1
|
Lao Z, Kamat KD, Jiang Z, Zhang B. OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 2024; 13:RP93223. [PMID: 39146200 PMCID: PMC11326778 DOI: 10.7554/elife.93223] [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: 08/17/2024] Open
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of 'fixed points' within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
Collapse
Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Kartik D Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| |
Collapse
|
2
|
Combriat T, Olsen PA, Låstad SB, Malthe-Sørenssen A, Krauss S, Dysthe DK. Acoustic Wave-Induced Stroboscopic Optical Mechanotyping of Adherent Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307929. [PMID: 38417124 DOI: 10.1002/advs.202307929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/02/2024] [Indexed: 03/01/2024]
Abstract
In this study, a novel, high content technique using a cylindrical acoustic transducer, stroboscopic fast imaging, and homodyne detection to recover the mechanical properties (dynamic shear modulus) of living adherent cells at low ultrasonic frequencies is presented. By analyzing the micro-oscillations of cells, whole populations are simultaneously mechanotyped with sub-cellular resolution. The technique can be combined with standard fluorescence imaging allowing to further cross-correlate biological and mechanical information. The potential of the technique is demonstrated by mechanotyping co-cultures of different cell types with significantly different mechanical properties.
Collapse
Affiliation(s)
- Thomas Combriat
- Njord Centre, Department of Physics, University of Oslo, P.O. Box 1048 Blindern, Oslo, 0316, Norway
- Hybrid Technology Hub, University of Oslo, Institute of Basic Medical Sciences P.O. Box 1110 Blindern, Oslo, 0317, Norway
- Center for Computing in Science Education, University of Oslo, P.O. Box 1048 Blindern, Oslo, 0316, Norway
| | - Petter Angell Olsen
- Hybrid Technology Hub, University of Oslo, Institute of Basic Medical Sciences P.O. Box 1110 Blindern, Oslo, 0317, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, P.O. Box 4950, Nydalen, Oslo, 0424, Norway
| | - Silja Borring Låstad
- Njord Centre, Department of Physics, University of Oslo, P.O. Box 1048 Blindern, Oslo, 0316, Norway
| | - Anders Malthe-Sørenssen
- Njord Centre, Department of Physics, University of Oslo, P.O. Box 1048 Blindern, Oslo, 0316, Norway
- Center for Computing in Science Education, University of Oslo, P.O. Box 1048 Blindern, Oslo, 0316, Norway
| | - Stefan Krauss
- Hybrid Technology Hub, University of Oslo, Institute of Basic Medical Sciences P.O. Box 1110 Blindern, Oslo, 0317, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, P.O. Box 4950, Nydalen, Oslo, 0424, Norway
| | - Dag Kristian Dysthe
- Njord Centre, Department of Physics, University of Oslo, P.O. Box 1048 Blindern, Oslo, 0316, Norway
| |
Collapse
|
3
|
Lao Z, Kamat K, Jiang Z, Zhang B. OpenNucleome for high resolution nuclear structural and dynamical modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562451. [PMID: 37905090 PMCID: PMC10614770 DOI: 10.1101/2023.10.16.562451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of "fixed points" within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
Collapse
Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
4
|
Wallace M, Fedorchak GR, Agrawal R, Gilbert RM, Patel J, Park S, Paszek M, Lammerding J. The lamin A/C Ig-fold undergoes cell density-dependent changes that alter epitope binding. Nucleus 2023; 14:2180206. [PMID: 36809122 PMCID: PMC9980629 DOI: 10.1080/19491034.2023.2180206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Lamins A/C are nuclear intermediate filament proteins that are involved in diverse cellular mechanical and biochemical functions. Here, we report that recognition of Lamins A/C by a commonly used antibody (JOL-2) that binds the Lamin A/C Ig-fold and other antibodies targeting similar epitopes is highly dependent on cell density, even though Lamin A/Clevels do not change. We propose that the effect is caused by partial unfolding or masking of the C'E and/or EF loops of the Ig-fold in response to cell spreading. Surprisingly, JOL-2 antibody labeling was insensitive to disruption of cytoskeletal filaments or the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. Furthermore, neither nuclear stiffness nor nucleo-cytoskeletal force transmission changed with cell density. These findings are important for the interpretation of immunofluorescence data for Lamin A/C and also raise the intriguing prospect that the conformational changes may play a role in Lamin A/C mediated cellular function.
Collapse
Affiliation(s)
- Melanie Wallace
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Gregory R. Fedorchak
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Richa Agrawal
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Rachel M. Gilbert
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Jineet Patel
- Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA
| | - Sangwoo Park
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, USA
| | - Matthew Paszek
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, USA,Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Jan Lammerding
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA,Weill Institute for Cell and Molecular Biology, Ithaca, NY, USA,CONTACT Jan Lammerding Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14853, USA
| |
Collapse
|
5
|
Buxboim A, Kronenberg-Tenga R, Salajkova S, Avidan N, Shahak H, Thurston A, Medalia O. Scaffold, mechanics and functions of nuclear lamins. FEBS Lett 2023; 597:2791-2805. [PMID: 37813648 DOI: 10.1002/1873-3468.14750] [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: 06/16/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Nuclear lamins are type-V intermediate filaments that are involved in many nuclear processes. In mammals, A- and B-type lamins assemble into separate physical meshwork underneath the inner nuclear membrane, the nuclear lamina, with some residual fraction localized within the nucleoplasm. Lamins are the major part of the nucleoskeleton, providing mechanical strength and flexibility to protect the genome and allow nuclear deformability, while also contributing to gene regulation via interactions with chromatin. While lamins are the evolutionary ancestors of all intermediate filament family proteins, their ultimate filamentous assembly is markedly different from their cytoplasmic counterparts. Interestingly, hundreds of genetic mutations in the lamina proteins have been causally linked with a broad range of human pathologies, termed laminopathies. These include muscular, neurological and metabolic disorders, as well as premature aging diseases. Recent technological advances have contributed to resolving the filamentous structure of lamins and the corresponding lamina organization. In this review, we revisit the multiscale lamin organization and discuss its implications on nuclear mechanics and chromatin organization within lamina-associated domains.
Collapse
Affiliation(s)
- Amnon Buxboim
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Sarka Salajkova
- Department of Biochemistry, University of Zurich, Switzerland
| | - Nili Avidan
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Hen Shahak
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Alice Thurston
- Department of Biochemistry, University of Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Switzerland
| |
Collapse
|
6
|
Bastianello G, Foiani M. Mechanisms controlling the mechanical properties of the nuclei. Curr Opin Cell Biol 2023; 84:102222. [PMID: 37619290 DOI: 10.1016/j.ceb.2023.102222] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/26/2023]
Abstract
The mechanical properties of the nucleus influence different cellular and nuclear functions and have relevant implications for several human diseases. The nucleus protects genetic information while acting as a mechano-sensory hub in response to internal and external forces. Cells have evolved mechano-transduction signaling to respond to physical cellular and nuclear perturbations and adopted a multitude of molecular pathways to maintain nuclear shape stability and prevent morphological abnormalities of the nucleus. Here we describe those key biological processes that control nuclear mechanics and discuss emerging perspectives on the mechanobiology of the nucleus as a diagnostic tool and clinical target.
