lobo M, Vilaseca M, Ampe C, Van Troys M, Madder A. Furan warheads for covalent trapping of weak protein-protein interactions: cross-linking of thymosin β4 to actin. Chem Commun (Camb) 2021; 57:6054-6057. [PMID: 34036992 DOI: 10.1039/d1cc01731d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe furan as a triggerable 'warhead' for site-specific cross-linking using the actin and thymosin β4 (Tβ4)-complex as model of a weak and dynamic protein-protein interaction (PPI) with known 3D structure and with application potential in disease contexts. The identified cross-linked residues demonstrate that lysine is a target for the furan warhead. The presented in vitro validation of covalently acting 'furan-armed' Tβ4-variants provides initial proof to further exploit furan-technology for covalent drug design targeting lysines.
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Affiliation(s)
- Laia Miret-Casals
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281 S4, Ghent B-9000, Belgium.
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7
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Vanslembrouck B, Ampe C, Hengel J. Time for rethinking the different β‐actin transgenic mouse models? Cytoskeleton (Hoboken) 2020; 77:527-543. [DOI: 10.1002/cm.21647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Bieke Vanslembrouck
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences Ghent University Ghent Belgium
| | - Christophe Ampe
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences Ghent University Ghent Belgium
| | - Jolanda Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences Ghent University Ghent Belgium
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8
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Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker GJ, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Dévédec SEL, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, Roudot P, Schuster M, Sergeant G, Strömblad S, Swedlow JR, van Erp M, Van Troys M, Zaritsky A, Sansone SA, Martens L. Community standards for open cell migration data. Gigascience 2020; 9:giaa041. [PMID: 32396199 PMCID: PMC7317087 DOI: 10.1093/gigascience/giaa041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.
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Affiliation(s)
- Alejandra N Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Paola Masuzzo
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Institute for Globally Distributed Open Research and Education (IGDORE), Kabupaten Gianyar, Bali 80571, Indonesia
| | - Christophe Ampe
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Gert-Jan Bakker
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
| | - Sébastien Besson
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Robert H Eibl
- German Cancer Research Center, DKFZ Alumni Association, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Peter Friedl
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
- David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, 6767 Bertner Ave, Mitchell Basic Science Research Building, 77030 Houston, TX, USA
- Cancer Genomics Center, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
- Leibniz Institute for Analytical Sciences, ISAS, Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany
| | - Mark Kittisopikul
- Department of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO box 9502 2300 RA Leiden, The Netherlands
| | - Simone Leo
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
- Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Loc. Piscina Manna, Edificio 1, 09050 Pula (CA) , Italy
| | - Josh Moore
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Yael Paran
- IDEA Bio-Medical Ltd, 2 Prof. Bergman St., Rehovot 76705, Israel
| | - Jaime Prilusky
- Life Science Core Facilities, Weizmann Institute of Science, P.O. Box 26 Rehovot 76100, Israel
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA
| | - Marc Schuster
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Gwendolien Sergeant
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Staffan Strömblad
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, SE-141 83 Huddinge, Sweden
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Merijn van Erp
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
| | - Marleen Van Troys
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501 Beer-Sheva, Israel
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
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9
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Witjes L, Van Troys M, Verhasselt B, Ampe C. Prevalence of Cytoplasmic Actin Mutations in Diffuse Large B-Cell Lymphoma and Multiple Myeloma: A Functional Assessment Based on Actin Three-Dimensional Structures. Int J Mol Sci 2020; 21:ijms21093093. [PMID: 32349449 PMCID: PMC7247664 DOI: 10.3390/ijms21093093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 02/06/2023] Open
Abstract
Mutations in actins have been linked to several developmental diseases. Their occurrence across different cancers has, however, not been investigated. Using the cBioPortal database we show that human actins are infrequently mutated in patient samples of various cancers types. Nevertheless, ranking these studies by mutational frequency suggest that some have a higher percentage of patients with ACTB and ACTG1 mutations. Within studies on hematological cancers, mutations in ACTB and ACTG1 are associated with lymphoid cancers since none have currently been reported in myeloid cancers. Within the different types of lymphoid cancers ACTB mutations are most frequent in diffuse large B-cell lymphoma (DLBCL) and ACTG1 mutations in multiple myeloma. We mapped the ACTB and ACTG1 mutations found in these two cancer types on the 3D-structure of actin showing they are in regions important for actin polymer formation or binding to myosin. The potential effects of the mutations on actin properties imply that mutations in cytoplasmic actins deserve dedicated research in DLBCL and multiple myeloma.
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Affiliation(s)
- Laura Witjes
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University Hospital, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Marleen Van Troys
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Bruno Verhasselt
- Department of Diagnostic Sciences, Ghent University Hospital, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Christophe Ampe
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Correspondence:
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10
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Schuster M, Moeller M, Bornemann L, Bessen C, Sobczak C, Schmitz S, Witjes L, Kruithoff K, Kohn C, Just O, Kündgen A, Pundt N, Pelzer B, Ampe C, Van Troys M, Nusch A, Haas R, Germing U, Martens L, Jöckel KH, Gunzer M. Surveillance of Myelodysplastic Syndrome via Migration Analyses of Blood Neutrophils: A Potential Prognostic Tool. J Immunol 2018; 201:3546-3557. [PMID: 30446567 DOI: 10.4049/jimmunol.1801071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 11/19/2022]
Abstract
Autonomous migration is a central characteristic of immune cells, and changes in this function have been correlated to the progression and severity of diseases. Hence, the identification of pathologically altered leukocyte migration patterns might be a promising approach for disease surveillance and prognostic scoring. However, because of the lack of standardized and robust assays, migration patterns have not been clinically exploited so far. In this study, we introduce an easy-to-use and cross-laboratory, standardized two-dimensional migration assay for neutrophil granulocytes from peripheral blood. By combining time-lapse video microscopy and automated cell tracking, we calculated the average migration of neutrophils from 111 individual participants of the German Heinz Nixdorf Recall MultiGeneration study under steady-state, formyl-methionyl-leucyl-phenylalanine-, CXCL1-, and CXCL8-stimulated conditions. Comparable values were obtained in an independent laboratory from a cohort in Belgium, demonstrating the robustness and transferability of the assay. In a double-blinded retrospective clinical analysis, we found that neutrophil migration strongly correlated with the Revised International Prognostic Scoring System scoring and risk category of myelodysplastic syndrome (MDS) patients. In fact, patients suffering from high-risk subtypes MDS with excess blasts I or II displayed highly significantly reduced neutrophil migration. Hence, the determination of neutrophil migration patterns might represent a useful tool in the surveillance of MDS. Taken together, we suggest that standardized migration assays of neutrophils and other leukocyte subtypes might be broadly applicable as prognostic and surveillance tools for MDS and potentially for other diseases.
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Affiliation(s)
- Marc Schuster
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Mischa Moeller
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Lea Bornemann
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Clara Bessen
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Charlyn Sobczak
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Saskia Schmitz
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Laura Witjes
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Katja Kruithoff
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Christina Kohn
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Olga Just
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Andrea Kündgen
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Noreen Pundt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Benedikt Pelzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | | | - Arnd Nusch
- Onkologische Praxis Velbert, 40822 Mettmann, Germany; and
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Lennart Martens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, 45147 Essen, Germany;
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11
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Simiczyjew A, Dratkiewicz E, Van Troys M, Ampe C, Styczeń I, Nowak D. Combination of EGFR Inhibitor Lapatinib and MET Inhibitor Foretinib Inhibits Migration of Triple Negative Breast Cancer Cell Lines. Cancers (Basel) 2018; 10:cancers10090335. [PMID: 30227653 PMCID: PMC6162814 DOI: 10.3390/cancers10090335] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 07/24/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most challenging subtype to treat due to the lack of estrogen receptor, progesterone receptor, and HER2 expression, which excludes the usage of directed targeted therapy against them. Promising therapeutic targets are the hepatocyte growth factor receptor (MET) and epidermal growth factor receptor (EGFR), which expression is frequently elevated in TNBC. Inhibitors of these receptors used as monotherapy are often ineffective. Due to that, we studied the efficacy of combined therapy targeting MET and EGFR simultaneously. Two TNBC cell lines were treated with lapatinib (a dual EGFR and HER2 inhibitor), foretinib (a MET inhibitor), or a combination of the two. After the inhibitors treatment, we verified the cell viability (XTT assay), distribution of the cell cycle phases, the activation of signaling pathways (Western blotting), distribution of invadopodia, fluorescent gelatin digestion (immunofluorescence), and the invasion capacity of cells. A combination of foretinib and lapatinib effectively reduced the viability of examined cells, led to G2/M arrest and reduction of pAKT. There was also a decreasein number of invadopodia formed by cells, their ability to digest gelatin and reduction of cells migration/invasion capacity. Therapy targeting of both EGFR and MET receptors was much more effective against tested cells than monotherapy. We selected a combination of drugs that could be successfully used against this breast cancer subtype.
