1
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Schaeffer A, Buracco S, Gazzola M, Gelin M, Vianay B, de Pascalis C, Blanchoin L, Théry M. Microtubule-driven cell shape changes and actomyosin flow synergize to position the centrosome. J Cell Biol 2025; 224:e202405126. [PMID: 40243666 PMCID: PMC12005118 DOI: 10.1083/jcb.202405126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 01/12/2025] [Accepted: 03/25/2025] [Indexed: 04/18/2025] Open
Abstract
The regulation of centrosome position is critical to the alignment of intracellular structures with extracellular cues. The exact nature and spatial distribution of the mechanical forces that balance at the centrosome are unknown. Here, we used laser-based nanoablations in adherent cells and found that forces along microtubules were damped by their anchoring to the actin network, rendering them ineffective in moving the microtubule aster. In contrast, the actomyosin contractile network was responsible for the generation of a centripetal flow that robustly drives the centrosome toward the geometrical center of the cell, even in the absence of microtubules. Unexpectedly, we discovered that the remodeling of cell shape around the centrosome was instrumental in aster centering. The radial array of microtubules and cytoplasmic dyneins appeared to direct this reorganization. This revised view of the respective roles of actin and microtubules in centrosome positioning offers a new perspective for understanding the establishment of cell polarity.
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Affiliation(s)
- Alexandre Schaeffer
- CytoMorpho Lab, CBI, UMR8132, Université Paris Sciences et Lettres, CEA/CNRS, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Institut Pierre Gilles De Gennes, Paris, France
| | - Simona Buracco
- CytoMorpho Lab, LPCV, UMR5168, Université Grenoble-Alpes, CEA/INRA/CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble, France
| | - Morgan Gazzola
- CytoMorpho Lab, CBI, UMR8132, Université Paris Sciences et Lettres, CEA/CNRS, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Institut Pierre Gilles De Gennes, Paris, France
| | - Matthieu Gelin
- CytoMorpho Lab, CBI, UMR8132, Université Paris Sciences et Lettres, CEA/CNRS, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Institut Pierre Gilles De Gennes, Paris, France
| | - Benoit Vianay
- CytoMorpho Lab, LPCV, UMR5168, Université Grenoble-Alpes, CEA/INRA/CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble, France
| | - Chiara de Pascalis
- CytoMorpho Lab, CBI, UMR8132, Université Paris Sciences et Lettres, CEA/CNRS, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Institut Pierre Gilles De Gennes, Paris, France
| | - Laurent Blanchoin
- CytoMorpho Lab, LPCV, UMR5168, Université Grenoble-Alpes, CEA/INRA/CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble, France
- CytoMorpho Lab, CBI, UMR8132, Université Paris Sciences et Lettres, CEA/CNRS, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Institut Pierre Gilles De Gennes, Paris, France
| | - Manuel Théry
- CytoMorpho Lab, LPCV, UMR5168, Université Grenoble-Alpes, CEA/INRA/CNRS, Interdisciplinary Research Institute of Grenoble, Grenoble, France
- CytoMorpho Lab, CBI, UMR8132, Université Paris Sciences et Lettres, CEA/CNRS, Ecole Supérieure de Physique et Chimie Industrielles de la Ville de Paris, Institut Pierre Gilles De Gennes, Paris, France
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2
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Zhou H, Liu R, Xu Y, Fan J, Liu X, Chen L, Wei Q. Viscoelastic mechanics of living cells. Phys Life Rev 2025; 53:91-116. [PMID: 40043484 DOI: 10.1016/j.plrev.2025.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2025] [Accepted: 02/25/2025] [Indexed: 05/18/2025]
Abstract
In cell mechanotransduction, cells respond to external forces or to perceive mechanical properties of their supporting substrates by remodeling themselves. This ability is endowed by modulating cells' viscoelastic properties, which dominates over various complex cellular processes. The viscoelasticity of living cells, a concept adapted from rheology, exhibits substantially spatial and temporal variability. This review aims not only to discuss the rheological properties of cells but also to clarify the complexity of cellular rheology, emphasizing its dependence on both the size scales and time scales of the measurements. Like typical viscoelastic materials, the storage and loss moduli of cells often exhibit robust power-law rheological characteristics with respect to loading frequency. This intrinsic feature is consistent across cell types and is attributed to internal structures, such as cytoskeleton, cortex, cytoplasm and nucleus, all of which contribute to the complexity of cellular rheology. Moreover, the rheological properties of cells are dynamic and play a crucial role in various cellular and tissue functions. In this review, we focus on elucidating time- and size-dependent aspects of cell rheology, the origins of intrinsic rheological properties and how these properties adapt to cellular functions, with the goal of interpretation of rheology into the language of cell biology.
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Affiliation(s)
- Hui Zhou
- State Key Laboratory of Polymer Materials and Engineering, College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Ruye Liu
- State Key Laboratory of Polymer Materials and Engineering, College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Yizhou Xu
- State Key Laboratory of Polymer Materials and Engineering, College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Jierui Fan
- State Key Laboratory of Polymer Materials and Engineering, College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Xinyue Liu
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai, 200072, China
| | - Longquan Chen
- School of Physics, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Qiang Wei
- State Key Laboratory of Polymer Materials and Engineering, College of Polymer Science and Engineering, Sichuan University, Chengdu 610065, China.
