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Bonaiuti P, Chiroli E, Gross F, Corno A, Vernieri C, Štefl M, Cosentino Lagomarsino M, Knop M, Ciliberto A. Cells Escape an Operational Mitotic Checkpoint through a Stochastic Process. Curr Biol 2017; 28:28-37.e7. [PMID: 29249657 DOI: 10.1016/j.cub.2017.11.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022]
Abstract
Improperly attached chromosomes activate the mitotic checkpoint that arrests cell division before anaphase. Cells can maintain an arrest for several hours but eventually will resume proliferation, a process we refer to as adaptation. Whether adapting cells bypass an active block or whether the block has to be removed to resume proliferation is not clear. Likewise, it is not known whether all cells of a genetically homogeneous population are equally capable to adapt. Here, we show that the mitotic checkpoint is operational when yeast cells adapt and that each cell has the same propensity to adapt. Our results are consistent with a model of the mitotic checkpoint where adaptation is driven by random fluctuations of APC/CCdc20, the molecular species inhibited by the checkpoint. Our data provide a quantitative framework for understanding how cells overcome a constant stimulus that halts cell cycle progression.
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Affiliation(s)
- Paolo Bonaiuti
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Elena Chiroli
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Fridolin Gross
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Andrea Corno
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy
| | - Claudio Vernieri
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy; Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, via Venezian 1, 20133 Milan, Italy
| | - Martin Štefl
- DKFZ-ZMBH Alliance, Centre for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marco Cosentino Lagomarsino
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy; Sorbonne Universités, UPMC Univ Paris 06, 5 Place Jussieu, 75005 Paris, France; CNRS, UMR 7238 "Biologie Computationnelle et Quantitative," UPMC, Institut de Biologie Paris Seine, 4 Place Jussieu, 75005 Paris, France
| | - Michael Knop
- DKFZ-ZMBH Alliance, Centre for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; DKFZ-ZMBH Alliance, Department of Cell and Tumour Biology, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Andrea Ciliberto
- Istituto Firc di Oncologia Molecolare, IFOM, via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso 207, 27100 Pavia, Italy.
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Kallepitis C, Bergholt MS, Mazo MM, Leonardo V, Skaalure SC, Maynard SA, Stevens MM. Quantitative volumetric Raman imaging of three dimensional cell cultures. Nat Commun 2017; 8:14843. [PMID: 28327660 PMCID: PMC5364421 DOI: 10.1038/ncomms14843] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/03/2017] [Indexed: 02/07/2023] Open
Abstract
The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.
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Affiliation(s)
- Charalambos Kallepitis
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Mads S. Bergholt
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Manuel M. Mazo
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Vincent Leonardo
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Stacey C. Skaalure
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Stephanie A. Maynard
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Molly M. Stevens
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
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Jacobson E, Perry JK, Long DS, Vickers MH, O'Sullivan JM. A potential role for genome structure in the translation of mechanical force during immune cell development. Nucleus 2016; 7:462-475. [PMID: 27673560 PMCID: PMC5120600 DOI: 10.1080/19491034.2016.1238998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/11/2016] [Accepted: 09/13/2016] [Indexed: 12/29/2022] Open
Abstract
Immune cells react to a wide range of environments, both chemical and physical. While the former has been extensively studied, there is growing evidence that physical and in particular mechanical forces also affect immune cell behavior and development. In order to elicit a response that affects immune cell behavior or development, environmental signals must often reach the nucleus. Chemical and mechanical signals can initiate signal transduction pathways, but mechanical forces may also have a more direct route to the nucleus, altering nuclear shape via mechanotransduction. The three-dimensional organization of DNA allows for the possibility that altering nuclear shape directly remodels chromatin, redistributing critical regulatory elements and proteins, and resulting in wide-scale gene expression changes. As such, integrating mechanotransduction and genome architecture into the immunology toolkit will improve our understanding of immune development and disease.