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Affiliation(s)
- Aleksandra Simiczyjew
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Ewelina Dratkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Marleen Van Troys
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
| | - Christophe Ampe
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
| | - Ilona Styczeń
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Dorota Nowak
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
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12
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Sala S, Ampe C. An emerging link between LIM domain proteins and nuclear receptors. Cell Mol Life Sci 2018; 75:1959-1971. [PMID: 29428964 PMCID: PMC11105726 DOI: 10.1007/s00018-018-2774-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 12/13/2022]
Abstract
Nuclear receptors are ligand-activated transcription factors that partake in several biological processes including development, reproduction and metabolism. Over the last decade, evidence has accumulated that group 2, 3 and 4 LIM domain proteins, primarily known for their roles in actin cytoskeleton organization, also partake in gene transcription regulation. They shuttle between the cytoplasm and the nucleus, amongst other as a consequence of triggering cells with ligands of nuclear receptors. LIM domain proteins act as important coregulators of nuclear receptor-mediated gene transcription, in which they can either function as coactivators or corepressors. In establishing interactions with nuclear receptors, the LIM domains are important, yet pleiotropy of LIM domain proteins and nuclear receptors frequently occurs. LIM domain protein-nuclear receptor complexes function in diverse physiological processes. Their association is, however, often linked to diseases including cancer.
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Affiliation(s)
- Stefano Sala
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium.
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13
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Abstract
Chemical cross-linking is well-established for investigating protein-protein interactions. Traditionally, photo cross-linking is used but is associated with problems of selectivity and UV toxicity in a biological context. We here describe, with live cells and under normal growth conditions, selective cross-linking of a furan-modified peptide ligand to its membrane-presented receptor with zero toxicity, high efficiency, and spatio-specificity. Furan-modified kisspeptin-10 is covalently coupled to its glycosylated membrane receptor, GPR54(KISS1R). This newly expands the applicability of furan-mediated cross-linking not only to protein-protein cross-linking but also to cross-linking in situ. Moreover, in our earlier reports on nucleic acid interstrand cross-linking, furan activation required external triggers of oxidation (via addition of N-bromo succinimide or singlet oxygen). In contrast, we here show, for multiple cell lines, the spontaneous endogenous oxidation of the furan moiety with concurrent selective cross-link formation. We propose that reactive oxygen species produced by NADPH oxidase (NOX) enzymes form the cellular source establishing furan oxidation.
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Affiliation(s)
- Willem Vannecke
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Christophe Ampe
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Marleen Van Troys
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Massimiliano Beltramo
- Equipe
Neuroendocrinologie Moleculaire de la Reproduction, Physiologie de
la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Annemieke Madder
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
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14
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Sala S, Catillon M, Hadzic E, Schaffner-Reckinger E, Van Troys M, Ampe C. The PET and LIM1-2 domains of testin contribute to intramolecular and homodimeric interactions. PLoS One 2017; 12:e0177879. [PMID: 28542564 PMCID: PMC5436826 DOI: 10.1371/journal.pone.0177879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 10/06/2016] [Accepted: 05/04/2017] [Indexed: 12/18/2022] Open
Abstract
The focal adhesion protein testin is a modular scaffold and tumour suppressor that consists of an N-terminal cysteine rich (CR) domain, a PET domain of unknown function and three C-terminal LIM domains. Testin has been proposed to have an open and a closed conformation based on the observation that its N-terminal half and C-terminal half directly interact. Here we extend the testin conformational model by demonstrating that testin can also form an antiparallel homodimer. In support of this extended model we determined that the testin region (amino acids 52–233) harbouring the PET domain interacts with the C-terminal LIM1-2 domains in vitro and in cells, and assign a critical role to tyrosine 288 in this interaction.
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Affiliation(s)
- Stefano Sala
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Marie Catillon
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | - Ermin Hadzic
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | - Elisabeth Schaffner-Reckinger
- Cytoskeleton and Cell Plasticity Lab, Life Sciences Research Unit - FSTC, University of Luxembourg, Luxembourg, Luxembourg
| | | | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium
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15
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Sala S, Van Troys M, Medves S, Catillon M, Timmerman E, Staes A, Schaffner-Reckinger E, Gevaert K, Ampe C. Expanding the Interactome of TES by Exploiting TES Modules with Different Subcellular Localizations. J Proteome Res 2017; 16:2054-2071. [DOI: 10.1021/acs.jproteome.7b00034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefano Sala
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
| | | | - Sandrine Medves
- Cytoskeleton
and Cell Plasticity Lab, Life Sciences Research Unit − FSTC, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
- Laboratory of Experimental Cancer Research, LIH, 1445 Strassen, Luxembourg
| | - Marie Catillon
- Cytoskeleton
and Cell Plasticity Lab, Life Sciences Research Unit − FSTC, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Evy Timmerman
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
- VIB Medical Biotechnology Center, 9000 Gent, Belgium
| | - An Staes
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
- VIB Medical Biotechnology Center, 9000 Gent, Belgium
| | - Elisabeth Schaffner-Reckinger
- Cytoskeleton
and Cell Plasticity Lab, Life Sciences Research Unit − FSTC, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
- VIB Medical Biotechnology Center, 9000 Gent, Belgium
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, 9000 Gent, Belgium
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16
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Masuzzo P, Huyck L, Simiczyjew A, Ampe C, Martens L, Van Troys M. An end-to-end software solution for the analysis of high-throughput single-cell migration data. Sci Rep 2017; 7:42383. [PMID: 28205527 PMCID: PMC5304333 DOI: 10.1038/srep42383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 06/24/2016] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
The systematic study of single-cell migration requires the availability of software for assisting data inspection, quality control and analysis. This is especially important for high-throughput experiments, where multiple biological conditions are tested in parallel. Although the field of cell migration can count on different computational tools for cell segmentation and tracking, downstream data visualization, parameter extraction and statistical analysis are still left to the user and are currently not possible within a single tool. This article presents a completely new module for the open-source, cross-platform CellMissy software for cell migration data management. This module is the first tool to focus specifically on single-cell migration data downstream of image processing. It allows fast comparison across all tested conditions, providing automated data visualization, assisted data filtering and quality control, extraction of various commonly used cell migration parameters, and non-parametric statistical analysis. Importantly, the module enables parameters computation both at the trajectory- and at the step-level. Moreover, this single-cell analysis module is complemented by a new data import module that accommodates multiwell plate data obtained from high-throughput experiments, and is easily extensible through a plugin architecture. In conclusion, the end-to-end software solution presented here tackles a key bioinformatics challenge in the cell migration field, assisting researchers in their high-throughput data processing.
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Affiliation(s)
- Paola Masuzzo
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lynn Huyck
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Aleksandra Simiczyjew
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
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17
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Vanhercke T, Ampe C, Tirry L, Denolf P. Rescue and In Situ Selection and Evaluation (RISE): A Method for High-Throughput Panning of Phage Display Libraries. ACTA ACUST UNITED AC 2016; 10:108-17. [PMID: 15799954 DOI: 10.1177/1087057104271956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/16/2022]
Abstract
Phage display has proven to be an invaluable instrument in the search for proteins and peptides with optimized or novel functions. The amplification and selection of phage libraries typically involve several operations and handling large bacterial cultures during each round. Purification of the assembled phage particles after rescue adds to the labor and time demand. The authors therefore devised a method, termed rescue and in situ selection and evaluation (RISE), which combines all steps from rescue to binding in a single microwell. To test this concept, wells were precoated with different antibodies, which allowed newly formed phage particles to be captured directly in situ during overnight rescue. Following 6 washing steps, the retained phages could be easily detected in an enzyme-linked immunosorbent assay (ELISA), thus eliminating the need for purification or concentration of the viral particles. As a consequence, RISE enables a rapid characterization of phage-displayed proteins. In addition, this method allowed for the selective enrichment of phages displaying a hemagglutinin (HA) epitope tag, spiked in a 104-fold excess of wild-type background. Because the combination of phage rescue, selection, or evaluation in a single microwell is amenable to automation, RISE may boost the high-throughput screening of smaller sized phage display libraries.