Collapse
Affiliation(s)
- Giulia Bastianello
- IFOM, The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Oncology and Haemato-Oncology Department, University of Milan, Milan 20122, Italy.
| | - Marco Foiani
- IFOM, The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Oncology and Haemato-Oncology Department, University of Milan, Milan 20122, Italy.
| |
Collapse
|
7
|
Blunt EL, Choi J, Sussman H, Christopherson RC, Keen P, Rahmati Ishka M, Li LY, Idrovo JM, Julkowska MM, Van Eck J, Richards EJ. The nuclear lamina is required for proper development and nuclear shape distortion in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5500-5513. [PMID: 37503569 PMCID: PMC10540737 DOI: 10.1093/jxb/erad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
The nuclear lamina in plant cells is composed of plant-specific proteins, including nuclear matrix constituent proteins (NMCPs), which have been postulated to be functional analogs of lamin proteins that provide structural integrity to the organelle and help stabilize the three-dimensional organization of the genome. Using genomic editing, we generated alleles for the three genes encoding NMCPs in cultivated tomato (Solanum lycopersicum) to determine if the consequences of perturbing the nuclear lamina in this crop species were similar to or distinct from those observed in the model Arabidopsis thaliana. Loss of the sole NMCP2-class protein was lethal in tomato but is tolerated in Arabidopsis. Moreover, depletion of NMCP1-type nuclear lamina proteins leads to distinct developmental phenotypes in tomato, including leaf morphology defects and reduced root growth rate (in nmcp1b mutants), compared with cognate mutants in Arabidopsis. These findings suggest that the nuclear lamina interfaces with different developmental and signaling pathways in tomato compared with Arabidopsis. At the subcellular level, however, tomato nmcp mutants resembled their Arabidopsis counterparts in displaying smaller and more spherical nuclei in differentiated cells. This result argues that the plant nuclear lamina facilitates nuclear shape distortion in response to forces exerted on the organelle within the cell.
Collapse
Affiliation(s)
- Endia L Blunt
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Junsik Choi
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Hayley Sussman
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | | | - Patricia Keen
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | | | - Linda Y Li
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Joanna M Idrovo
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | | | - Joyce Van Eck
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Eric J Richards
- The Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| |
Collapse
|
8
|
Svoren M, Camerini E, van Erp M, Yang FW, Bakker GJ, Wolf K. Approaches to Determine Nuclear Shape in Cells During Migration Through Collagen Matrices. Methods Mol Biol 2023; 2608:97-114. [PMID: 36653704 DOI: 10.1007/978-1-0716-2887-4_7] [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] [Indexed: 01/20/2023]
Abstract
Fibrillar collagen is an abundant extracellular matrix (ECM) component of interstitial tissues which supports the structure of many organs, including the skin and breast. Many different physiological processes, but also pathological processes such as metastatic cancer invasion, involve interstitial cell migration. Often, cell movement takes place through small ECM gaps and pores and depends upon the ability of the cell and its stiff nucleus to deform. Such nuclear deformation during cell migration may impact nuclear integrity, such as of chromatin or the nuclear envelope, and therefore the morphometric analysis of nuclear shapes can provide valuable insight into a broad variety of biological processes. Here, we describe a protocol on how to generate a cell-collagen model in vitro and how to use confocal microscopy for the static and dynamic visualization of labeled nuclei in single migratory cells. We developed, and here provide, two scripts that (Fidler, Nat Rev Cancer 3(6):453-458, 2003) enable the semi-automated and fast quantification of static single nuclear shape descriptors, such as aspect ratio or circularity, and the nuclear irregularity index that forms a combination of four distinct shape descriptors, as well as (Frantz et al., J Cell Sci 123 (Pt 24):4195-4200, 2010) a quantification of their changes over time. Finally, we provide quantitative measurements on nuclear shapes from cells that migrated through collagen either in the presence or the absence of an inhibitor of collagen degradation, showing the distinctive power of this approach. This pipeline can also be applied to cell migration studied in different assays, ranging from 3D microfluidics to migration in the living organism.
Collapse
Affiliation(s)
- Martin Svoren
- Department of Cell Biology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elena Camerini
- Department of Cell Biology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Merijn van Erp
- Department of Cell Biology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Feng Wei Yang
- Department of Mathematics, School of Mathematical and Physical Sciences, University of Sussex, Brighton, Falmer, UK
| | - Gert-Jan Bakker
- Department of Cell Biology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Katarina Wolf
- Department of Cell Biology, Radboud University Medical Center, Nijmegen, the Netherlands.
| |
Collapse
|
9
|
Kalukula Y, Stephens AD, Lammerding J, Gabriele S. Mechanics and functional consequences of nuclear deformations. Nat Rev Mol Cell Biol 2022; 23:583-602. [PMID: 35513718 PMCID: PMC9902167 DOI: 10.1038/s41580-022-00480-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 02/08/2023]
Abstract
As the home of cellular genetic information, the nucleus has a critical role in determining cell fate and function in response to various signals and stimuli. In addition to biochemical inputs, the nucleus is constantly exposed to intrinsic and extrinsic mechanical forces that trigger dynamic changes in nuclear structure and morphology. Emerging data suggest that the physical deformation of the nucleus modulates many cellular and nuclear functions. These functions have long been considered to be downstream of cytoplasmic signalling pathways and dictated by gene expression. In this Review, we discuss an emerging perspective on the mechanoregulation of the nucleus that considers the physical connections from chromatin to nuclear lamina and cytoskeletal filaments as a single mechanical unit. We describe key mechanisms of nuclear deformations in time and space and provide a critical review of the structural and functional adaptive responses of the nucleus to deformations. We then consider the contribution of nuclear deformations to the regulation of important cellular functions, including muscle contraction, cell migration and human disease pathogenesis. Collectively, these emerging insights shed new light on the dynamics of nuclear deformations and their roles in cellular mechanobiology.