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Affiliation(s)
- Elsie Jacobson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Jo K. Perry
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - David S. Long
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Mark H. Vickers
- Liggins Institute, University of Auckland, Auckland, New Zealand
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Barrero JJ, Papanikou E, Casler JC, Day KJ, Glick BS. An improved reversibly dimerizing mutant of the FK506-binding protein FKBP. CELLULAR LOGISTICS 2016; 6:e1204848. [PMID: 27738551 PMCID: PMC5058350 DOI: 10.1080/21592799.2016.1204848] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 01/10/2023]
Abstract
FK506-binding protein (FKBP) is a monomer that binds to FK506, rapamycin, and related ligands. The F36M substitution, in which Phe36 in the ligand-binding pocket is changed to Met, leads to formation of antiparallel FKBP dimers, which can be dissociated into monomers by ligand binding. This FKBP(M) mutant has been employed in the mammalian secretory pathway to generate aggregates that can be dissolved by ligand addition to create cargo waves. However, when testing this approach in yeast, we found that dissolution of FKBP(M) aggregates was inefficient. An improved reversibly dimerizing FKBP formed aggregates that dissolved more readily. This FKBP(L,V) mutant carries the F36L mutation, which increases the affinity of ligand binding, and the I90V mutation, which accelerates ligand-induced dissociation of the dimers. The FKBP(L,V) mutant expands the utility of reversibly dimerizing FKBP.
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Affiliation(s)
- Juan J Barrero
- Department of Molecular Genetics and Cell Biology, University of Chicago , Chicago, IL, USA
| | - Effrosyni Papanikou
- Department of Molecular Genetics and Cell Biology, University of Chicago , Chicago, IL, USA
| | - Jason C Casler
- Department of Molecular Genetics and Cell Biology, University of Chicago , Chicago, IL, USA
| | - Kasey J Day
- Department of Molecular Genetics and Cell Biology, University of Chicago , Chicago, IL, USA
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago , Chicago, IL, USA
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Fievet A, Ducret A, Mignot T, Valette O, Robert L, Pardoux R, Dolla AR, Aubert C. Single-Cell Analysis of Growth and Cell Division of the Anaerobe Desulfovibrio vulgaris Hildenborough. Front Microbiol 2015; 6:1378. [PMID: 26696987 PMCID: PMC4672049 DOI: 10.3389/fmicb.2015.01378] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/20/2015] [Indexed: 01/08/2023] Open
Abstract
Recent years have seen significant progress in understanding basic bacterial cell cycle properties such as cell growth and cell division. While characterization and regulation of bacterial cell cycle is quite well-documented in the case of fast growing aerobic model organisms, no data has been so far reported for anaerobic bacteria. This lack of information in anaerobic microorganisms can mainly be explained by the absence of molecular and cellular tools such as single cell microscopy and fluorescent probes usable for anaerobes and essential to study cellular events and/or subcellular localization of the actors involved in cell cycle. In this study, single-cell microscopy has been adapted to study for the first time, in real time, the cell cycle of a bacterial anaerobe, Desulfovibrio vulgaris Hildenborough (DvH). This single-cell analysis provides mechanistic insights into the cell division cycle of DvH, which seems to be governed by the recently discussed so-called incremental model that generates remarkably homogeneous cell sizes. Furthermore, cell division was reversibly blocked during oxygen exposure. This may constitute a strategy for anaerobic cells to cope with transient exposure to oxygen that they may encounter in their natural environment, thereby contributing to their aerotolerance. This study lays the foundation for the first molecular, single-cell assay that will address factors that cannot otherwise be resolved in bulk assays and that will allow visualization of a wide range of molecular mechanisms within living anaerobic cells.