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Affiliation(s)
- Thomas Vanhercke
- Department of Crop Protection, Faculty of Agricultural and Applied Biological Sciences, Ghent University, Ghent, Belgium, Bayer BioScience N.V., Ghent, Belgium.
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18
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Abstract
Actin is the central building block of the actin cytoskeleton, a highly regulated filamentous network enabling dynamic processes of cells and simultaneously providing structure. Mammals have six actin isoforms that are very conserved and thus share common functions. Tissue-specific expression in part underlies their differential roles, but actin isoforms also coexist in various cell types and tissues, suggesting specific functions and preferential interaction partners. Gene deletion models, antibody-based staining patterns, gene silencing effects, and the occurrence of isoform-specific mutations in certain diseases have provided clues for specificity on the subcellular level and its consequences on the organism level. Yet, the differential actin isoform functions are still far from understood in detail. Biochemical studies on the different isoforms in pure form are just emerging, and investigations in cells have to deal with a complex and regulated system, including compensatory actin isoform expression.
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Affiliation(s)
- Christophe Ampe
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium.
| | - Marleen Van Troys
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000, Ghent, Belgium
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19
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Simiczyjew A, Mazur AJ, Ampe C, Malicka-Błaszkiewicz M, van Troys M, Nowak D. Active invadopodia of mesenchymally migrating cancer cells contain both β and γ cytoplasmic actin isoforms. Exp Cell Res 2015; 339:206-19. [PMID: 26548725 DOI: 10.1016/j.yexcr.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 10/25/2022]
Abstract
Invadopodia are actin-rich protrusions formed by mesenchymally migrating cancer cells. They are mainly composed of actin, actin-associated proteins, integrins and proteins of signaling machineries. These protrusions display focalized proteolytic activity towards the extracellular matrix. It is well known that polymerized (F-)actin is present in these structures, but the nature of the actin isoform has not been studied before. We here show that both cytoplasmic actin isoforms, β- and γ-actin, are present in the invadopodia of MDA-MB-231 breast cancer cells cultured on a 2D-surface, where they colocalize with the invadopodial marker cortactin. Invadopodial structures formed by the cells in a 3D-collagen matrix also contain β- and γ-actin. We demonstrate this using isoform-specific antibodies and expression of fluorescently-tagged actin isoforms. Additionally, using simultaneous expression of differentially tagged β- and γ-actin in cells, we show that the actin isoforms are present together in a single invadopodium. Cells with an increased level of β- or γ-actin, display a similar increase in the number and size of invadopodia in comparison to control cells. Moreover, increasing the level of either actin isoforms also increases invasion velocity.
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Affiliation(s)
- Aleksandra Simiczyjew
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Antonina Joanna Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Christophe Ampe
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Maria Malicka-Błaszkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Marleen van Troys
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Dorota Nowak
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
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20
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Hadzic E, Catillon M, Halavatyi A, Medves S, Van Troys M, Moes M, Baird MA, Davidson MW, Schaffner-Reckinger E, Ampe C, Friederich E. Delineating the Tes Interaction Site in Zyxin and Studying Cellular Effects of Its Disruption. PLoS One 2015; 10:e0140511. [PMID: 26509500 PMCID: PMC4624954 DOI: 10.1371/journal.pone.0140511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/25/2015] [Indexed: 01/21/2023] Open
Abstract
Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain protein zyxin localizes to focal adhesions where it participates in the regulation of the actin cytoskeleton. Because of its interactions with a variety of binding partners, zyxin has been proposed to act as a molecular scaffold. Here, we studied the interaction of zyxin with such a partner: Tes. Similar to zyxin, Tes harbors three highly conserved LIM domains of which the LIM1 domain directly interacts with zyxin. Using different zyxin variants in pull-down assays and ectopic recruitment experiments, we identified the Tes binding site in zyxin and showed that four highly conserved amino acids are crucial for its interaction with Tes. Based upon these findings, we used a zyxin mutant defective in Tes-binding to assess the functional consequences of abrogating the zyxin-Tes interaction in focal adhesions. Performing fluorescence recovery after photobleaching, we showed that zyxin recruits Tes to focal adhesions and modulates its turnover in these structures. However, we also provide evidence for zyxin-independent localization of Tes to focal adhesions. Zyxin increases focal adhesion numbers and reduces focal adhesion lifetimes, but does so independent of Tes. Quantitative analysis showed that the loss of interaction between zyxin and Tes affects the process of cell spreading. We conclude that zyxin influences focal adhesion dynamics, that it recruits Tes and that this interaction is functional in regulating cell spreading.
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Affiliation(s)
- Ermin Hadzic
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Marie Catillon
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Aliaksandr Halavatyi
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Sandrine Medves
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | | | - Michèle Moes
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Michelle A. Baird
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Michael W. Davidson
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, Tallahassee, Florida, United States of America
| | - Elisabeth Schaffner-Reckinger
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
| | - Christophe Ampe
- Department of Biochemistry, Ghent University, Ghent, Belgium
- * E-mail:
| | - Evelyne Friederich
- Laboratory of Cytoskeleton and Cell Plasticity, Life Sciences Research Unit, University of Luxembourg, Luxemburg, Luxembourg
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21
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Masuzzo P, Martens L, Ampe C, Anderson KI, Barry J, De Wever O, Debeir O, Decaestecker C, Dolznig H, Friedl P, Gaggioli C, Geiger B, Goldberg IG, Horn E, Horwitz R, Kam Z, Le Dévédec SE, Vignjevic DM, Moore J, Olivo-Marin JC, Sahai E, Sansone SA, Sanz-Moreno V, Strömblad S, Swedlow J, Textor J, Van Troys M, Zantl R. An open data ecosystem for cell migration research. Trends Cell Biol 2015; 25:55-8. [PMID: 25484346 DOI: 10.1016/j.tcb.2014.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 11/11/2014] [Accepted: 11/14/2014] [Indexed: 11/22/2022]
Abstract
Cell migration research has recently become both a high content and a high throughput field thanks to technological, computational, and methodological advances. Simultaneously, however, urgent bioinformatics needs regarding data management, standardization, and dissemination have emerged. To address these concerns, we propose to establish an open data ecosystem for cell migration research.
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Affiliation(s)
- Paola Masuzzo
- Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium.
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22
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Jedynska A, Hoek G, Wang M, Eeftens M, Cyrys J, Keuken M, Ampe C, Beelen R, Cesaroni G, Forastiere F, Cirach M, de Hoogh K, De Nazelle A, Nystad W, Declercq C, Eriksen KT, Dimakopoulou K, Lanki T, Meliefste K, Nieuwenhuijsen MJ, Yli-Tuomi T, Raaschou-Nielsen O, Brunekreef B, Kooter IM. Development of land use regression models for elemental, organic carbon, PAH, and hopanes/steranes in 10 ESCAPE/TRANSPHORM European study areas. Environ Sci Technol 2014; 48:14435-44. [PMID: 25317817 DOI: 10.1021/es502568z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Land use regression (LUR) models have been used to model concentrations of mainly traffic-related air pollutants (nitrogen oxides (NOx), particulate matter (PM) mass or absorbance). Few LUR models are published of PM composition, whereas the interest in health effects related to particle composition is increasing. The aim of our study was to evaluate LUR models of polycyclic aromatic hydrocarbons (PAH), hopanes/steranes, and elemental and organic carbon (EC/OC) content of PM2.5. In 10 European study areas, PAH, hopanes/steranes, and EC/OC concentrations were measured at 16-40 sites per study area. LUR models for each study area were developed on the basis of annual average concentrations and predictor variables including traffic, population, industry, natural land obtained from geographic information systems. The highest median model explained variance (R(2)) was found for EC - 84%. The median R(2) was 51% for OC, 67% for benzo[a]pyrene, and 38% for sum of hopanes/steranes, with large variability between study areas. Traffic predictors were included in most models. Population and natural land were included frequently as additional predictors. The moderate to high explained variance of LUR models and the overall moderate correlation with PM2.5 model predictions support the application of especially the OC and PAH models in epidemiological studies.