Collapse
Affiliation(s)
- Yohalie Kalukula
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Sylvain Gabriele
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
| |
Collapse
|
10
|
Currey ML, Kandula V, Biggs R, Marko JF, Stephens AD. A Versatile Micromanipulation Apparatus for Biophysical Assays of the Cell Nucleus. Cell Mol Bioeng 2022; 15:303-312. [PMID: 36119136 PMCID: PMC9474788 DOI: 10.1007/s12195-022-00734-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
Intro Force measurements of the nucleus, the strongest organelle, have propelled the field of mechanobiology to understand the basic mechanical components of the nucleus and how these components properly support nuclear morphology and function. Micromanipulation force measurement provides separation of the relative roles of nuclear mechanical components chromatin and lamin A. Methods To provide access to this technique, we have developed a universal micromanipulation apparatus for inverted microscopes. We outline how to engineer and utilize this apparatus through dual micromanipulators, fashion and calibrate micropipettes, and flow systems to isolate a nucleus and provide force vs. extensions measurements. This force measurement approach provides the unique ability to measure the separate contributions of chromatin at short extensions and lamin A strain stiffening at long extensions. We then investigated the apparatus' controllable and programmable micromanipulators through compression, isolation, and extension in conjunction with fluorescence to develop new assays for nuclear mechanobiology. Results Using this methodology, we provide the first rebuilding of the micromanipulation setup outside of its lab of origin and recapitulate many key findings including spring constant of the nucleus and strain stiffening across many cell types. Furthermore, we have developed new micromanipulation-based techniques to compress nuclei inducing nuclear deformation and/or rupture, track nuclear shape post-isolation, and fluorescence imaging during micromanipulation force measurements. Conclusion We provide the workflow to build and use a micromanipulation apparatus with any inverted microscope to perform nucleus isolation, force measurements, and various other biophysical techniques. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-022-00734-y.
Collapse
Affiliation(s)
| | - Viswajit Kandula
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, USA
- Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ronald Biggs
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, USA
| | - John F. Marko
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, USA
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, USA
- Molecular and Cellular Biosciences, University of Massachusetts Amherst, Amherst, USA
| |
Collapse
|
11
|
Villa S, Palamidessi A, Frittoli E, Scita G, Cerbino R, Giavazzi F. Non-invasive measurement of nuclear relative stiffness from quantitative analysis of microscopy data. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:50. [PMID: 35604494 PMCID: PMC9165292 DOI: 10.1140/epje/s10189-022-00189-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/28/2022] [Indexed: 05/21/2023]
Abstract
The connection between the properties of a cell tissue and those of the single constituent cells remains to be elucidated. At the purely mechanical level, the degree of rigidity of different cellular components, such as the nucleus and the cytoplasm, modulates the interplay between the cell inner processes and the external environment, while simultaneously mediating the mechanical interactions between neighboring cells. Being able to quantify the correlation between single-cell and tissue properties would improve our mechanobiological understanding of cell tissues. Here we develop a methodology to quantitatively extract a set of structural and motility parameters from the analysis of time-lapse movies of nuclei belonging to jammed and flocking cell monolayers. We then study in detail the correlation between the dynamical state of the tissue and the deformation of the nuclei. We observe that the nuclear deformation rate linearly correlates with the local divergence of the velocity field, which leads to a non-invasive estimate of the elastic modulus of the nucleus relative to the one of the cytoplasm. We also find that nuclei belonging to flocking monolayers, subjected to larger mechanical perturbations, are about two time stiffer than nuclei belonging to dynamically arrested monolayers, in agreement with atomic force microscopy results. Our results demonstrate a non-invasive route to the determination of nuclear relative stiffness for cells in a monolayer.
Collapse
Affiliation(s)
- Stefano Villa
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, 20090 Segrate, Italy
| | | | | | - Giorgio Scita
- IFOM-FIRC Institute of Molecular Oncology, 20139 Milan, Italy
- Dipartimento di Oncologia e Emato-Oncologia, Universitá degli Studi di Milano, 20133 Milan, Italy
| | - Roberto Cerbino
- University of Vienna, Faculty of Physics, 1090 Vienna, Austria
| | - Fabio Giavazzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, 20090 Segrate, Italy
| |
Collapse
|
12
|
Atanasova KR, Chakraborty S, Ratnayake R, Khare KD, Luesch H, Lele TP. An epigenetic small molecule screen to target abnormal nuclear morphology in human cells. Mol Biol Cell 2022; 33:ar45. [PMID: 35323046 PMCID: PMC9265153 DOI: 10.1091/mbc.e21-10-0528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Irregular nuclear shapes are a hallmark of human cancers. Recent studies suggest that alterations to chromatin regulators may cause irregular nuclear morphologies. Here we screened an epigenetic small molecule library consisting of 145 compounds against chromatin regulators, for their ability to revert abnormal nuclear shapes that were induced by gene knockdown in non-cancerous MCF10A human mammary breast epithelial cells. We leveraged a previously validated quantitative Fourier approach to quantify the elliptical Fourier coefficient (EFC ratio) as a measure of nuclear irregularities, which allowed us to perform rigorous statistical analyses of screening data. Top hit compounds fell into three major mode of action categories, targeting three separate epigenetic modulation routes: 1) Histone deacetylase (HDAC) inhibitors; 2) Bromodomain and extra-terminal domain (BET) protein inhibitors; and 3) Methyl-transferase inhibitors. Some of the top hit compounds were also efficacious in reverting nuclear irregularities in MDA-MB-231 triple negative breast cancer cells and in PANC-1 pancreatic cancer cells in a cell type dependent manner. Regularization of nuclear shapes was compound-specific, cell-type specific, and dependent on the specific molecular perturbation that induced nuclear irregularities. Our approach of targeting nuclear abnormalities may be potentially useful in screening new types of cancer therapies targeted toward chromatin structure.
Collapse
Affiliation(s)
- Kalina R Atanasova
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville FL 32610, USA
| | - Saptarshi Chakraborty
- Department of Biostatistics, State University of New York at Buffalo, Buffalo NY 14214, USA
| | - Ranjala Ratnayake
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville FL 32610, USA
| | - Kshitij D Khare
- Department of Statistics, University of Florida, Gainesville FL 32611, USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville FL 32610, USA
| | - Tanmay P Lele
- Department of Biomedical Engineering, Department of Chemical Engineering, and Department of Translational Medical Sciences, Texas A&M University, College Station TX 77843, USA
| |
Collapse
|
13
|
Vahabikashi A, Adam SA, Medalia O, Goldman RD. Nuclear lamins: Structure and function in mechanobiology. APL Bioeng 2022; 6:011503. [PMID: 35146235 PMCID: PMC8810204 DOI: 10.1063/5.0082656] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
Nuclear lamins are type V intermediate filament proteins that polymerize into complex filamentous meshworks at the nuclear periphery and in less structured forms throughout the nucleoplasm. Lamins interact with a wide range of nuclear proteins and are involved in numerous nuclear and cellular functions. Within the nucleus, they play roles in chromatin organization and gene regulation, nuclear shape, size, and mechanics, and the organization and anchorage of nuclear pore complexes. At the whole cell level, they are involved in the organization of the cytoskeleton, cell motility, and mechanotransduction. The expression of different lamin isoforms has been associated with developmental progression, differentiation, and tissue-specific functions. Mutations in lamins and their binding proteins result in over 15 distinct human diseases, referred to as laminopathies. The laminopathies include muscular (e.g., Emery-Dreifuss muscular dystrophy and dilated cardiomyopathy), neurological (e.g., microcephaly), and metabolic (e.g., familial partial lipodystrophy) disorders as well as premature aging diseases (e.g., Hutchinson-Gilford Progeria and Werner syndromes). How lamins contribute to the etiology of laminopathies is still unknown. In this review article, we summarize major recent findings on the structure, organization, and multiple functions of lamins in nuclear and more global cellular processes.