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Affiliation(s)
- Anouchka Fievet
- Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne UMR 7283, Aix Marseille Université Marseille, France
| | - Adrien Ducret
- Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne UMR 7283, Aix Marseille Université Marseille, France
| | - Tâm Mignot
- Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne UMR 7283, Aix Marseille Université Marseille, France
| | - Odile Valette
- Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne UMR 7283, Aix Marseille Université Marseille, France
| | - Lydia Robert
- INRA, UMR1319 Micalis Jouy-en-Josas, France ; AgroParisTech, UMR Micalis Jouy-en-Josas, France
| | - Romain Pardoux
- Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne UMR 7283, Aix Marseille Université Marseille, France
| | - Alain R Dolla
- Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne UMR 7283, Aix Marseille Université Marseille, France
| | - Corinne Aubert
- Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne UMR 7283, Aix Marseille Université Marseille, France
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Methods for rectifying cell motions in vitro: breaking symmetry using microfabrication and microfluidics. Methods Cell Biol 2015. [PMID: 25640443 DOI: 10.1016/bs.mcb.2014.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cell motility is an important phenomenon in cell biology, developmental biology, and cancer. Here we report methods that we designed to identify and characterize external factors which direct cell motions by breaking locally the symmetry. We used microfabrication and microfluidics techniques to impose and combine mechanical and chemical cues to moving fibroblasts. Gradients can thereby be engineered at the cellular scale and this approach has allowed to disentangle roles of the nucleus and protrusion activity in setting cell directions.
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Bheda P, Schneider R. Epigenetics reloaded: the single-cell revolution. Trends Cell Biol 2014; 24:712-23. [PMID: 25283892 DOI: 10.1016/j.tcb.2014.08.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 01/15/2023]
Abstract
Mechanistically, how epigenetic states are inherited through cellular divisions remains an important open question in the chromatin field and beyond. Defining the heritability of epigenetic states and the underlying chromatin-based mechanisms within a population of cells is complicated due to cell heterogeneity combined with varying levels of stability of these states; thus, efforts must be focused toward single-cell analyses. The approaches presented here constitute the forefront of epigenetics research at the single-cell level using classic and innovative methods to dissect epigenetics mechanisms from the limited material available in a single cell. This review further outlines exciting future avenues of research to address the significance of epigenetic heterogeneity and the contributions of microfluidics technologies to single-cell isolation and analysis.
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Affiliation(s)
- Poonam Bheda
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104/Inserm U964/Université de Strasbourg, 67400 Illkirch, France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104/Inserm U964/Université de Strasbourg, 67400 Illkirch, France.
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Gasset-Rosa F, Coquel AS, Moreno-Del Álamo M, Chen P, Song X, Serrano AM, Fernández-Tresguerres ME, Moreno-Díaz de la Espina S, Lindner AB, Giraldo R. Direct assessment in bacteria of prionoid propagation and phenotype selection by Hsp70 chaperone. Mol Microbiol 2014; 91:1070-87. [PMID: 24417419 DOI: 10.1111/mmi.12518] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2014] [Indexed: 11/28/2022]
Abstract
Protein amyloid aggregates epigenetically determine either advantageous or proteinopathic phenotypes. Prions are infectious amyloidogenic proteins, whereas prionoids lack infectivity but spread from mother to daughter cells. While prion amyloidosis has been studied in yeast and mammalian cells models, the dynamics of transmission of an amyloid proteinopathy has not been addressed yet in bacteria. Using time-lapse microscopy and a microfluidic set-up, we have assessed in Escherichia coli the vertical transmission of the amyloidosis caused by the synthetic bacterial model prionoid RepA-WH1 at single cell resolution within their lineage context. We identify in vivo the coexistence of two strain-like types of amyloid aggregates within a genetically identical population and a controlled homogeneous environment. The amyloids are either toxic globular particles or single comet-shaped aggregates that split during cytokinesis and exhibit milder toxicity. Both segregate and propagate in sublineages, yet show interconversion. ClpB (Hsp104) chaperone, key for spreading of yeast prions, has no effect on the dynamics of the two RepA-WH1 aggregates. However, the propagation of the comet-like species is DnaK (Hsp70)-dependent. The bacterial RepA-WH1 prionoid thus provides key qualitative and quantitative clues on the biology of intracellular amyloid proteinopathies.
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Affiliation(s)
- Fátima Gasset-Rosa
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas - CSIC, C/ Ramiro de Maeztu 9, Madrid, E-28040, Spain
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