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Affiliation(s)
- Aleksandra Jedynska
- TNO, Netherlands Organization for Applied Scientific Research, Utrecht, The Netherlands
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Kolmus K, Van Troys M, Van Wesemael K, Ampe C, Haegeman G, Tavernier J, Gerlo S. β-agonists selectively modulate proinflammatory gene expression in skeletal muscle cells via non-canonical nuclear crosstalk mechanisms. PLoS One 2014; 9:e90649. [PMID: 24603712 PMCID: PMC3946252 DOI: 10.1371/journal.pone.0090649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 02/04/2014] [Indexed: 02/04/2023] Open
Abstract
The proinflammatory cytokine Tumour Necrosis Factor (TNF)-α is implicated in a variety of skeletal muscle pathologies. Here, we have investigated how in vitro cotreatment of skeletal muscle C2C12 cells with β-agonists modulates the TNF-α-induced inflammatory program. We observed that C2C12 myotubes express functional TNF receptor 1 (TNF-R1) and β2-adrenoreceptors (β2-ARs). TNF-α activated the canonical Nuclear Factor-κB (NF-κB) pathway and Mitogen-Activated Protein Kinases (MAPKs), culminating in potent induction of NF-κB-dependent proinflammatory genes. Cotreatment with the β-agonist isoproterenol potentiated the expression of inflammatory mediators, including Interleukin-6 (IL-6) and several chemokines. The enhanced production of chemotactic factors upon TNF-α/isoproterenol cotreatment was also suggested by the results from migrational analysis. Whereas we could not explain our observations by cytoplasmic crosstalk, we found that TNF-R1-and β2-AR-induced signalling cascades cooperate in the nucleus. Using the IL-6 promoter as a model, we demonstrated that TNF-α/isoproterenol cotreatment provoked phosphorylation of histone H3 at serine 10, concomitant with enhanced promoter accessibility and recruitment of the NF-κB p65 subunit, cAMP-response element-binding protein (CREB), CREB-binding protein (CBP) and RNA polymerase II. In summary, we show that β-agonists potentiate TNF-α action, via nuclear crosstalk, that promotes chromatin relaxation at selected gene promoters. Our data warrant further study into the mode of action of β-agonists and urge for caution in their use as therapeutic agents for muscular disorders.
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Affiliation(s)
- Krzysztof Kolmus
- Department of Medical Protein Research, VIB, Gent, Belgium
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Marleen Van Troys
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | | | - Christophe Ampe
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Guy Haegeman
- Department of Physiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Jan Tavernier
- Department of Medical Protein Research, VIB, Gent, Belgium
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Sarah Gerlo
- Department of Medical Protein Research, VIB, Gent, Belgium
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
- * E-mail:
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Abstract
The mouse genome consists of six functional actin genes of which the expression patterns are temporally and spatially regulated during development and in the adult organism. Deletion of beta-actin in mouse is lethal during embryonic development, although there is compensatory expression of other actin isoforms. This suggests different isoform specific functions and, more in particular, an important function for beta-actin during early mammalian development. We here report a role for beta-actin during neural crest ontogeny. Although beta-actin null neural crest cells show expression of neural crest markers, less cells delaminate and their migration arrests shortly after. These phenotypes were associated with elevated apoptosis levels in neural crest cells, whereas proliferation levels were unchanged. Specifically the pre-migratory neural crest cells displayed higher levels of apoptosis, suggesting increased apoptosis in the neural tube accounts for the decreased amount of migrating neural crest cells seen in the beta-actin null embryos. These cells additionally displayed a lack of membrane bound N-cadherin and dramatic decrease in cadherin-11 expression which was more pronounced in the pre-migratory neural crest population, potentially indicating linkage between the cadherin-11 expression and apoptosis. By inhibiting ROCK ex vivo, the knockout neural crest cells regained migratory capacity and cadherin-11 expression was upregulated. We conclude that the presence of beta-actin is vital for survival, specifically of pre-migratory neural crest cells, their proper emigration from the neural tube and their subsequent migration. Furthermore, the absence of beta-actin affects cadherin-11 and N-cadherin function, which could partly be alleviated by ROCK inhibition, situating the Rho-ROCK signaling in a feedback loop with cadherin-11.
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Affiliation(s)
- Davina Tondeleir
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Rivka Noelanders
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Karima Bakkali
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Christophe Ampe
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
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Ampe C, Libbrecht J, Van Troys M. β-actin knock-out mouse embryonic fibroblasts show increased expression of LIM-, CH-, EFh-domain containing proteins with predicted common upstream regulators. Cytoskeleton (Hoboken) 2013; 70:766-74. [DOI: 10.1002/cm.21147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/22/2013] [Accepted: 09/26/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Christophe Ampe
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Ghent
| | - Jelle Libbrecht
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Ghent
| | - Marleen Van Troys
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Ghent
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Ampe C, Machesky LM, Nyitrai M. Biophysical approaches for investigation of the cytoskeleton. A special issue stemming from research presented at the 2012 ECF meeting: a FEBS/EMBO workshop lecture course in Pécs, Hungary. Cytoskeleton (Hoboken) 2013; 70:539. [PMID: 24166833 DOI: 10.1002/cm.21145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Masuzzo P, Hulstaert N, Huyck L, Ampe C, Van Troys M, Martens L. CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays. ACTA ACUST UNITED AC 2013; 29:2661-3. [PMID: 23918247 PMCID: PMC3789541 DOI: 10.1093/bioinformatics/btt437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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] [Indexed: 11/14/2022]
Abstract
SUMMARY Automated image processing has allowed cell migration research to evolve to a high-throughput research field. As a consequence, there is now an unmet need for data management in this domain. The absence of a generic management system for the quantitative data generated in cell migration assays results in each dataset being treated in isolation, making data comparison across experiments difficult. Moreover, by integrating quality control and analysis capabilities into such a data management system, the common practice of having to manually transfer data across different downstream analysis tools will be markedly sped up and made more robust. In addition, access to a data management solution creates gateways for data standardization, meta-analysis and structured public data dissemination. We here present CellMissy, a cross-platform data management system for cell migration data with a focus on wound healing data. CellMissy simplifies and automates data management, storage and analysis from the initial experimental set-up to data exploration. AVAILABILITY AND IMPLEMENTATION CellMissy is a cross-platform open-source software developed in Java. Source code and cross-platform binaries are freely available under the Apache2 open source license at http://cellmissy.googlecode.com.
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Affiliation(s)
- Paola Masuzzo
- Department of Medical Protein Research, VIB and Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent 9000, Belgium
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Tondeleir D, Drogat B, Slowicka K, Bakkali K, Bartunkova S, Goossens S, Haigh JJ, Ampe C. Beta-Actin Is Involved in Modulating Erythropoiesis during Development by Fine-Tuning Gata2 Expression Levels. PLoS One 2013; 8:e67855. [PMID: 23840778 PMCID: PMC3694046 DOI: 10.1371/journal.pone.0067855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/28/2013] [Indexed: 12/22/2022] Open
Abstract
The functions of actin family members during development are poorly understood. To investigate the role of beta-actin in mammalian development, a beta-actin knockout mouse model was used. Homozygous beta-actin knockout mice are lethal at embryonic day (E)10.5. At E10.25 beta-actin knockout embryos are growth retarded and display a pale yolk sac and embryo proper that is suggestive of altered erythropoiesis. Here we report that lack of beta-actin resulted in a block of primitive and definitive hematopoietic development. Reduced levels of Gata2, were associated to this phenotype. Consistently, ChIP analysis revealed multiple binding sites for beta-actin in the Gata2 promoter. Gata2 mRNA levels were almost completely rescued by expression of an erythroid lineage restricted ROSA26-promotor based GATA2 transgene. As a result, erythroid differentiation was restored and the knockout embryos showed significant improvement in yolk sac and embryo vascularization. These results provide new molecular insights for a novel function of beta-actin in erythropoiesis by modulating the expression levels of Gata2 in vivo.