Collapse
Affiliation(s)
- Amir Vahabikashi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Stephen A. Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert D. Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| |
Collapse
|
14
|
Hobson CM, Falvo MR, Superfine R. A survey of physical methods for studying nuclear mechanics and mechanobiology. APL Bioeng 2021; 5:041508. [PMID: 34849443 PMCID: PMC8604565 DOI: 10.1063/5.0068126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022] Open
Abstract
It is increasingly appreciated that the cell nucleus is not only a home for DNA but also a complex material that resists physical deformations and dynamically responds to external mechanical cues. The molecules that confer mechanical properties to nuclei certainly contribute to laminopathies and possibly contribute to cellular mechanotransduction and physical processes in cancer such as metastasis. Studying nuclear mechanics and the downstream biochemical consequences or their modulation requires a suite of complex assays for applying, measuring, and visualizing mechanical forces across diverse length, time, and force scales. Here, we review the current methods in nuclear mechanics and mechanobiology, placing specific emphasis on each of their unique advantages and limitations. Furthermore, we explore important considerations in selecting a new methodology as are demonstrated by recent examples from the literature. We conclude by providing an outlook on the development of new methods and the judicious use of the current techniques for continued exploration into the role of nuclear mechanobiology.
Collapse
Affiliation(s)
| | - Michael R. Falvo
- Department of Physics and Astronomy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Richard Superfine
- Department of Applied Physical Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| |
Collapse
|
15
|
Kennedy Z, Newberg J, Goelzer M, Judex S, Fitzpatrick CK, Uzer G. Modeling stem cell nucleus mechanics using confocal microscopy. Biomech Model Mechanobiol 2021; 20:2361-2372. [PMID: 34424419 PMCID: PMC8599651 DOI: 10.1007/s10237-021-01513-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 08/14/2021] [Indexed: 11/24/2022]
Abstract
Nuclear mechanics is emerging as a key component of stem cell function and differentiation. While changes in nuclear structure can be visually imaged with confocal microscopy, mechanical characterization of the nucleus and its sub-cellular components require specialized testing equipment. A computational model permitting cell-specific mechanical information directly from confocal and atomic force microscopy of cell nuclei would be of great value. Here, we developed a computational framework for generating finite element models of isolated cell nuclei from multiple confocal microscopy scans and simple atomic force microscopy (AFM) tests. Confocal imaging stacks of isolated mesenchymal stem cells were converted into finite element models and siRNA-mediated Lamin A/C depletion isolated chromatin and Lamin A/C structures. Using AFM-measured experimental stiffness values, a set of conversion factors were determined for both chromatin and Lamin A/C to map the voxel intensity of the original images to the element stiffness, allowing the prediction of nuclear stiffness in an additional set of other nuclei. The developed computational framework will identify the contribution of a multitude of sub-nuclear structures and predict global nuclear stiffness of multiple nuclei based on simple nuclear isolation protocols, confocal images and AFM tests.
Collapse
Affiliation(s)
- Zeke Kennedy
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Joshua Newberg
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Matthew Goelzer
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Stefan Judex
- Biomedical Engineering, Stony Brook University, Stony Brook, USA
| | - Clare K Fitzpatrick
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA
| | - Gunes Uzer
- Department of Mechanical and Biomedical Engineering, Boise State University, 1910 University Drive, MSd-2085, Boise, ID, 83725-2085, USA.
| |
Collapse
|
16
|
Yeh CF, Chou C, Yang KC. Mechanotransduction in fibrosis: Mechanisms and treatment targets. CURRENT TOPICS IN MEMBRANES 2021; 87:279-314. [PMID: 34696888 DOI: 10.1016/bs.ctm.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
To perceive and integrate the environmental cues, cells and tissues sense and interpret various physical forces like shear, tensile, and compression stress. Mechanotransduction involves the sensing and translation of mechanical forces into biochemical and mechanical signals to guide cell fate and achieve tissue homeostasis. Disruption of this mechanical homeostasis by tissue injury elicits multiple cellular responses leading to pathological matrix deposition and tissue stiffening, and consequent evolution toward pro-inflammatory/pro-fibrotic phenotypes, leading to tissue/organ fibrosis. This review focuses on the molecular mechanisms linking mechanotransduction to fibrosis and uncovers the potential therapeutic targets to halt or resolve fibrosis.
Collapse
Affiliation(s)
- Chih-Fan Yeh
- Division of Cardiology, Department of Internal Medicine and Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan; Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Caroline Chou
- Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan; Washington University in St. Louis, St. Louis, MO, United States
| | - Kai-Chien Yang
- Division of Cardiology, Department of Internal Medicine and Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan; Department and Graduate Institute of Pharmacology, National Taiwan University College of Medicine, Taipei, Taiwan; Research Center for Developmental Biology & Regenerative Medicine, National Taiwan University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
17
|
Shah P, Hobson CM, Cheng S, Colville MJ, Paszek MJ, Superfine R, Lammerding J. Nuclear Deformation Causes DNA Damage by Increasing Replication Stress. Curr Biol 2021; 31:753-765.e6. [PMID: 33326770 PMCID: PMC7904640 DOI: 10.1016/j.cub.2020.11.037] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/22/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022]
Abstract
Cancer metastasis, i.e., the spreading of tumor cells from the primary tumor to distant organs, is responsible for the vast majority of cancer deaths. In the process, cancer cells migrate through narrow interstitial spaces substantially smaller in cross-section than the cell. During such confined migration, cancer cells experience extensive nuclear deformation, nuclear envelope rupture, and DNA damage. The molecular mechanisms responsible for the confined migration-induced DNA damage remain incompletely understood. Although in some cell lines, DNA damage is closely associated with nuclear envelope rupture, we show that, in others, mechanical deformation of the nucleus is sufficient to cause DNA damage, even in the absence of nuclear envelope rupture. This deformation-induced DNA damage, unlike nuclear-envelope-rupture-induced DNA damage, occurs primarily in S/G2 phase of the cell cycle and is associated with replication forks. Nuclear deformation, resulting from either confined migration or external cell compression, increases replication stress, possibly by increasing replication fork stalling, providing a molecular mechanism for the deformation-induced DNA damage. Thus, we have uncovered a new mechanism for mechanically induced DNA damage, linking mechanical deformation of the nucleus to DNA replication stress. This mechanically induced DNA damage could not only increase genomic instability in metastasizing cancer cells but could also cause DNA damage in non-migrating cells and tissues that experience mechanical compression during development, thereby contributing to tumorigenesis and DNA damage response activation.