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3
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Stamatov R, Uzunova S, Kicheva Y, Karaboeva M, Blagoev T, Stoynov S. Supra-second tracking and live-cell karyotyping reveal principles of mitotic chromosome dynamics. Nat Cell Biol 2025; 27:654-667. [PMID: 40185948 PMCID: PMC11991918 DOI: 10.1038/s41556-025-01637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/11/2025] [Indexed: 04/07/2025]
Abstract
Mitotic chromosome dynamics are essential for the three-dimensional organization of the genome during the cell cycle, but the spatiotemporal characteristics of this process remain unclear due to methodological challenges. While Hi-C methods capture interchromosomal contacts, they lack single-cell temporal dynamics, whereas microscopy struggles with bleaching and phototoxicity. Here, to overcome these limitations, we introduce Facilitated Segmentation and Tracking of Chromosomes in Mitosis Pipeline (FAST CHIMP), pairing time-lapse super-resolution microscopy with deep learning. FAST CHIMP tracked all human chromosomes with 8-s resolution from prophase to telophase, identified 15 out of 23 homologue pairs in single cells and compared chromosomal positioning between mother and daughter cells. It revealed a centrosome-motion-dependent flow that governs the mapping between chromosome locations at prophase and their metaphase plate position. In addition, FAST CHIMP measured supra-second dynamics of intra- and interchromosomal contacts. This tool adds a dynamic dimension to the study of chromatin behaviour in live cells, promising advances beyond the scope of existing methods.
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Affiliation(s)
- Rumen Stamatov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Sonya Uzunova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Yoana Kicheva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Karaboeva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tavian Blagoev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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4
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Ray D, Sinha DK. Dynamic crosstalk between cytoskeletal filaments regulates dorsoventral cytoplasmic mechanics. J Cell Sci 2025; 138:JCS263464. [PMID: 39886815 DOI: 10.1242/jcs.263464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 01/24/2025] [Indexed: 02/01/2025] Open
Abstract
The cytoplasm exhibits viscoelastic properties, displaying both solid and liquid-like behaviour, and can actively regulate its mechanical attributes. The cytoskeleton is a major regulator among the numerous factors influencing cytoplasmic mechanics. We explore the interdependence of various cytoskeletal filaments and the impact of their density on cytoplasmic viscoelasticity. The heterogeneous distribution of these filaments gives rise to polarised mechanical properties of the cytoplasm along the dorsoventral axis. Actin filament disassembly softens the ventral cytoplasm while stiffening the mid cytoplasm, due to increased vimentin filament assembly. Disruption of microtubules or depletion of vimentin softens both the ventral and mid cytoplasm. Cytochalasin D (Cyto D) treatment results in a localised increase of vimentin assembly in the mid cytoplasm, which is dependent on the cytolinker plectin. Nocodazole treatment has a negligible effect on F-actin distribution but significantly alters the spatial arrangement of vimentin. We demonstrate that Cyto D treatment upregulates vimentin expression via reactive oxygen species-mediated activation of NF-κΒ. This article investigates how different cytoskeletal filaments influence the rheological characteristics of various cytoplasmic regions.
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Affiliation(s)
- Dipanjan Ray
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Deepak Kumar Sinha
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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5
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Afonso O, Dumoulin L, Kruse K, Gonzalez-Gaitan M. Cytoplasmic flow is a cell size sensor that scales anaphase. Nat Cell Biol 2025; 27:273-282. [PMID: 39890956 PMCID: PMC11821524 DOI: 10.1038/s41556-024-01605-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 11/22/2024] [Indexed: 02/03/2025]
Abstract
During early embryogenesis, fast mitotic cycles without interphase lead to a decrease in cell size, while scaling mechanisms must keep cellular structures proportional to cell size. For instance, as cells become smaller, if the position of nuclear envelope reformation (NER) did not adapt, NER would have to occur beyond the cell boundary. Here we found that NER position in anaphase scales with cell size via changes in chromosome motility, mediated by cytoplasmic flows that themselves scale with cell size. Flows are a consequence of friction between viscous cytoplasm and bulky cargo transported by dynein on astral microtubules. As an emerging property, confinement in cells of different sizes yields scaling of cytoplasmic flows. Thus, flows behave like a cell geometry sensor: astral microtubules approach the boundary causing flow velocity changes, which then affect the velocity of chromosome separation, thus scaling NER.
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Affiliation(s)
- Olga Afonso
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland.
| | - Ludovic Dumoulin
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
- Department of Theoretical Physics, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Karsten Kruse
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland
- Department of Theoretical Physics, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Marcos Gonzalez-Gaitan
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland.
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6
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Xie J, Najafi J, Nommick A, Lederer L, Salle J, Dmitrieff S, Lacroix B, Dumont J, Minc N. Cell shape modulates mitotic spindle positioning forces via intracellular hydrodynamics. Curr Biol 2025; 35:413-421.e6. [PMID: 39755120 DOI: 10.1016/j.cub.2024.11.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 10/21/2024] [Accepted: 11/22/2024] [Indexed: 01/06/2025]
Abstract
The regulation of mitotic spindle positioning and orientation is central to the morphogenesis of developing embryos and tissues.1,2,3,4,5 In many multicellular contexts, cell geometry has been shown to have a major influence on spindle positioning, with spindles that commonly align along the longest cell shape axis.6,7,8,9,10,11,12,13,14 To date, however, we still lack an understanding of how the nature and amplitude of intracellular forces that position, orient, or hold mitotic spindles depend on cell geometry. Here, we used in vivo magnetic tweezers to directly measure the forces that maintain the mitotic spindle in the center of sea urchin cells that adopt different shapes during early embryo development. We found that spindles are held by viscoelastic forces that progressively increase in amplitude as cells become more elongated during early development. By coupling direct cell shape manipulations in microfabricated chambers with in vivo force measurements, we establish how spindle-associated forces increase in dose dependence with cell shape anisotropy. Cytoplasm flow analysis and hydrodynamic simulations suggest that this geometry-dependent mechanical enhancement results from a stronger hydrodynamic coupling between the spindle and cell boundaries, which dampens cytoplasm flows and spindle mobility as cells become more elongated. These findings establish how cell shape affects spindle-associated forces and suggest a novel mechanism for shape sensing and division positioning mediated by intracellular hydrodynamics with functional implications for early embryo morphogenesis.
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Affiliation(s)
- Jing Xie
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, 75013 Paris, France
| | - Javad Najafi
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, 75013 Paris, France
| | - Aude Nommick
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, 75013 Paris, France
| | - Luc Lederer
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, 75013 Paris, France
| | - Jeremy Salle
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, 75013 Paris, France
| | - Serge Dmitrieff
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, 75013 Paris, France
| | - Benjamin Lacroix
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Julien Dumont
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Nicolas Minc
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, 75013 Paris, France.