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Affiliation(s)
- Davina Tondeleir
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Benjamin Drogat
- Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Karolina Slowicka
- Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Karima Bakkali
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sonia Bartunkova
- Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Steven Goossens
- Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jody J. Haigh
- Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- * E-mail: * (CA); (JJH)
| | - Christophe Ampe
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- * E-mail: * (CA); (JJH)
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Eeftens M, Tsai MY, Ampe C, Anwander B, Beelen R, Bellander T, Cesaroni G, Cirach M, Cyrys J, de Hoogh K, De Nazelle A, de Vocht F, Declercq C, Dėdelė A, Eriksen K, Galassi C, Gražulevičienė R, Grivas G, Heinrich J, Hoffmann B, Iakovides M, Ineichen A, Katsouyanni K, Korek M, Krämer U, Kuhlbusch T, Lanki T, Madsen C, Meliefste K, Mölter A, Mosler G, Nieuwenhuijsen M, Oldenwening M, Pennanen A, Probst-Hensch N, Quass U, Raaschou-Nielsen O, Ranzi A, Stephanou E, Sugiri D, Udvardy O, Vaskövi É, Weinmayr G, Brunekreef B, Hoek G. Spatial variation of PM2.5, PM10, PM2.5 absorbance and PMcoarse concentrations between and within 20 European study areas and the relationship with NO2 – Results of the ESCAPE project. Atmospheric Environment 2012; 62:303-317. [PMID: 0 DOI: 10.1016/j.atmosenv.2012.08.038] [Citation(s) in RCA: 285] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Rochelle T, Daubon T, Van Troys M, Harnois T, Waterschoot D, Ampe C, Roy L, Bourmeyster N, Constantin B. p210bcr-abl induces amoeboid motility by recruiting ADF/destrin through RhoA/ROCK1. FASEB J 2012; 27:123-34. [PMID: 23047898 DOI: 10.1096/fj.12-205112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We previously demonstrated that the Bcr-Abl oncogene, p210(bcr-abl), through its unique GEF domain, specifically activates RhoA and induces spontaneous amoeboid motility. We intend to study the pathways downstream RhoA controlling amoeboid motility. Mouse prolymphoblastic cells (Ba/F3 cell line) expressing different forms of Bcr-Abl were embedded in 3-dimensional (3D) Matrigel to study motility and explore the effects of inhibiting Rho pathway (inhibitors and siRNAs). The phosphorylation levels of cofilin-1 and destrin were analyzed by 2-dimensional electrophoresis. Composition of Bcr-Abl signalplex in different conditions was determined by coimmunoprecipitation. Ba/F3p190 and Ba/F3 expressing a mutant form of p210(bcr-abl) (unable to activate RhoA) cells presented a spontaneous motility, but not an amoeboid type. p210(bcr-abl)-induced amoeboid motility in a 3D matrix requires isoform-specific RhoA/ROCK-1/destrin signaling. Next to the conventional Rho/ROCK/MLC/myosin pathway, this pathway is a crucial determinant for amoeboid motility, specific for the destrin isoform (and not its coexpressed homologue cofilin-1). Also, the presence of destrin (and not cofilin-1) in the p210(bcr-abl) complex is dependent on ROCK1, and this signalplex is required for amoeboid motility. This underscores isoform-specific function within the ADF/cofilin family and provides new insight into Bcr-Abl signaling to amoeboid motility and possible impact on understanding chronic myeloid leukemia progression.
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Affiliation(s)
- Tristan Rochelle
- Institut de Physiologie et Biologie Cellulaires, Unité Mixte de Recherche Centre National de Recherche Scientifique (CNRS) 6187, Poitiers, France
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Huyck L, Ampe C, Van Troys M. The XTT cell proliferation assay applied to cell layers embedded in three-dimensional matrix. Assay Drug Dev Technol 2012; 10:382-92. [PMID: 22574651 DOI: 10.1089/adt.2011.391] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cell proliferation, a main target in cancer therapy, is influenced by the surrounding three-dimensional (3D) extracellular matrix (ECM). In vitro drug screening is, thus, optimally performed under conditions in which cells are grown (embedded or trapped) in dense 3D matrices, as these most closely mimic the adhesive and mechanical properties of natural ECM. Measuring cell proliferation under these conditions is, however, technically more challenging compared with two-dimensional (2D) culture and other "3D culture conditions," such as growth on top of a matrix (pseudo-3D) or in spongy scaffolds with large pore sizes. Consequently, such measurements are only slowly applied on a wider scale. To advance this, we report on the equal quality (dynamic range, background, linearity) of measuring the proliferation of cell layers embedded in dense 3D matrices (collagen, Matrigel) compared with cells in 2D culture using the easy (one-step) and in 2D well-validated, 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT)-assay. The comparison stresses the differences in proliferation kinetics and drug sensitivity of matrix-embedded cells versus 2D culture. Using the specific cell-layer-embedded 3D matrix setup, quantitative measurements of cell proliferation and cell invasion are shown to be possible in similar assay conditions, and cytostatic, cytotoxic, and anti-invasive drug effects can thus be reliably determined and compared in physiologically relevant settings. This approach in the 3D matrix holds promise for improving early-stage, high-throughput drug screening, targeting either highly invasive or highly proliferative subpopulations of cancers or both.
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Affiliation(s)
- Lynn Huyck
- Department of Medical Protein Research, VIB, Ghent, Belgium
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Tondeleir D, Lambrechts A, Müller M, Jonckheere V, Doll T, Vandamme D, Bakkali K, Waterschoot D, Lemaistre M, Debeir O, Decaestecker C, Hinz B, Staes A, Timmerman E, Colaert N, Gevaert K, Vandekerckhove J, Ampe C. Cells lacking β-actin are genetically reprogrammed and maintain conditional migratory capacity. Mol Cell Proteomics 2012; 11:255-71. [PMID: 22448045 DOI: 10.1074/mcp.m111.015099] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Vertebrate nonmuscle cells express two actin isoforms: cytoplasmic β- and γ-actin. Because of the presence and localized translation of β-actin at the leading edge, this isoform is generally accepted to specifically generate protrusive forces for cell migration. Recent evidence also implicates β-actin in gene regulation. Cell migration without β-actin has remained unstudied until recently and it is unclear whether other actin isoforms can compensate for this cytoplasmic function and/or for its nuclear role. Primary mouse embryonic fibroblasts lacking β-actin display compensatory expression of other actin isoforms. Consistent with this preservation of polymerization capacity, β-actin knockout cells have unchanged lamellipodial protrusion rates despite a severe migration defect. To solve this paradox we applied quantitative proteomics revealing a broad genetic reprogramming of β-actin knockout cells. This also explains why reintroducing β-actin in knockout cells does not restore the affected cell migration. Pathway analysis suggested increased Rho-ROCK signaling, consistent with observed phenotypic changes. We therefore developed and tested a model explaining the phenotypes in β-actin knockout cells based on increased Rho-ROCK signaling and increased TGFβ production resulting in increased adhesion and contractility in the knockout cells. Inhibiting ROCK or myosin restores migration of β-actin knockout cells indicating that other actins compensate for β-actin in this process. Consequently, isoactins act redundantly in providing propulsive forces for cell migration, but β-actin has a unique nuclear function, regulating expression on transcriptional and post-translational levels, thereby preventing myogenic differentiation.
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Huyck L, Van Troys M, Ampe C. Phosphosite conservation in single domain orthologs versus paralogs: a way to combine differential regulation with redundant core functions. FEBS Lett 2012; 586:296-302. [PMID: 22265693 DOI: 10.1016/j.febslet.2012.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 12/15/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 11/19/2022]
Abstract
Evolutionary conservation for structure function relations is commonly accepted. Here we hypothesize that closely related single domain paralogous proteins, having similar expression profiles and redundant biochemical core functions, additionally evolved to allow and maintain isoform specific differential regulation by single conserved amino acid substitutions. To substantiate this, we considered two families of closely related actin binding proteins combined with data mining of phosphorylated residues in human and mouse proteins. We show that such residues are identical in other orthologs whereas paralogs have a different, but also conserved, non-phosphorylatable residue at the equivalent positions.