Collapse
Affiliation(s)
- Pragya Shah
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chad M Hobson
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Svea Cheng
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marshall J Colville
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Matthew J Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Richard Superfine
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
18
|
Jabre S, Hleihel W, Coirault C. Nuclear Mechanotransduction in Skeletal Muscle. Cells 2021; 10:cells10020318. [PMID: 33557157 PMCID: PMC7913907 DOI: 10.3390/cells10020318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Skeletal muscle is composed of multinucleated, mature muscle cells (myofibers) responsible for contraction, and a resident pool of mononucleated muscle cell precursors (MCPs), that are maintained in a quiescent state in homeostatic conditions. Skeletal muscle is remarkable in its ability to adapt to mechanical constraints, a property referred as muscle plasticity and mediated by both MCPs and myofibers. An emerging body of literature supports the notion that muscle plasticity is critically dependent upon nuclear mechanotransduction, which is transduction of exterior physical forces into the nucleus to generate a biological response. Mechanical loading induces nuclear deformation, changes in the nuclear lamina organization, chromatin condensation state, and cell signaling, which ultimately impacts myogenic cell fate decisions. This review summarizes contemporary insights into the mechanisms underlying nuclear force transmission in MCPs and myofibers. We discuss how the cytoskeleton and nuclear reorganizations during myogenic differentiation may affect force transmission and nuclear mechanotransduction. We also discuss how to apply these findings in the context of muscular disorders. Finally, we highlight current gaps in knowledge and opportunities for further research in the field.
Collapse
Affiliation(s)
- Saline Jabre
- Sorbonne Université, INSERM UMRS-974 and Institut de Myologie, 75013 Paris, France;
- Department of Biology, Faculty of Arts and Sciences, Holy Spirit University of Kasik (USEK), Jounieh 446, Lebanon;
| | - Walid Hleihel
- Department of Biology, Faculty of Arts and Sciences, Holy Spirit University of Kasik (USEK), Jounieh 446, Lebanon;
- Department of Basic Health Sciences, Faculty of Medicine, Holy Spirit University of Kaslik (USEK), Jounieh 446, Lebanon
| | - Catherine Coirault
- Sorbonne Université, INSERM UMRS-974 and Institut de Myologie, 75013 Paris, France;
- Correspondence:
| |
Collapse
|
19
|
Haftbaradaran Esfahani P, Knöll R. Cell shape: effects on gene expression and signaling. Biophys Rev 2020; 12:895-901. [PMID: 32671813 PMCID: PMC7429604 DOI: 10.1007/s12551-020-00722-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/02/2020] [Indexed: 02/06/2023] Open
Abstract
The perception of biophysical forces (mechanosensation) and their conversion into chemical signals (mechanotransduction) are fundamental biological processes. They are connected to hypertrophic and atrophic cellular responses, and defects in these processes have been linked to various diseases, especially in the cardiovascular system. Although cardiomyocytes generate, and are exposed to, considerable hemodynamic forces that affect their shapes, until recently, we did not know whether cell shape affects gene expression. However, new single-cell trapping strategies, followed by single-cell RNA sequencing, to profile the transcriptomes of individual cardiomyocytes of defined geometrical morphotypes have been developed that are characteristic for either normal or pathological (afterload or preload) conditions. This paper reviews the recent literature with regard to cell shape and the transcriptome and provides an overview of this newly emerging field, which has far-reaching implications for both biology, disease, and possibly therapy.
Collapse
Affiliation(s)
- Payam Haftbaradaran Esfahani
- ICMC (Integrated Cardio Metabolic Centre), Myocardial Genetics, Heart and Vascular Theme, Karolinska Institutet, University Hospital, Novum, Hiss A, våning 7, Hälsovägen 7-9, 141 57, Huddinge, Sweden
| | - Ralph Knöll
- ICMC (Integrated Cardio Metabolic Centre), Myocardial Genetics, Heart and Vascular Theme, Karolinska Institutet, University Hospital, Novum, Hiss A, våning 7, Hälsovägen 7-9, 141 57, Huddinge, Sweden. .,Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| |
Collapse
|
20
|
Zuela-Sopilniak N, Bar-Sela D, Charar C, Wintner O, Gruenbaum Y, Buxboim A. Measuring nucleus mechanics within a living multicellular organism: Physical decoupling and attenuated recovery rate are physiological protective mechanisms of the cell nucleus under high mechanical load. Mol Biol Cell 2020; 31:1943-1950. [PMID: 32583745 PMCID: PMC7525816 DOI: 10.1091/mbc.e20-01-0085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Nuclei within cells are constantly subjected to compressive, tensile, and shear forces, which regulate nucleoskeletal and cytoskeletal remodeling, activate signaling pathways, and direct cell-fate decisions. Multiple rheological methods have been adapted for characterizing the response to applied forces of isolated nuclei and nuclei within intact cells. However, in vitro measurements fail to capture the viscoelastic modulation of nuclear stress-strain relationships by the physiological tethering to the surrounding cytoskeleton, extracellular matrix and cells, and tissue-level architectures. Using an equiaxial stretching apparatus, we applied a step stress and measured nucleus deformation dynamics within living Caenorhabditis elegans nematodes. Nuclei deformed nonmonotonically under constant load. Nonmonotonic deformation was conserved across tissues and robust to nucleoskeletal and cytoskeletal perturbations, but it required intact linker of nucleoskeleton and cytoskeleton complex attachments. The transition from creep to strain recovery fits a tensile-compressive linear viscoelastic model that is indicative of nucleoskeletal–cytoskeletal decoupling under high load. Ce-lamin (lmn-1) knockdown softened the nucleus, whereas nematode aging stiffened the nucleus and decreased deformation recovery rate. Recovery lasted minutes rather than seconds due to physiological damping of the released mechanical energy, thus protecting nuclear integrity and preventing chromatin damage.