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7
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Tang W, Wang J, Jiang A, Sun Y. Stiffening of the Cytoplasm in Response to Intracellularly Applied Forces. NANO LETTERS 2024. [PMID: 39377302 DOI: 10.1021/acs.nanolett.4c03979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
Abstract
Cells constantly encounter mechanical forces that regulate various cellular functions, such as migration, division, and differentiation. Understanding how cells respond to forces at the intracellular level is essential for elucidating the mechanical adaptability of living cells. This study investigates how the cytoplasm alters its mechanical properties in response to forces applied inside a cell. The mechanical properties were measured through in situ characterization using magnetic tweezers to apply mechanical forces on magnetic beads internalized into cells. The findings reveal that the cytoplasm stiffens within seconds when force is applied to the cytoplasm. Macromolecular crowding and cytoskeletal structures, particularly F-actin, were found to significantly contribute to cytoplasm stiffening. The stiffening response was also observed across multiple length scales by using magnetic beads of varying diameters. These results highlight the rapid adaptation of the cytoplasm to mechanical forces applied to the inside of a cell.
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Affiliation(s)
- Wentian Tang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, Canada
| | - Jintian Wang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, Canada
| | - Aojun Jiang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, Canada
| | - Yu Sun
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, M5S 3G4, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 3G4, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, M5S 3G9, Canada
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8
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Anjur-Dietrich MI, Gomez Hererra V, Farhadifar R, Wu H, Merta H, Bahmanyar S, Shelley MJ, Needleman DJ. Mechanics of spindle orientation in human mitotic cells is determined by pulling forces on astral microtubules and clustering of cortical dynein. Dev Cell 2024; 59:2429-2442.e4. [PMID: 38866013 DOI: 10.1016/j.devcel.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 04/03/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024]
Abstract
The forces that orient the spindle in human cells remain poorly understood due to a lack of direct mechanical measurements in mammalian systems. We use magnetic tweezers to measure the force on human mitotic spindles. Combining the spindle's measured resistance to rotation, the speed at which it rotates after laser ablating astral microtubules, and estimates of the number of ablated microtubules reveals that each microtubule contacting the cell cortex is subject to ∼5 pN of pulling force, suggesting that each is pulled on by an individual dynein motor. We find that the concentration of dynein at the cell cortex and extent of dynein clustering are key determinants of the spindle's resistance to rotation, with little contribution from cytoplasmic viscosity, which we explain using a biophysically based mathematical model. This work reveals how pulling forces on astral microtubules determine the mechanics of spindle orientation and demonstrates the central role of cortical dynein clustering.
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Affiliation(s)
- Maya I Anjur-Dietrich
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
| | - Vicente Gomez Hererra
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Reza Farhadifar
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Haiyin Wu
- Department of Physics, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Holly Merta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Shirin Bahmanyar
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Michael J Shelley
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Daniel J Needleman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
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9
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Chang Z, Li LY, Shi ZJ, Liu W, Xu GK. Beyond stiffness: Multiscale viscoelastic features as biomechanical markers for assessing cell types and states. Biophys J 2024; 123:1869-1881. [PMID: 38835167 PMCID: PMC11267428 DOI: 10.1016/j.bpj.2024.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cell mechanics are pivotal in regulating cellular activities, diseases progression, and cancer development. However, the understanding of how cellular viscoelastic properties vary in physiological and pathological stimuli remains scarce. Here, we develop a hybrid self-similar hierarchical theory-microrheology approach to accurately and efficiently characterize cellular viscoelasticity. Focusing on two key cell types associated with livers fibrosis-the capillarized liver sinusoidal endothelial cells and activated hepatic stellate cells-we uncover a universal two-stage power-law rheology characterized by two distinct exponents, αshort and αlong. The mechanical profiles derived from both exponents exhibit significant potential for discriminating among diverse cells. This finding suggests a potential common dynamic creep characteristic across biological systems, extending our earlier observations in soft tissues. Using a tailored hierarchical model for cellular mechanical structures, we discern significant variations in the viscoelastic properties and their distribution profiles across different cell types and states from the cytoplasm (elastic stiffness E1 and viscosity η), to a single cytoskeleton fiber (elastic stiffness E2), and then to the cell level (transverse expansion stiffness E3). Importantly, we construct a logistic-regression-based machine-learning model using the dynamic parameters that outperforms conventional cell-stiffness-based classifiers in assessing cell states, achieving an area under the curve of 97% vs. 78%. Our findings not only advance a robust framework for monitoring intricate cell dynamics but also highlight the crucial role of cellular viscoelasticity in discerning cell states across a spectrum of liver diseases and prognosis, offering new avenues for developing diagnostic and therapeutic strategies based on cellular viscoelasticity.
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Affiliation(s)
- Zhuo Chang
- Laboratory for Multiscale Mechanics and Medical Science, Department of Engineering Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Li-Ya Li
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhi-Jun Shi
- Laboratory for Multiscale Mechanics and Medical Science, Department of Engineering Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Wenjia Liu
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
| | - Guang-Kui Xu
- Laboratory for Multiscale Mechanics and Medical Science, Department of Engineering Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an, China.
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10
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Singam A, Bhattacharya C, Park S. Aging-related changes in the mechanical properties of single cells. Heliyon 2024; 10:e32974. [PMID: 38994100 PMCID: PMC11238009 DOI: 10.1016/j.heliyon.2024.e32974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
Mechanical properties, along with biochemical and molecular properties, play crucial roles in governing cellular function and homeostasis. Cellular mechanics are influenced by various factors, including physiological and pathological states, making them potential biomarkers for diseases and aging. While several methods such as AFM, particle-tracking microrheology, optical tweezers/stretching, magnetic tweezers/twisting cytometry, microfluidics, and micropipette aspiration have been widely utilized to measure the mechanical properties of single cells, our understanding of how aging affects these properties remains limited. To fill this knowledge gap, we provide a brief overview of the commonly used methods to measure single-cell mechanical properties. We then delve into the effects of aging on the mechanical properties of different cell types. Finally, we discuss the importance of studying cellular viscous and viscoelastic properties as well as aging induced by different stressors to gain a deeper understanding of the aging process and aging-related diseases.