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Affiliation(s)
- Lynn Huyck
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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Bourry D, Sinnaeve D, Gheysen K, Fritzinger B, Vandenborre G, Van Damme EJM, Wieruszeski JM, Lippens G, Ampe C, Martins JC. Intermolecular interaction studies using small volumes. Magn Reson Chem 2011; 49:9-15. [PMID: 21162136 DOI: 10.1002/mrc.2699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 09/15/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
We present the use of 1-mm room-temperature probe technology to perform intermolecular interaction studies using chemical shift perturbation methods and saturation transfer difference (STD) spectroscopy using small sample volumes. The use of a small sample volume (5-10 µl) allows for an alternative titration protocol where individual samples are prepared for each titration point, rather than the usual protocol used for a 5-mm probe setup where the ligand is added consecutively to the solution containing the protein or host of interest. This allows for considerable economy in the consumption and cost of the protein and ligand amounts required for interaction studies. For titration experiments, the use of the 1-mm setup consumes less than 10% of the ligand amount required using a 5-mm setup. This is especially significant when complex ligands that are only available in limited quantities, typically because they are obtained from natural sources or through elaborate synthesis efforts, need to be investigated. While the use of smaller volumes does increase the measuring time, we demonstrate that the use of commercial small volume probes allows the study of interactions that would otherwise be impossible to address by NMR.
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Affiliation(s)
- David Bourry
- Department of Chemistry, Ghent University, Ghent, Belgium
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35
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Meixner A, Boldt K, Van Troys M, Askenazi M, Gloeckner CJ, Bauer M, Marto JA, Ampe C, Kinkl N, Ueffing M. A QUICK screen for Lrrk2 interaction partners--leucine-rich repeat kinase 2 is involved in actin cytoskeleton dynamics. Mol Cell Proteomics 2010; 10:M110.001172. [PMID: 20876399 DOI: 10.1074/mcp.m110.001172] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Mutations in human leucine-rich repeat kinase 2 (Lrrk2), a protein of yet unknown function, are linked to Parkinson's disease caused by degeneration of midbrain dopaminergic neurons. The protein comprises several domains including a GTPase and a kinase domain both affected by several pathogenic mutations. To elucidate the molecular interaction network of endogenous Lrrk2 under stoichiometric constraints, we applied QUICK (quantitative immunoprecipitation combined with knockdown) in NIH3T3 cells. The identified interactome reveals actin isoforms as well as actin-associated proteins involved in actin filament assembly, organization, rearrangement, and maintenance, suggesting that the biological function of Lrrk2 is linked to cytoskeletal dynamics. In fact, we demonstrate Lrrk2 de novo binding to F-actin and its ability to modulate its assembly in vitro. When tested in intact cells, knockdown of Lrrk2 causes morphological alterations in NIH3T3 cells. In developing dopaminergic midbrain primary neurons, Lrrk2 knockdown results in shortened neurite processes, indicating a physiological role of Lrrk2 in cytoskeletal organization and dynamics of dopaminergic neurons. Hence, our results demonstrate that molecular interactions as well as the physiological function of Lrrk2 are closely related to the organization of the actin-based cytoskeleton, a crucial feature of neuronal development and neuron function.
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Affiliation(s)
- Andrea Meixner
- Department of Protein Science, Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany
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36
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Veniere S, Waterschoot D, Vandekerckhove J, Lambrechts A, Ampe C. Identification and expression analysis of splice variants of mouse enabled homologue during development and in adult tissues. BMC Mol Biol 2010; 11:45. [PMID: 20565797 PMCID: PMC2898656 DOI: 10.1186/1471-2199-11-45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/28/2009] [Accepted: 06/17/2010] [Indexed: 11/30/2022] Open
Abstract
Background The Enabled/Vasodilator stimulated phosphoprotein (Ena/VASP) gene family comprises three genes in vertebrates: Vasp, Enabled homologue (Enah) and Ena-VASP like (Evl). Enah has the most complex gene structure. It has extra alternatively included exons compared to Vasp and Evl, and possibly one alternatively excluded intron S. The aim of this mapping study was to probe the occurrence of combinations of exon usage in Enah thereby identifying possible vertebrate ENAH splice variants. We investigated this via an in silico analysis and by performing a reverse transcription-polymerase chain reaction (RT-PCR) screen on mouse samples. We further probed the expression pattern of mouse Enah splice variants during development and in a selection of mouse adult tissues and mouse cell lines. Results In silico analysis of the vertebrate Ena/VASP gene family reveals that birds do not have Vasp, while fish have two Evl genes. Analysis of expressed sequence tags of vertebrate Enah splice variants confirms that an Enah transcript without alternative exons is ubiquitously expressed, but yields only limited information about the existence of other possible alternatively spliced Enah transcripts. Via a RT-PCR screen, we provide evidence that during mouse development and in adult mice at least eight and maximally sixteen different Enah transcripts are expressed. We also show that tissues and cell lines display specific expression profiles of these different transcripts. Exons previously associated with neuronal expression of Enah splice variants are also present in other tissues, in particular in heart. Conclusions We propose a more uniform nomenclature for alternative exons in Enah. We provide an overview of distinct expression profiles of mouse Enah splice variants during mouse development, in adult mouse tissues and in a subset of mouse cell lines.
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Affiliation(s)
- Sylvie Veniere
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
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Tondeleir D, Vandamme D, Vandekerckhove J, Ampe C, Lambrechts A. Actin isoform expression patterns during mammalian development and in pathology: insights from mouse models. ACTA ACUST UNITED AC 2009; 66:798-815. [PMID: 19296487 DOI: 10.1002/cm.20350] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [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: 11/07/2022]
Abstract
The dynamic actin cytoskeleton, consisting of six actin isoforms in mammals and a variety of actin binding proteins is essential for all developmental processes and for the viability of the adult organism. Actin isoform specific functions have been proposed for muscle contraction, cell migration, endo- and exocytosis and maintaining cell shape. However, these specific functions for each of the actin isoforms during development are not well understood. Based on transgenic mouse models, we will discuss the expression patterns of the six conventional actin isoforms in mammals during development and adult life. Ablation of actin genes usually leads to lethality and affects expression of other actin isoforms at the cell or tissue level. A good knowledge of their expression and functions will contribute to fully understand severe phenotypes or diseases caused by mutations in actin isoforms.
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Affiliation(s)
- Davina Tondeleir
- Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (VIB), Albert Baertsoenkaai 3, Ghent, Belgium
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Leyman S, Sidani M, Ritsma L, Waterschoot D, Eddy R, Dewitte D, Debeir O, Decaestecker C, Vandekerckhove J, van Rheenen J, Ampe C, Condeelis J, Van Troys M. Unbalancing the phosphatidylinositol-4,5-bisphosphate-cofilin interaction impairs cell steering. Mol Biol Cell 2009; 20:4509-23. [PMID: 19741095 DOI: 10.1091/mbc.e09-02-0121] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cofilin is a key player in actin dynamics during cell migration. Its activity is regulated by (de)phosphorylation, pH, and binding to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P(2)]. Here, we here use a human cofilin-1 (D122K) mutant with increased binding affinity for PI(4,5)P(2) and slower release from the plasma membrane to study the role of the PI(4,5)P(2)-cofilin interaction in migrating cells. In fibroblasts in a background of endogenous cofilin, D122K cofilin expression negatively affects cell turning frequency. In carcinoma cells with down-regulated endogenous cofilin, D122K cofilin neither rescues the drastic morphological defects nor restores the effects in cell turning capacity, unlike what has been reported for wild-type cofilin. In cofilin knockdown cells, D122K cofilin expression promotes outgrowth of an existing lamellipod in response to epidermal growth factor (EGF) but does not result in initiation of new lamellipodia. This indicates that, next to phospho- and pH regulation, the normal release kinetics of cofilin from PI(4,5)P(2) is crucial as a local activation switch for lamellipodia initiation and as a signal for migrating cells to change direction in response to external stimuli. Our results demonstrate that the PI(4,5)P(2) regulatory mechanism, that is governed by EGF-dependent phospholipase C activation, is a determinant for the spatial and temporal control of cofilin activation required for lamellipodia initiation.