Collapse
Affiliation(s)
- Noam Zuela-Sopilniak
- Departments of Genetics, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daniel Bar-Sela
- Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Chayki Charar
- Departments of Genetics, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Oren Wintner
- Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yosef Gruenbaum
- Departments of Genetics, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Amnon Buxboim
- Cell and Developmental Biology, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Alexander Grass Center for Bioengineering, The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190416, Israel
| |
Collapse
|
21
|
Fischer T, Hayn A, Mierke CT. Effect of Nuclear Stiffness on Cell Mechanics and Migration of Human Breast Cancer Cells. Front Cell Dev Biol 2020; 8:393. [PMID: 32548118 PMCID: PMC7272586 DOI: 10.3389/fcell.2020.00393] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 04/29/2020] [Indexed: 12/18/2022] Open
Abstract
The migration and invasion of cancer cells through 3D confined extracellular matrices is coupled to cell mechanics and the mechanics of the extracellular matrix. Cell mechanics is mainly determined by both the mechanics of the largest organelle in the cell, the nucleus, and the cytoskeletal architecture of the cell. Hence, cytoskeletal and nuclear mechanics are the major contributors to cell mechanics. Among other factors, steric hindrances of the extracellular matrix confinement are supposed to affect nuclear mechanics and thus also influence cell mechanics. Therefore, we propose that the percentage of invasive cells and their invasion depths into loose and dense 3D extracellular matrices is regulated by both nuclear and cytoskeletal mechanics. In order to investigate the effect of both nuclear and cytoskeletal mechanics on the overall cell mechanics, we firstly altered nuclear mechanics by the chromatin de-condensing reagent Trichostatin A (TSA) and secondly altered cytoskeletal mechanics by addition of actin polymerization inhibitor Latrunculin A and the myosin inhibitor Blebbistatin. In fact, we found that TSA-treated MDA-MB-231 human breast cancer cells increased their invasion depth in dense 3D extracellular matrices, whereas the invasion depths in loose matrices were decreased. Similarly, the invasion depths of TSA-treated MCF-7 human breast cancer cells in dense matrices were significantly increased compared to loose matrices, where the invasion depths were decreased. These results are also valid in the presence of a matrix-metalloproteinase inhibitor GM6001. Using atomic force microscopy (AFM), we found that the nuclear stiffnesses of both MDA-MB-231 and MCF-7 breast cancer cells were pronouncedly higher than their cytoskeletal stiffness, whereas the stiffness of the nucleus of human mammary epithelial cells was decreased compared to their cytoskeleton. TSA treatment reduced cytoskeletal and nuclear stiffness of MCF-7 cells, as expected. However, a softening of the nucleus by TSA treatment may induce a stiffening of the cytoskeleton of MDA-MB-231 cells and subsequently an apparent stiffening of the nucleus. Inhibiting actin polymerization using Latrunculin A revealed a softer nucleus of MDA-MB-231 cells under TSA treatment. This indicates that the actin-dependent cytoskeletal stiffness seems to be influenced by the TSA-induced nuclear stiffness changes. Finally, the combined treatment with TSA and Latrunculin A further justifies the hypothesis of apparent nuclear stiffening, indicating that cytoskeletal mechanics seem to be regulated by nuclear mechanics.
Collapse
Affiliation(s)
- Tony Fischer
- Biological Physics Division, Peter Debye Institute of Soft Matter Physics, Faculty of Physics and Earth Sciences, Leipzig University, Leipzig, Germany
| | - Alexander Hayn
- Biological Physics Division, Peter Debye Institute of Soft Matter Physics, Faculty of Physics and Earth Sciences, Leipzig University, Leipzig, Germany
| | - Claudia Tanja Mierke
- Biological Physics Division, Peter Debye Institute of Soft Matter Physics, Faculty of Physics and Earth Sciences, Leipzig University, Leipzig, Germany
| |
Collapse
|
22
|
Gaetani R, Zizzi EA, Deriu MA, Morbiducci U, Pesce M, Messina E. When Stiffness Matters: Mechanosensing in Heart Development and Disease. Front Cell Dev Biol 2020; 8:334. [PMID: 32671058 PMCID: PMC7326078 DOI: 10.3389/fcell.2020.00334] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
During embryonic morphogenesis, the heart undergoes a complex series of cellular phenotypic maturations (e.g., transition of myocytes from proliferative to quiescent or maturation of the contractile apparatus), and this involves stiffening of the extracellular matrix (ECM) acting in concert with morphogenetic signals. The maladaptive remodeling of the myocardium, one of the processes involved in determination of heart failure, also involves mechanical cues, with a progressive stiffening of the tissue that produces cellular mechanical damage, inflammation, and ultimately myocardial fibrosis. The assessment of the biomechanical dependence of the molecular machinery (in myocardial and non-myocardial cells) is therefore essential to contextualize the maturation of the cardiac tissue at early stages and understand its pathologic evolution in aging. Because systems to perform multiscale modeling of cellular and tissue mechanics have been developed, it appears particularly novel to design integrated mechano-molecular models of heart development and disease to be tested in ex vivo reconstituted cells/tissue-mimicking conditions. In the present contribution, we will discuss the latest implication of mechanosensing in heart development and pathology, describe the most recent models of cell/tissue mechanics, and delineate novel strategies to target the consequences of heart failure with personalized approaches based on tissue engineering and induced pluripotent stem cell (iPSC) technologies.
Collapse
Affiliation(s)
- Roberto Gaetani
- Department of Molecular Medicine, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome, Italy.,Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, San Diego, CA, United States
| | - Eric Adriano Zizzi
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Agostino Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Umberto Morbiducci
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Maurizio Pesce
- Tissue Engineering Research Unit, "Centro Cardiologico Monzino," IRCCS, Milan, Italy
| | - Elisa Messina
- Department of Maternal, Infantile, and Urological Sciences, "Umberto I" Hospital, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
23
|
Stephens AD. Chromatin rigidity provides mechanical and genome protection. Mutat Res 2020; 821:111712. [PMID: 32590202 PMCID: PMC8186544 DOI: 10.1016/j.mrfmmm.2020.111712] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
The nucleus is the organelle in the cell that contains the genome and its associate proteins which is collectively called chromatin. New work has shown that chromatin and its compaction level, dictated largely through histone modification state, provides rigidity to protect and stabilize the nucleus. Alterations in chromatin, its mechanics, and downstream loss of nuclear shape and stability are hallmarks of human disease. Weakened nuclear mechanics and abnormal morphology have been shown to cause rupturing of the nucleus which results in nuclear dysfunction including DNA damage. Thus, the rigidity provided by chromatin to maintain nuclear mechanical stability also provides its own protection from DNA damage via compartmentalization maintenance.