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Affiliation(s)
- Amarnath Singam
- Department of Mechanical Engineering, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Chandrabali Bhattacharya
- Department of Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
- Interdisciplinary Biomedical Engineering Program, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Seungman Park
- Department of Mechanical Engineering, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
- Interdisciplinary Biomedical Engineering Program, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
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11
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Mendová K, Otáhal M, Drab M, Daniel M. Size Matters: Rethinking Hertz Model Interpretation for Cell Mechanics Using AFM. Int J Mol Sci 2024; 25:7186. [PMID: 39000293 PMCID: PMC11241038 DOI: 10.3390/ijms25137186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
Cell mechanics are a biophysical indicator of cell state, such as cancer metastasis, leukocyte activation, and cell cycle progression. Atomic force microscopy (AFM) is a widely used technique to measure cell mechanics, where the Young modulus of a cell is usually derived from the Hertz contact model. However, the Hertz model assumes that the cell is an elastic, isotropic, and homogeneous material and that the indentation is small compared to the cell size. These assumptions neglect the effects of the cytoskeleton, cell size and shape, and cell environment on cell deformation. In this study, we investigated the influence of cell size on the estimated Young's modulus using liposomes as cell models. Liposomes were prepared with different sizes and filled with phosphate buffered saline (PBS) or hyaluronic acid (HA) to mimic the cytoplasm. AFM was used to obtain the force indentation curves and fit them to the Hertz model. We found that the larger the liposome, the lower the estimated Young's modulus for both PBS-filled and HA-filled liposomes. This suggests that the Young modulus obtained from the Hertz model is not only a property of the cell material but also depends on the cell dimensions. Therefore, when comparing or interpreting cell mechanics using the Hertz model, it is essential to account for cell size.
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Affiliation(s)
- Katarína Mendová
- Department of Mechanics, Biomechanics and Mechatronics, Faculty of Mechanical Engineering, Czech Technical University in Prague, Technická 4, 16000 Prague, Czech Republic;
| | - Martin Otáhal
- Department of Natural Sciences, Faculty of Biomedical Engineering, Czech Technical University in Prague, Náměstí Sítná 3105, 27201 Kladno, Czech Republic;
| | - Mitja Drab
- Laboratory of Biophysics, Faculty of Electrical Engineering, University of Ljubljana, Trzaska 25, 1000 Ljubljana, Slovenia;
| | - Matej Daniel
- Department of Mechanics, Biomechanics and Mechatronics, Faculty of Mechanical Engineering, Czech Technical University in Prague, Technická 4, 16000 Prague, Czech Republic;
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12
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Sakai K, Kondo Y, Goto Y, Aoki K. Cytoplasmic fluidization contributes to breaking spore dormancy in fission yeast. Proc Natl Acad Sci U S A 2024; 121:e2405553121. [PMID: 38889144 PMCID: PMC11214080 DOI: 10.1073/pnas.2405553121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The cytoplasm is a complex, crowded environment that influences myriad cellular processes including protein folding and metabolic reactions. Recent studies have suggested that changes in the biophysical properties of the cytoplasm play a key role in cellular homeostasis and adaptation. However, it still remains unclear how cells control their cytoplasmic properties in response to environmental cues. Here, we used fission yeast spores as a model system of dormant cells to elucidate the mechanisms underlying regulation of the cytoplasmic properties. By tracking fluorescent tracer particles, we found that particle mobility decreased in spores compared to vegetative cells and rapidly increased at the onset of dormancy breaking upon glucose addition. This cytoplasmic fluidization depended on glucose-sensing via the cyclic adenosine monophosphate-protein kinase A pathway. PKA activation led to trehalose degradation through trehalase Ntp1, thereby increasing particle mobility as the amount of trehalose decreased. In contrast, the rapid cytoplasmic fluidization did not require de novo protein synthesis, cytoskeletal dynamics, or cell volume increase. Furthermore, the measurement of diffusion coefficients with tracer particles of different sizes suggests that the spore cytoplasm impedes the movement of larger protein complexes (40 to 150 nm) such as ribosomes, while allowing free diffusion of smaller molecules (~3 nm) such as second messengers and signaling proteins. Our experiments have thus uncovered a series of signaling events that enable cells to quickly fluidize the cytoplasm at the onset of dormancy breaking.
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Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
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13
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Raja Venkatesh A, Le KH, Weld DM, Brandman O. Diffusive lensing as a mechanism of intracellular transport and compartmentalization. eLife 2024; 12:RP89794. [PMID: 38896469 PMCID: PMC11186627 DOI: 10.7554/elife.89794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
While inhomogeneous diffusivity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales remain largely unexplored. In this work, we use agent-based simulations of diffusion to investigate how heterogeneous diffusivity affects the movement and concentration of diffusing particles. We propose that a nonequilibrium mode of membrane-less compartmentalization arising from the convergence of diffusive trajectories into low-diffusive sinks, which we call 'diffusive lensing,' is relevant for living systems. Our work highlights the phenomenon of diffusive lensing as a potentially key driver of mesoscale dynamics in the cytoplasm, with possible far-reaching implications for biochemical processes.