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Affiliation(s)
- Shirley Leyman
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
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Tondeleir D, Müller M, Jonckheere V, Waterschoot D, Bakkali K, Vandekerckhove J, Ampe C, Lambrechts A. Impaired neural crest migration contributes to midgestation lethality of beta-actin knock-out mouse. Dev Biol 2009. [DOI: 10.1016/j.ydbio.2009.05.316] [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: 10/20/2022]
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Veniere S, Ampe C, Vandekerckhove J, Lambrechts A. The interaction of proline-rich ligands with profilin probed with an enzyme-linked immunosorbent assay. ACTA ACUST UNITED AC 2009; 14:350-9. [PMID: 19403918 DOI: 10.1177/1087057109332594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To detect interactions of different proline-rich ligands with profilins, the authors developed a simple analytical antibody-based screening method. Profilin I or profilin IIa was coated in microplates, and ligand binding was monitored via antibody detection. Using purified components, the authors show that the assay is very sensitive as nanomolar concentrations of recombinant profilin ligands can be used. They further apply this technique to detect interaction of profilin with various proline-rich partners, either endogenously present or ectopically expressed as tagged fusions, using lysates. With this assay, the authors identify Shootin1 as a novel profilin IIa partner. In addition, they demonstrate that this assay can be used for studying competition or ternary complex formation. In conclusion, they developed a sensitive, easy-to-use, and versatile method for the study of the interaction between profilin and different ligands.
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Affiliation(s)
- Sylvie Veniere
- Department of Medical Protein Research, VIB, Ghent, Belgium
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Vandamme D, Lambert E, Waterschoot D, Cognard C, Vandekerckhove J, Ampe C, Constantin B, Rommelaere H. alpha-Skeletal muscle actin nemaline myopathy mutants cause cell death in cultured muscle cells. Biochim Biophys Acta 2009; 1793:1259-71. [PMID: 19393268 DOI: 10.1016/j.bbamcr.2009.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 03/24/2009] [Accepted: 04/14/2009] [Indexed: 11/24/2022]
Abstract
Nemaline myopathy is a neuromuscular disorder, characterized by muscle weakness and hypotonia and is, in 20% of the cases, caused by mutations in the gene encoding alpha-skeletal muscle actin, ACTA1. It is a heterogeneous disease with various clinical phenotypes and severities. In patients the ultrastructure of muscle cells is often disturbed by nemaline rods and it is thought this is the cause for muscle weakness. To search for possible defects during muscle cell differentiation we expressed alpha-actin mutants in myoblasts and allowed these cells to differentiate into myotubes. Surprisingly, we observed two striking new phenotypes in differentiating myoblasts: rounding up of cells and bleb formation, two features reminiscent of apoptosis. Indeed expression of these mutants induced cell death with apoptotic features in muscle cell culture, using AIF and endonuclease G, in a caspase-independent but calpain-dependent pathway. This is the first report on a common cellular defect induced by NM causing actin mutants, independent of their biochemical phenotypes or rod and aggregate formation capacity. These data suggest that lack of type II fibers or atrophy observed in nemaline myopathy patients may be also due to an increased number of dying muscle cells.
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Affiliation(s)
- Drieke Vandamme
- Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, B-9000, Gent, Belgium
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Vandamme D, Rommelaere H, Lambert E, Waterschoot D, Vandekerckhove J, Constantin B, Ampe C. α-Skeletal muscle actin mutants causing different congenital myopathies induce similar cytoskeletal defects in cell line cultures. ACTA ACUST UNITED AC 2009; 66:179-92. [DOI: 10.1002/cm.20340] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Dhaese S, Vandepoele K, Waterschoot D, Vanloo B, Vandekerckhove J, Ampe C, Van Troys M. The mouse thymosin beta15 gene family displays unique complexity and encodes a functional thymosin repeat. J Mol Biol 2009; 387:809-25. [PMID: 19233202 DOI: 10.1016/j.jmb.2009.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 02/10/2009] [Accepted: 02/12/2009] [Indexed: 11/24/2022]
Abstract
We showed earlier that human beta-thymosin 15 (Tb15) is up-regulated in prostate cancer, confirming studies from others that propagated Tb15 as a prostate cancer biomarker. In this first report on mouse Tb15, we show that, unlike in humans, four Tb15-like isoforms are present in mouse. We used phylogenetic analysis of deuterostome beta-thymosins to show that these four new isoforms cluster within the vertebrate Tb15-clade. Intriguingly, one of these mouse beta-thymosins, Tb15r, consists of two beta-thymosin domains. The existence of such a repeat beta-thymosin is so far unique in vertebrates, though common in lower eukaryotes. Biochemical data indicate that Tb15r potently sequesters actin. In a cellular context, Tb15r behaves as a bona fide beta-thymosin, lowering central stress fibre content. We reveal that a complex genomic organization underlies Tb15r expression: Tb15r results from read-through transcription and alternative splicing of two tandem duplicated mouse Tb15 genes. Transcript profiling of all mouse beta-thymosin isoforms (Tb15s, Tb4 and Tb10) reveals that two isoform switches occur between embryonic and adult tissues, and indicates Tb15r as the major mouse Tb15 isoform in adult cells. Tb15r is present also in mouse prostate cancer cell lines. This insight into the mouse Tb15 family is fundamental for future studies on Tb15 in mouse (prostate) cancer models.
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Affiliation(s)
- Stien Dhaese
- Department of Medical Protein Research, VIB, Ghent, Belgium
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Van Troys M, Huyck L, Leyman S, Dhaese S, Vandekerkhove J, Ampe C. Ins and outs of ADF/cofilin activity and regulation. Eur J Cell Biol 2008; 87:649-67. [PMID: 18499298 DOI: 10.1016/j.ejcb.2008.04.001] [Citation(s) in RCA: 253] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/25/2008] [Accepted: 04/02/2008] [Indexed: 12/15/2022] Open
Abstract
The actin-binding proteins of the actin-depolymerisation factor (ADF)/cofilin family were first described more than three decades ago, but research on these proteins still occupies a front role in the actin and cell migration field. Moreover, cofilin activity is implicated in the malignant, invasive properties of cancer cells. The effects of ADF/cofilins on actin dynamics are diverse and their regulation is complex. In stimulated cells, multiple signalling pathways can be initiated resulting in different activation/deactivation switches that control ADF/cofilin activity. The output of this entire regulatory system, in combination with spatial and temporal segregation of the activation mechanisms, underlies the contribution of ADF/cofilins to various cell migration/invasion phenotypes. In this framework, we describe current views on how ADF/cofilins function in migrating and invading cells.
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Thomas C, Moreau F, Dieterle M, Hoffmann C, Gatti S, Hofmann C, Van Troys M, Ampe C, Steinmetz A. The LIM domains of WLIM1 define a new class of actin bundling modules. J Biol Chem 2007; 282:33599-33608. [PMID: 17827159 DOI: 10.1074/jbc.m703691200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [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
Actin filament bundling, i.e. the formation of actin cables, is an important process that relies on proteins able to directly bind and cross-link subunits of adjacent actin filaments. Animal cysteine-rich proteins and their plant counterparts are two LIM domain-containing proteins that were recently suggested to define a new family of actin cytoskeleton regulators involved in actin filament bundling. We here identified the LIM domains as responsible for F-actin binding and bundling activities of the tobacco WLIM1. The deletion of one of the two LIM domains reduced significantly, but did not entirely abolish, the ability of WLIM1 to bind actin filaments. Individual LIM domains were found to interact directly with actin filaments, although with a reduced affinity compared with the native protein. Variants lacking the C-terminal or the inter-LIM domain were only weakly affected in their F-actin stabilizing and bundling activities and trigger the formation of thick cables containing tightly packed actin filaments as does the native protein. In contrast, the deletion of one of the two LIM domains negatively impacted both activities and resulted in the formation of thinner and wavier cables. In conclusion, we demonstrate that the LIM domains of WLIM1 are new autonomous actin binding and bundling modules that cooperate to confer WLIM1 high actin binding and bundling activities.