Collapse
Affiliation(s)
- Andrew D Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, United States.
| |
Collapse
|
24
|
Chromatin and Cytoskeletal Tethering Determine Nuclear Morphology in Progerin-Expressing Cells. Biophys J 2020; 118:2319-2332. [PMID: 32320674 DOI: 10.1016/j.bpj.2020.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/18/2020] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
The nuclear morphology of eukaryotic cells is determined by the interplay between the lamina forming the nuclear skeleton, the chromatin inside the nucleus, and the coupling with the cytoskeleton. Nuclear alterations are often associated with pathological conditions as in Hutchinson-Gilford progeria syndrome, in which a mutation in the lamin A gene yields an altered form of the protein, named progerin, and an aberrant nuclear shape. Here, we introduce an inducible cellular model of Hutchinson-Gilford progeria syndrome in HeLa cells in which increased progerin expression leads to alterations in the coupling of the lamin shell with cytoskeletal or chromatin tethers as well as with polycomb group proteins. Furthermore, our experiments show that progerin expression leads to enhanced nuclear shape fluctuations in response to cytoskeletal activity. To interpret the experimental results, we introduce a computational model of the cell nucleus that explicitly includes chromatin fibers, the nuclear shell, and coupling with the cytoskeleton. The model allows us to investigate how the geometrical organization of the chromatin-lamin tether affects nuclear morphology and shape fluctuations. In sum, our findings highlight the crucial role played by lamin-chromatin and lamin-cytoskeletal alterations in determining nuclear shape morphology and in affecting cellular functions and gene regulation.
Collapse
|
25
|
Erdel F. Biophysical mechanisms of chromatin patterning. Curr Opin Genet Dev 2020; 61:62-68. [DOI: 10.1016/j.gde.2020.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/08/2023]
|
26
|
Hoffman LM, Smith MA, Jensen CC, Yoshigi M, Blankman E, Ullman KS, Beckerle MC. Mechanical stress triggers nuclear remodeling and the formation of transmembrane actin nuclear lines with associated nuclear pore complexes. Mol Biol Cell 2020; 31:1774-1787. [PMID: 31967947 PMCID: PMC7521858 DOI: 10.1091/mbc.e19-01-0027] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mechanical stimulation of fibroblasts induces changes in the actin cytoskeleton including stress fiber (SF) reinforcement and realignment. Here we characterize the nuclear response to mechanical stimulation (uniaxial cyclic stretch). Using fluorescence microscopy and quantitative image analysis we find that stretch-induced nuclear elongation and alignment perpendicular to the stretch vector are dependent on formin-regulated actin polymerization. The mechanosensitive transcription factors Yes-associated protein/Transcriptional coactivator with PDZ domain (YAP/TAZ) and myocardin-related transcription factor (MRTF-A, also known as MKL1 and MAL1) accumulate in the nucleus and activate their target genes in response to uniaxial cyclic stretch. We show that transmembrane actin nuclear (TAN) lines are induced by stretch stimulation and nuclear envelope (NE) proteins including nesprins, SUN2, and lamins form Linkers of the Nucleoskeleton and Cytoskeleton (LINC) complexes aligned with actin SFs. These NE structures are altered by pharmacological treatments (Cytochalasin D and Jasplakinolide) or genetic disruption (zyxin gene deletion) that alter actin, and their persistence requires maintenance of stretch stimulation. Nuclear pore complexes (NPCs) accumulate at TAN lines providing a potential mechanism for linking mechanical cues to NPC function.
Collapse
Affiliation(s)
- Laura M Hoffman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112.,Department of Biology, University of Utah, Salt Lake City, UT 84112
| | - Mark A Smith
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112.,Department of Biology, University of Utah, Salt Lake City, UT 84112
| | | | - Masaaki Yoshigi
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84112
| | | | - Katharine S Ullman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Mary C Beckerle
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112.,Department of Biology, University of Utah, Salt Lake City, UT 84112.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
| |
Collapse
|
27
|
Gallardo P, Barrales RR, Daga RR, Salas-Pino S. Nuclear Mechanics in the Fission Yeast. Cells 2019; 8:cells8101285. [PMID: 31635174 PMCID: PMC6829894 DOI: 10.3390/cells8101285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022] Open
Abstract
In eukaryotic cells, the organization of the genome within the nucleus requires the nuclear envelope (NE) and its associated proteins. The nucleus is subjected to mechanical forces produced by the cytoskeleton. The physical properties of the NE and the linkage of chromatin in compacted conformation at sites of cytoskeleton contacts seem to be key for withstanding nuclear mechanical stress. Mechanical perturbations of the nucleus normally occur during nuclear positioning and migration. In addition, cell contraction or expansion occurring for instance during cell migration or upon changes in osmotic conditions also result innuclear mechanical stress. Recent studies in Schizosaccharomyces pombe (fission yeast) have revealed unexpected functions of cytoplasmic microtubules in nuclear architecture and chromosome behavior, and have pointed to NE-chromatin tethers as protective elements during nuclear mechanics. Here, we review and discuss how fission yeast cells can be used to understand principles underlying the dynamic interplay between genome organization and function and the effect of forces applied to the nucleus by the microtubule cytoskeleton.
Collapse
Affiliation(s)
- Paola Gallardo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Silvia Salas-Pino
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| |
Collapse
|
28
|
Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O’Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF. Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. Mol Biol Cell 2019; 30:2320-2330. [PMID: 31365328 PMCID: PMC6743459 DOI: 10.1091/mbc.e19-05-0286] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleus houses, organizes, and protects chromatin to ensure genome integrity and proper gene expression, but how the nucleus adapts mechanically to changes in the extracellular environment is poorly understood. Recent studies have revealed that extracellular physical stresses induce chromatin compaction via mechanotransductive processes. We report that increased extracellular multivalent cations lead to increased heterochromatin levels through activation of mechanosensitive ion channels (MSCs), without large-scale cell stretching. In cells with perturbed chromatin or lamins, this increase in heterochromatin suppresses nuclear blebbing associated with nuclear rupture and DNA damage. Through micromanipulation force measurements, we show that this increase in heterochromatin increases chromatin-based nuclear rigidity, which protects nuclear morphology and function. In addition, transduction of elevated extracellular cations rescues nuclear morphology in model and patient cells of human diseases, including progeria and the breast cancer model cell line MDA-MB-231. We conclude that nuclear mechanics, morphology, and function can be modulated by cell sensing of the extracellular environment through MSCs and consequent changes to histone modification state and chromatin-based nuclear rigidity.