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Affiliation(s)
- Achuthan Raja Venkatesh
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) MohaliMohaliIndia
| | - Kathy H Le
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - David M Weld
- Department of Physics, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Onn Brandman
- Department of Biochemistry, Stanford UniversityStanfordUnited States
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14
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Vos BE, Muenker TM, Betz T. Characterizing intracellular mechanics via optical tweezers-based microrheology. Curr Opin Cell Biol 2024; 88:102374. [PMID: 38824902 DOI: 10.1016/j.ceb.2024.102374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 06/04/2024]
Abstract
Intracellular organization is a highly regulated homeostatic state maintained to ensure eukaryotic cells' correct and efficient functioning. Thanks to decades of research, vast knowledge of the proteins involved in intracellular transport and organization has been acquired. However, how these influence and potentially regulate the intracellular mechanical properties of the cell is largely unknown. There is a deep knowledge gap between the understanding of cortical mechanics, which is accessible by a series of experimental tools, and the intracellular situation that has been largely neglected due to the difficulty of performing intracellular mechanics measurements. Recently, tools required for such quantitative and localized analysis of intracellular mechanics have been introduced. Here, we review how these approaches and the resulting viscoelastic models lead the way to a full mechanical description of the cytoplasm, which is instrumental for a quantitative characterization of the intracellular life of cells.
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Affiliation(s)
- Bart E Vos
- Third Institute of Physics, Georg August University, Göttingen, Germany
| | - Till M Muenker
- Third Institute of Physics, Georg August University, Göttingen, Germany
| | - Timo Betz
- Third Institute of Physics, Georg August University, Göttingen, Germany; Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), Georg August University, Göttingen, Germany.
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15
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Ye Y, Homer HA. A surge in cytoplasmic viscosity triggers nuclear remodeling required for Dux silencing and pre-implantation embryo development. Cell Rep 2024; 43:113917. [PMID: 38446665 DOI: 10.1016/j.celrep.2024.113917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/17/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Embryonic genome activation (EGA) marks the transition from dependence on maternal transcripts to an embryonic transcriptional program. The precise temporal regulation of gene expression, specifically the silencing of the Dux/murine endogenous retrovirus type L (MERVL) program during late 2-cell interphase, is crucial for developmental progression in mouse embryos. How this finely tuned regulation is achieved within this specific window is poorly understood. Here, using particle-tracking microrheology throughout the mouse oocyte-to-embryo transition, we identify a surge in cytoplasmic viscosity specific to late 2-cell interphase brought about by high microtubule and endomembrane density. Importantly, preventing the rise in 2-cell viscosity severely impairs nuclear reorganization, resulting in a persistently open chromatin configuration and failure to silence Dux/MERVL. This, in turn, derails embryo development beyond the 2- and 4-cell stages. Our findings reveal a mechanical role of the cytoplasm in regulating Dux/MERVL repression via nuclear remodeling during a temporally confined period in late 2-cell interphase.
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Affiliation(s)
- Yunan Ye
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia
| | - Hayden Anthony Homer
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia.
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16
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de-Carvalho J, Tlili S, Saunders TE, Telley IA. The positioning mechanics of microtubule asters in Drosophila embryo explants. eLife 2024; 12:RP90541. [PMID: 38426416 PMCID: PMC10911390 DOI: 10.7554/elife.90541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Microtubule asters are essential in localizing the action of microtubules in processes including mitosis and organelle positioning. In large cells, such as the one-cell sea urchin embryo, aster dynamics are dominated by hydrodynamic pulling forces. However, in systems with more densely positioned nuclei such as the early Drosophila embryo, which packs around 6000 nuclei within the syncytium in a crystalline-like order, it is unclear what processes dominate aster dynamics. Here, we take advantage of a cell cycle regulation Drosophila mutant to generate embryos with multiple asters, independent from nuclei. We use an ex vivo assay to further simplify this biological system to explore the forces generated by and between asters. Through live imaging, drug and optical perturbations, and theoretical modeling, we demonstrate that these asters likely generate an effective pushing force over short distances.
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Affiliation(s)
- Jorge de-Carvalho
- Instituto Gulbenkian de Ciência, Fundação Calouste GulbenkianOeirasPortugal
| | - Sham Tlili
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Timothy E Saunders
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Institute of Molecular and Cellular Biology, A*Star, ProteosSingaporeSingapore
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of WarwickWarwickUnited Kingdom
| | - Ivo A Telley
- Instituto Gulbenkian de Ciência, Fundação Calouste GulbenkianOeirasPortugal
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17
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Xie J, Levy DL, Minc N, Sallé J. Manipulation of Embryonic Cleavage Geometry Using Magnetic Tweezers. Methods Mol Biol 2024; 2740:125-140. [PMID: 38393473 PMCID: PMC11059781 DOI: 10.1007/978-1-0716-3557-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The geometry of reductive divisions that mark the development of early embryos instructs cell fates, sizes, and positions, by mechanisms that remain unclear. In that context, new methods to mechanically manipulate these divisions are starting to emerge in different model systems. These are key to develop future innovative approaches and understand developmental mechanisms controlled by cleavage geometry. In particular, how cell cycle pace is regulated in rapidly reducing blastomeres and how fate diversity can arise from blastomere size and position within embryos are fundamental questions that remain at the heart of ongoing research. In this chapter, we provide a detailed protocol to assemble and use magnetic tweezers in the sea urchin model and generate spatially controlled asymmetric and oriented divisions during early embryonic development.
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Affiliation(s)
- Jing Xie
- CNRS, Institut Jacques Monod, Université Paris Cité, Paris, France
- Equipe Labellisée LIGUE Contre le Cancer, Paris, France
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Nicolas Minc
- CNRS, Institut Jacques Monod, Université Paris Cité, Paris, France
- Equipe Labellisée LIGUE Contre le Cancer, Paris, France
| | - Jérémy Sallé
- CNRS, Institut Jacques Monod, Université Paris Cité, Paris, France.
- Equipe Labellisée LIGUE Contre le Cancer, Paris, France.