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Affiliation(s)
- Clément Thomas
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg.
| | - Flora Moreau
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Monika Dieterle
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Céline Hoffmann
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Sabrina Gatti
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
| | - Christina Hofmann
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, F-67084 Strasbourg, France
| | - Marleen Van Troys
- VIB Department of Medical Protein Research, Ugent and Department of Biochemistry, Faculty of Medicine and Health Sciences, B-9052 Ghent, Belgium
| | - Christophe Ampe
- VIB Department of Medical Protein Research, Ugent and Department of Biochemistry, Faculty of Medicine and Health Sciences, B-9052 Ghent, Belgium
| | - André Steinmetz
- Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg
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Dhaese S, Jonckheere V, Goethals M, Waltregny D, Vandekerckhove J, Ampe C, Van Troys M. Functional and profiling studies prove that prostate cancer upregulated neuroblastoma thymosin β is the true human homologue of rat thymosin β15. FEBS Lett 2007; 581:4809-15. [PMID: 17888914 DOI: 10.1016/j.febslet.2007.09.003] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 08/24/2007] [Accepted: 09/01/2007] [Indexed: 11/30/2022]
Abstract
A peptide with a sequence identical to rat thymosin beta(Tb)15 was reported to be upregulated in human prostate cancer. However, in this report we provide evidence that TbNB, initially identified in human neuroblastoma, is the only Tb isoform upregulated in human prostate cancer and that the Tb15 sequence is not present herein. In addition, we demonstrate that human TbNB has a higher affinity for actin in comparison to Tb4 and promotes cell migration. In combination, this experimentally validates TbNB as functional homologue of rat Tb15 in the human organism and clarifies the current composition of the human Tb family.
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Affiliation(s)
- S Dhaese
- VIB Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
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Polet D, Lambrechts A, Vandepoele K, Vandekerckhove J, Ampe C. On the origin and evolution of vertebrate and viral profilins. FEBS Lett 2006; 581:211-7. [PMID: 17187785 DOI: 10.1016/j.febslet.2006.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [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: 11/10/2006] [Accepted: 12/06/2006] [Indexed: 11/23/2022]
Abstract
The three dimensional structures of profilins from invertebrates and vertebrates are remarkably similar despite low sequence similarity. Their evolutionary relationship remains thus enigmatic. A phylogenetic analysis of profilins from Deuterostoma indicates that profilin III and IV isoforms each form distinct groups. Profilin IV is most related to invertebrate profilins and originated prior to vertebrate evolution whereas separation of profilin I, II and III isoforms occurred early in vertebrate evolution. Viral profilins are most similar to profilin III. In silico analysis of representative profilin gene structures corroborates the phylogenetic result and we discuss this in terms of biochemical differences.
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Affiliation(s)
- Debby Polet
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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Thomas C, Hoffmann C, Dieterle M, Van Troys M, Ampe C, Steinmetz A. Tobacco WLIM1 is a novel F-actin binding protein involved in actin cytoskeleton remodeling. Plant Cell 2006; 18:2194-206. [PMID: 16905656 PMCID: PMC1560925 DOI: 10.1105/tpc.106.040956] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 06/22/2006] [Accepted: 07/13/2006] [Indexed: 05/05/2023]
Abstract
We used confocal microscopy and in vitro analyses to show that Nicotiana tabacum WLIM1, a LIM domain protein related to animal Cys-rich proteins, is a novel actin binding protein in plants. Green fluorescent protein (GFP)-tagged WLIM1 protein accumulated in the nucleus and cytoplasm of tobacco BY2 cells. It associated predominantly with actin cytoskeleton, as demonstrated by colabeling and treatment with actin-depolymerizing latrunculin B. High-speed cosedimentation assays revealed the ability of WLIM1 to bind directly to actin filaments with high affinity. Fluorescence recovery after photobleaching and fluorescence loss in photobleaching showed a highly dynamic in vivo interaction of WLIM1-GFP with actin filaments. Expression of WLIM1-GFP in BY2 cells significantly delayed depolymerization of the actin cytoskeleton induced by latrunculin B treatment. WLIM1 also stabilized actin filaments in vitro. Importantly, expression of WLIM1-GFP in Nicotiana benthamiana leaves induces significant changes in actin cytoskeleton organization, specifically, fewer and thicker actin bundles than in control cells, suggesting that WLIM1 functions as an actin bundling protein. This hypothesis was confirmed by low-speed cosedimentation assays and direct observation of F-actin bundles that formed in vitro in the presence of WLIM1. Taken together, these data identify WLIM1 as a novel actin binding protein that increases actin cytoskeleton stability by promoting bundling of actin filaments.
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Martens L, Monsieur G, Ampe C, Gevaert K, Vandekerckhove J. Cell_motility: a cross-platform, open source application for the study of cell motion paths. BMC Bioinformatics 2006; 7:289. [PMID: 16762054 PMCID: PMC1523222 DOI: 10.1186/1471-2105-7-289] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Accepted: 06/08/2006] [Indexed: 12/04/2022] Open
Abstract
Background Migration is an important aspect of cellular behaviour and is therefore widely studied in cell biology. Numerous components are known to participate in this process in a highly dynamic manner. In order to obtain a better insight in cell migration, mutants or drugs are used and their motive phenotype is then linked with the disturbing factors. One of the typical approaches to study motion paths of individual cells relies on fitting mean square displacements to a persistent random walk function. Since the numerous calculations involved often rely on diverse commercial software packages, the analysis can be expensive, labour-intensive and error-prone work. Additionally, due to the nature of algorithms employed the calculations involved are not readily reproducible without access to the exact software package(s) used. Results We here present the cell_motility software, an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data. The application features an intuitive graphical user interface as well as full user and developer documentation and both source and binary files can be freely downloaded from the project website at . Conclusion In providing a free, open source software solution for the automated processing of cell motion data, we aim to achieve two important goals: labs can greatly simplify their data analysis pipeline as switching between different computational software packages becomes obsolete (thus reducing the chances for human error during data manipulation and transfer) and secondly, to provide scientists in the field with a freely available common platform to perform their analyses, enabling more efficient data quality control through peer reviewing.
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Affiliation(s)
- Lennart Martens
- Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A, Baertsoenkaai 3, B-9000 Ghent, Belgium.
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Vermeulen W, Van Troys M, Bourry D, Dewitte D, Rossenu S, Goethals M, Borremans FAM, Vandekerckhove J, Martins JC, Ampe C. Identification of the PXW sequence as a structural gatekeeper of the headpiece C-terminal subdomain fold. J Mol Biol 2006; 359:1277-92. [PMID: 16697408 DOI: 10.1016/j.jmb.2006.04.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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: 01/08/2006] [Revised: 04/16/2006] [Accepted: 04/20/2006] [Indexed: 11/22/2022]
Abstract
The HeadPiece (HP) domain, present in several F-actin-binding multi-domain proteins, features a well-conserved, solvent-exposed PXWK motif in its C-terminal subdomain. The latter is an autonomously folding subunit comprised of three alpha-helices organised around a hydrophobic core, with the sequence motif preceding the last helix. We report the contributions of each conserved residue in the PXWK motif to human villin HP function and structure, as well as the structural implications of the naturally occurring Pro to Ala mutation in dematin HP. NMR shift perturbation mapping reveals that substitution of each residue by Ala induces only minor, local perturbations in the full villin HP structure. CD spectroscopic thermal analysis, however, shows that the Pro and Trp residues in the PXWK motif afford stabilising interactions. This indicates that, in addition to the residues in the hydrophobic core, the Trp-Pro stacking within the motif contributes to HP stability. This is reinforced by our data on isolated C-terminal HP subdomains where the Pro is also essential for structure formation, since the villin, but not the dematin, C-terminal subdomain is structured. Proper folding can be induced in the dematin C-terminal subdomain by exchanging the Ala for Pro. Conversely, the reverse substitution in the villin C-terminal subdomain leads to loss of structure. Thus, we demonstrate a crucial role for this proline residue in structural stability and folding potential of HP (sub)domains consistent with Pro-Trp stacking as a more general determinant of protein stability.
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Affiliation(s)
- Wim Vermeulen
- NMR and Structure Analysis Unit, Department of Organic Chemistry, Faculty of Sciences, Ghent University, Belgium
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