Collapse
Affiliation(s)
- Andrew D. Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Patrick Z. Liu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Viswajit Kandula
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Haimei Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Thomas O’Halloran
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Stephen A. Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Robert D. Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Edward J. Banigan
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - John F. Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
| |
Collapse
|
29
|
Abstract
Cellular behavior is continuously affected by microenvironmental forces through the process of mechanotransduction, in which mechanical stimuli are rapidly converted to biochemical responses. Mounting evidence suggests that the nucleus itself is a mechanoresponsive element, reacting to cytoskeletal forces and mediating downstream biochemical responses. The nucleus responds through a host of mechanisms, including partial unfolding, conformational changes, and phosphorylation of nuclear envelope proteins; modulation of nuclear import/export; and altered chromatin organization, resulting in transcriptional changes. It is unclear which of these events present direct mechanotransduction processes and which are downstream of other mechanotransduction pathways. We critically review and discuss the current evidence for nuclear mechanotransduction, particularly in the context of stem cell fate, a largely unexplored topic, and in disease, where an improved understanding of nuclear mechanotransduction is beginning to open new treatment avenues. Finally, we discuss innovative technological developments that will allow outstanding questions in the rapidly growing field of nuclear mechanotransduction to be answered.
Collapse
Affiliation(s)
- Melanie Maurer
- Meinig School of Biomedical Engineering and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA; ,
| | - Jan Lammerding
- Meinig School of Biomedical Engineering and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA; ,
| |
Collapse
|
30
|
Stephens AD, Banigan EJ, Marko JF. Chromatin's physical properties shape the nucleus and its functions. Curr Opin Cell Biol 2019; 58:76-84. [PMID: 30889417 PMCID: PMC6692209 DOI: 10.1016/j.ceb.2019.02.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/06/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
The cell nucleus encloses, organizes, and protects the genome. Chromatin maintains nuclear mechanical stability and shape in coordination with lamins and the cytoskeleton. Abnormal nuclear shape is a diagnostic marker for human diseases, and it can cause nuclear dysfunction. Chromatin mechanics underlies this link, as alterations to chromatin and its physical properties can disrupt or rescue nuclear shape. The cell can regulate nuclear shape through mechanotransduction pathways that sense and respond to extracellular cues, thus modulating chromatin compaction and rigidity. These findings reveal how chromatin's physical properties can regulate cellular function and drive abnormal nuclear morphology and dysfunction in disease.
Collapse
Affiliation(s)
- Andrew D Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, United States.
| | - Edward J Banigan
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, United States; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, United States.
| |
Collapse
|
31
|
Maeshima K, Tamura S, Shimamoto Y. Chromatin as a nuclear spring. Biophys Physicobiol 2018; 15:189-195. [PMID: 30349803 PMCID: PMC6194950 DOI: 10.2142/biophysico.15.0_189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
The nucleus in eukaryotic cells is the site for genomic functions such as RNA transcription, DNA replication, and DNA repair/recombination. However, the nucleus is subjected to various mechanical forces associated with diverse cellular activities, including contraction, migration, and adhesion. Although it has long been assumed that the lamina structure, underlying filamentous mesh-work of the nuclear envelope, plays an important role in resisting mechanical forces, the involvement of compact chromatin in mechanical resistance has also recently been suggested. However, it is still unclear how chromatin functions to cope with the stresses. To address this issue, we studied the mechanical responses of human cell nuclei by combining a force measurement microscopy setup with controlled biochemical manipulation of chromatin. We found that nuclei with condensed chromatin possess significant elastic rigidity, whereas the nuclei with a decondensed chromatin are considerably soft. Further analyses revealed that the linker DNA and nucleosome-nucleosome interactions via histone tails in the chromatin act together to generate a spring-like restoring force that resists nuclear deformation. The elastic restoring force is likely to be generated by condensed chromatin domains, consisting of interdigitated or "melted" 10-nm nucleosome fibers. Together with other recent studies, it is suggested that chromatin functions not only as a "memory device" to store, replicate, and express the genetic information for various cellular functions but also as a "nuclear spring" to resist and respond to mechanical forces.
Collapse
Affiliation(s)
- Kazuhiro Maeshima
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuta Shimamoto
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.,Quantitative Mechanobiology Laboratory, Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
32
|
Broders-Bondon F, Nguyen Ho-Bouldoires TH, Fernandez-Sanchez ME, Farge E. Mechanotransduction in tumor progression: The dark side of the force. J Cell Biol 2018; 217:1571-1587. [PMID: 29467174 PMCID: PMC5940296 DOI: 10.1083/jcb.201701039] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 01/19/2018] [Accepted: 02/01/2018] [Indexed: 12/11/2022] Open
Abstract
Broders-Bondon et al. review the pathological mechanical properties of tumor tissues and how abnormal mechanical signals result in oncogenic biochemical signals during tumor progression. Cancer has been characterized as a genetic disease, associated with mutations that cause pathological alterations of the cell cycle, adhesion, or invasive motility. Recently, the importance of the anomalous mechanical properties of tumor tissues, which activate tumorigenic biochemical pathways, has become apparent. This mechanical induction in tumors appears to consist of the destabilization of adult tissue homeostasis as a result of the reactivation of embryonic developmental mechanosensitive pathways in response to pathological mechanical strains. These strains occur in many forms, for example, hypervascularization in late tumors leads to high static hydrodynamic pressure that can promote malignant progression through hypoxia or anomalous interstitial liquid and blood flow. The high stiffness of tumors directly induces the mechanical activation of biochemical pathways enhancing the cell cycle, epithelial–mesenchymal transition, and cell motility. Furthermore, increases in solid-stress pressure associated with cell hyperproliferation activate tumorigenic pathways in the healthy epithelial cells compressed by the neighboring tumor. The underlying molecular mechanisms of the translation of a mechanical signal into a tumor inducing biochemical signal are based on mechanically induced protein conformational changes that activate classical tumorigenic signaling pathways. Understanding these mechanisms will be important for the development of innovative treatments to target such mechanical anomalies in cancer.
Collapse
Affiliation(s)
- Florence Broders-Bondon
- Mechanics and Genetics of Embryonic and Tumor Development Group, Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, UMR168, Inserm, Sorbonne Universities, Paris, France
| | - Thanh Huong Nguyen Ho-Bouldoires
- Mechanics and Genetics of Embryonic and Tumor Development Group, Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, UMR168, Inserm, Sorbonne Universities, Paris, France
| | - Maria-Elena Fernandez-Sanchez
- Mechanics and Genetics of Embryonic and Tumor Development Group, Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, UMR168, Inserm, Sorbonne Universities, Paris, France
| | - Emmanuel Farge
- Mechanics and Genetics of Embryonic and Tumor Development Group, Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, UMR168, Inserm, Sorbonne Universities, Paris, France
| |
Collapse
|