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18
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Arjona MI, Najafi J, Minc N. Cytoplasm mechanics and cellular organization. Curr Opin Cell Biol 2023; 85:102278. [PMID: 37979412 DOI: 10.1016/j.ceb.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/20/2023]
Abstract
As cells organize spatially or divide, they translocate many micron-scale organelles in their cytoplasm. These include endomembrane vesicles, nuclei, microtubule asters, mitotic spindles, or chromosomes. Organelle motion is powered by cytoskeleton forces but is opposed by viscoelastic forces imparted by the surrounding crowded cytoplasm medium. These resistive forces associated to cytoplasm physcial properties remain generally underappreciated, yet reach significant values to slow down organelle motion or even limit their displacement by springing them back towards their original position. The cytoplasm may also be itself organized in time and space, being for example stiffer or more fluid at certain locations or during particular cell cycle phases. Thus, cytoplasm mechanics may be viewed as a labile module that contributes to organize cells. We here review emerging methods, mechanisms, and concepts to study cytoplasm mechanical properties and their function in organelle positioning, cellular organization and division.
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Affiliation(s)
- María Isabel Arjona
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Javad Najafi
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Nicolas Minc
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France.
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19
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Bonucci M, Shu T, Holt LJ. How it feels in a cell. Trends Cell Biol 2023; 33:924-938. [PMID: 37286396 PMCID: PMC10592589 DOI: 10.1016/j.tcb.2023.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Life emerges from thousands of biochemical processes occurring within a shared intracellular environment. We have gained deep insights from in vitro reconstitution of isolated biochemical reactions. However, the reaction medium in test tubes is typically simple and diluted. The cell interior is far more complex: macromolecules occupy more than a third of the space, and energy-consuming processes agitate the cell interior. Here, we review how this crowded, active environment impacts the motion and assembly of macromolecules, with an emphasis on mesoscale particles (10-1000 nm diameter). We describe methods to probe and analyze the biophysical properties of cells and highlight how changes in these properties can impact physiology and signaling, and potentially contribute to aging, and diseases, including cancer and neurodegeneration.
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Affiliation(s)
- Martina Bonucci
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA.
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20
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Anjur-Dietrich MI, Hererra VG, Farhadifar R, Wu H, Merta H, Bahmanyar S, Shelley MJ, Needleman DJ. Clustering of cortical dynein regulates the mechanics of spindle orientation in human mitotic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557210. [PMID: 37745442 PMCID: PMC10515834 DOI: 10.1101/2023.09.11.557210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The forces which orient the spindle in human cells remain poorly understood due to a lack of direct mechanical measurements in mammalian systems. We use magnetic tweezers to measure the force on human mitotic spindles. Combining the spindle's measured resistance to rotation, the speed it rotates after laser ablating astral microtubules, and estimates of the number of ablated microtubules reveals that each microtubule contacting the cell cortex is subject to ~1 pN of pulling force, suggesting that each is pulled on by an individual dynein motor. We find that the concentration of dynein at the cell cortex and extent of dynein clustering are key determinants of the spindle's resistance to rotation, with little contribution from cytoplasmic viscosity, which we explain using a biophysically based mathematical model. This work reveals how pulling forces on astral microtubules determine the mechanics of spindle orientation and demonstrates the central role of cortical dynein clustering.
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Affiliation(s)
- Maya I. Anjur-Dietrich
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Vicente Gomez Hererra
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Reza Farhadifar
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Haiyin Wu
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Holly Merta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Shirin Bahmanyar
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Michael J. Shelley
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Daniel J. Needleman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
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21
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Najafi J, Dmitrieff S, Minc N. Size- and position-dependent cytoplasm viscoelasticity through hydrodynamic interactions with the cell surface. Proc Natl Acad Sci U S A 2023; 120:e2216839120. [PMID: 36802422 PMCID: PMC9992773 DOI: 10.1073/pnas.2216839120] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 01/23/2023] [Indexed: 02/23/2023] Open
Abstract
Many studies of cytoplasm rheology have focused on small components in the submicrometer scale. However, the cytoplasm also baths large organelles like nuclei, microtubule asters, or spindles that often take significant portions of cells and move across the cytoplasm to regulate cell division or polarization. Here, we translated passive components of sizes ranging from few up to ~50 percents of the cell diameter, through the vast cytoplasm of live sea urchin eggs, with calibrated magnetic forces. Creep and relaxation responses indicate that for objects larger than the micron size, the cytoplasm behaves as a Jeffreys material, viscoelastic at short timescales, and fluidizing at longer times. However, as component size approached that of cells, cytoplasm viscoelastic resistance increased in a nonmonotonic manner. Flow analysis and simulations suggest that this size-dependent viscoelasticity emerges from hydrodynamic interactions between the moving object and the static cell surface. This effect also yields to position-dependent viscoelasticity with objects initially closer to the cell surface being harder to displace. These findings suggest that the cytoplasm hydrodynamically couples large organelles to the cell surface to restrain their motion, with important implications for cell shape sensing and cellular organization.
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Affiliation(s)
- Javad Najafi
- Université de Paris, CNRS, Institut Jacques Monod,75006Paris, France
- Equipe Labellisée Ligue Contre le Cancer, 75013Paris, France
| | - Serge Dmitrieff
- Université de Paris, CNRS, Institut Jacques Monod,75006Paris, France
- Equipe Labellisée Ligue Contre le Cancer, 75013Paris, France
| | - Nicolas Minc
- Université de Paris, CNRS, Institut Jacques Monod,75006Paris, France
- Equipe Labellisée Ligue Contre le Cancer, 75013Paris, France
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22
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Floyd C, Vaikuntanathan S, Dinner AR. Simulating structured fluids with tensorial viscoelasticity. J Chem Phys 2023; 158:054906. [PMID: 36754798 DOI: 10.1063/5.0123470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We consider an immersed elastic body that is actively driven through a structured fluid by a motor or an external force. The behavior of such a system generally cannot be solved analytically, necessitating the use of numerical methods. However, current numerical methods omit important details of the microscopic structure and dynamics of the fluid, which can modulate the magnitudes and directions of viscoelastic restoring forces. To address this issue, we develop a simulation platform for modeling viscoelastic media with tensorial elasticity. We build on the lattice Boltzmann algorithm and incorporate viscoelastic forces, elastic immersed objects, a microscopic orientation field, and coupling between viscoelasticity and the orientation field. We demonstrate our method by characterizing how the viscoelastic restoring force on a driven immersed object depends on various key parameters as well as the tensorial character of the elastic response. We find that the restoring force depends non-monotonically on the rate of diffusion of the stress and the size of the object. We further show how the restoring force depends on the relative orientation of the microscopic structure and the pulling direction. These results imply that accounting for previously neglected physical features, such as stress diffusion and the microscopic orientation field, can improve the realism of viscoelastic simulations. We discuss possible applications and extensions to the method.
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Affiliation(s)
- Carlos Floyd
- Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, USA
| | | | - Aaron R Dinner
- Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, USA
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23
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Di Bari D, Timr S, Guiral M, Giudici-Orticoni MT, Seydel T, Beck C, Petrillo C, Derreumaux P, Melchionna S, Sterpone F, Peters J, Paciaroni A. Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death. ACS CENTRAL SCIENCE 2023; 9:93-102. [PMID: 36712493 PMCID: PMC9881203 DOI: 10.1021/acscentsci.2c01078] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 05/30/2023]
Abstract
Temperature variations have a big impact on bacterial metabolism and death, yet an exhaustive molecular picture of these processes is still missing. For instance, whether thermal death is determined by the deterioration of the whole or a specific part of the proteome is hotly debated. Here, by monitoring the proteome dynamics of E. coli, we clearly show that only a minor fraction of the proteome unfolds at the cell death. First, we prove that the dynamical state of the E. coli proteome is an excellent proxy for temperature-dependent bacterial metabolism and death. The proteome diffusive dynamics peaks at about the bacterial optimal growth temperature, then a dramatic dynamical slowdown is observed that starts just below the cell's death temperature. Next, we show that this slowdown is caused by the unfolding of just a small fraction of proteins that establish an entangling interprotein network, dominated by hydrophobic interactions, across the cytoplasm. Finally, the deduced progress of the proteome unfolding and its diffusive dynamics are both key to correctly reproduce the E. coli growth rate.
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Affiliation(s)
- Daniele Di Bari
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
| | - Stepan Timr
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- J.
Heyrovský
Institute of Physical Chemistry, Czech Academy
of Sciences, 182 23Prague 8, Czechia
| | - Marianne Guiral
- Laboratoire
de Bioénergétique et Ingénierie des Protéines, BIP, CNRS, Aix-Marseille Université, 13400Marseille, France
| | | | - Tilo Seydel
- Institut
Laue-Langevin, 38000Grenoble, France
| | | | - Caterina Petrillo
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut Universitaire de France, 75005Paris, France
| | - Simone Melchionna
- ISC-CNR,
Dipartimento di Fisica, Università
Sapienza, 00185Rome, Italy
- Lexma
Technology1337 Massachusetts
Avenue, Arlington, Massachusetts02476, United States
| | - Fabio Sterpone
- Laboratoire
de Biochimie Théorique (UPR9080), CNRS, Université de Paris Cité, 13 Rue Pierre et Marie Curie, 75005Paris, France
- Institut
de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005Paris, France
| | - Judith Peters
- Université
Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38400Saint-Martin-d’Héres, France
- Institut
Laue-Langevin, 38000Grenoble, France
- Institut Universitaire de France, 75005Paris, France
| | - Alessandro Paciaroni
- Università
degli Studi di Perugia, Dipartimento di
Fisica e Geologia, Via
A. Pascoli, 06123Perugia PG, Italy
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24
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Qu J, Shao C, Ying Y, Wu Y, Liu W, Tian Y, Yin Z, Li X, Yu Z, Shuai J. The spring-like effect of microRNA-31 in balancing inflammatory and regenerative responses in colitis. Front Microbiol 2022; 13:1089729. [PMID: 36590397 PMCID: PMC9800619 DOI: 10.3389/fmicb.2022.1089729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders caused by the disruption of immune tolerance to the gut microbiota. MicroRNA-31 (MIR31) has been proven to be up-regulated in intestinal tissues from patients with IBDs and colitis-associated neoplasias. While the functional role of MIR31 in colitis and related diseases remain elusive. Combining mathematical modeling and experimental analysis, we systematically explored the regulatory mechanism of MIR31 in inflammatory and epithelial regeneration responses in colitis. Level of MIR31 presents an "adaptation" behavior in dextran sulfate sodium (DSS)-induced colitis, and the similar behavior is also observed for the key cytokines of p65 and STAT3. Simulation analysis predicts MIR31 suppresses the activation of p65 and STAT3 but accelerates the recovery of epithelia in colitis, which are validated by our experimental observations. Further analysis reveals that the number of proliferative epithelial cells, which characterizes the inflammatory process and the recovery of epithelia in colitis, is mainly determined by the inhibition of MIR31 on IL17RA. MIR31 promotes epithelial regeneration in low levels of DSS-induced colitis but inhibits inflammation with high DSS levels, which is dominated by the competition for MIR31 to either inhibit inflammation or promote epithelial regeneration by binding to different targets. The binding probability determines the functional transformation of MIR31, but the functional strength is determined by MIR31 levels. Thus, the role of MIR31 in the inflammatory response can be described as the "spring-like effect," where DSS, MIR31 action strength, and proliferative epithelial cell number are regarded as external force, intrinsic spring force, and spring length, respectively. Overall, our study uncovers the vital roles of MIR31 in balancing inflammation and the recovery of epithelia in colitis, providing potential clues for the development of therapeutic targets in drug design.
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Affiliation(s)
- Jing Qu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Chunlei Shao
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yongfa Ying
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yuning Wu
- Department of Mathematics and Physics, Fujian Jiangxia University, Fuzhou, China
| | - Wen Liu
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Yuhua Tian
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhiyong Yin
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Xiang Li
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jianwei Shuai
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), University of Chinese Academy of Sciences, Wenzhou, China
- Wenzhou Institute, Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, China
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25
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Yamamoto S, Gaillard J, Vianay B, Guerin C, Orhant-Prioux M, Blanchoin L, Théry M. Actin network architecture can ensure robust centering or sensitive decentering of the centrosome. EMBO J 2022; 41:e111631. [PMID: 35916262 PMCID: PMC9574749 DOI: 10.15252/embj.2022111631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 01/17/2023] Open
Abstract
The orientation of cell polarity depends on the position of the centrosome, the main microtubule-organizing center (MTOC). Microtubules (MTs) transmit pushing forces to the MTOC as they grow against the cell periphery. How the actin network regulates these forces remains unclear. Here, in a cell-free assay, we used purified proteins to reconstitute the interaction of a microtubule aster with actin networks of various architectures in cell-sized microwells. In the absence of actin filaments, MTOC positioning was highly sensitive to variations in microtubule length. The presence of a bulk actin network limited microtubule displacement, and MTOCs were held in place. In contrast, the assembly of a branched actin network along the well edges centered the MTOCs by maintaining an isotropic balance of pushing forces. An anisotropic peripheral actin network caused the MTOC to decenter by focusing the pushing forces. Overall, our results show that actin networks can limit the sensitivity of MTOC positioning to microtubule length and enforce robust MTOC centering or decentering depending on the isotropy of its architecture.
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Affiliation(s)
- Shohei Yamamoto
- Interdisciplinary Research Institute of Grenoble, UMR5168-LPCV, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Jérémie Gaillard
- Interdisciplinary Research Institute of Grenoble, UMR5168-LPCV, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Benoit Vianay
- Institut de Recherche Saint Louis, UMRS1160-HIPI, CytoMorpho Lab, University of Paris, CEA, INSERM, Paris, France
| | - Christophe Guerin
- Interdisciplinary Research Institute of Grenoble, UMR5168-LPCV, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Magali Orhant-Prioux
- Interdisciplinary Research Institute of Grenoble, UMR5168-LPCV, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Laurent Blanchoin
- Interdisciplinary Research Institute of Grenoble, UMR5168-LPCV, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France.,Institut de Recherche Saint Louis, UMRS1160-HIPI, CytoMorpho Lab, University of Paris, CEA, INSERM, Paris, France
| | - Manuel Théry
- Interdisciplinary Research Institute of Grenoble, UMR5168-LPCV, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France.,Institut de Recherche Saint Louis, UMRS1160-HIPI, CytoMorpho Lab, University of Paris, CEA, INSERM, Paris, France
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26
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Kelkar M, Bohec P, Smith MB, Sreenivasan V, Lisica A, Valon L, Ferber E, Baum B, Salbreux G, Charras G. Spindle reorientation in response to mechanical stress is an emergent property of the spindle positioning mechanisms. Proc Natl Acad Sci U S A 2022; 119:e2121868119. [PMID: 35727980 PMCID: PMC9245638 DOI: 10.1073/pnas.2121868119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
Proper orientation of the mitotic spindle plays a crucial role in embryos, during tissue development, and in adults, where it functions to dissipate mechanical stress to maintain tissue integrity and homeostasis. While mitotic spindles have been shown to reorient in response to external mechanical stresses, the subcellular cues that mediate spindle reorientation remain unclear. Here, we used a combination of optogenetics and computational modeling to investigate how mitotic spindles respond to inhomogeneous tension within the actomyosin cortex. Strikingly, we found that the optogenetic activation of RhoA only influences spindle orientation when it is induced at both poles of the cell. Under these conditions, the sudden local increase in cortical tension induced by RhoA activation reduces pulling forces exerted by cortical regulators on astral microtubules. This leads to a perturbation of the balance of torques exerted on the spindle, which causes it to rotate. Thus, spindle rotation in response to mechanical stress is an emergent phenomenon arising from the interaction between the spindle positioning machinery and the cell cortex.
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Affiliation(s)
- Manasi Kelkar
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | - Pierre Bohec
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | | | - Varun Sreenivasan
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE1 1UL, United Kingdom
- Medical Research Council Centre for Neurodevelopmental Disorders, King’s College London, London SE1 1UL, United Kingdom
| | - Ana Lisica
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | - Léo Valon
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 75015 Paris , France
| | - Emma Ferber
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | - Buzz Baum
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Guillaume Salbreux
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Genetics and Evolution, Quai Ernest-Ansermet 30, 1205 Geneva, Switzerland
| | - Guillaume Charras
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom
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27
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Mittag T, Pappu RV. A conceptual framework for understanding phase separation and addressing open questions and challenges. Mol Cell 2022; 82:2201-2214. [PMID: 35675815 PMCID: PMC9233049 DOI: 10.1016/j.molcel.2022.05.018] [Citation(s) in RCA: 351] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/04/2022] [Accepted: 05/13/2022] [Indexed: 12/11/2022]
Abstract
Macromolecular phase separation is being recognized for its potential importance and relevance as a driver of spatial organization within cells. Here, we describe a framework based on synergies between networking (percolation or gelation) and density (phase separation) transitions. Accordingly, the phase transitions in question are referred to as phase separation coupled to percolation (PSCP). The condensates that result from PSCP are viscoelastic network fluids. Such systems have sequence-, composition-, and topology-specific internal network structures that give rise to time-dependent interplays between viscous and elastic properties. Unlike pure phase separation, the process of PSCP gives rise to sequence-, chemistry-, and structure-specific distributions of clusters that can form at concentrations that lie well below the threshold concentration for phase separation. PSCP, influenced by specific versus solubility-determining interactions, also provides a bridge between different observations and helps answer questions and address challenges that have arisen regarding the role of macromolecular phase separation in biology.
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Affiliation(s)
- Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA.
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28
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Bai L, Mitchison TJ. Spring-like behavior of cytoplasm holds the mitotic spindle in place. Proc Natl Acad Sci U S A 2022; 119:e2203036119. [PMID: 35324318 PMCID: PMC9169080 DOI: 10.1073/pnas.2203036119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Luolan Bai
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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