1
|
Caillier A, Oleksyn D, Fowell DJ, Miller J, Oakes PW. T cells use focal adhesions to pull themselves through confined environments. J Cell Biol 2024; 223:e202310067. [PMID: 38889096 PMCID: PMC11187980 DOI: 10.1083/jcb.202310067] [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: 10/16/2023] [Revised: 05/16/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
Immune cells are highly dynamic and able to migrate through environments with diverse biochemical and mechanical compositions. Their migration has classically been defined as amoeboid under the assumption that it is integrin independent. Here, we show that activated primary Th1 T cells require both confinement and extracellular matrix proteins to migrate efficiently. This migration is mediated through small and dynamic focal adhesions that are composed of the same proteins associated with canonical mesenchymal cell focal adhesions, such as integrins, talin, and vinculin. These focal adhesions, furthermore, localize to sites of contractile traction stresses, enabling T cells to pull themselves through confined spaces. Finally, we show that Th1 T cells preferentially follow tracks of other T cells, suggesting that these adhesions modify the extracellular matrix to provide additional environmental guidance cues. These results demonstrate not only that the boundaries between amoeboid and mesenchymal migration modes are ambiguous, but that integrin-mediated focal adhesions play a key role in T cell motility.
Collapse
Affiliation(s)
- Alexia Caillier
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - David Oleksyn
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY, USA
| | - Deborah J. Fowell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jim Miller
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY, USA
| | - Patrick W. Oakes
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| |
Collapse
|
2
|
Montes AR, Barroso A, Wang W, O'Connell GD, Tepole AB, Mofrad MRK. Integrin mechanosensing relies on a pivot-clip mechanism to reinforce cell adhesion. Biophys J 2024:S0006-3495(24)00391-6. [PMID: 38872310 DOI: 10.1016/j.bpj.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/01/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024] Open
Abstract
Cells intricately sense mechanical forces from their surroundings, driving biophysical and biochemical activities. This mechanosensing phenomenon occurs at the cell-matrix interface, where mechanical forces resulting from cellular motion, such as migration or matrix stretching, are exchanged through surface receptors, primarily integrins, and their corresponding matrix ligands. A pivotal player in this interaction is the α5β1 integrin and fibronectin (FN) bond, known for its role in establishing cell adhesion sites for migration. However, upregulation of the α5β1-FN bond is associated with uncontrolled cell metastasis. This bond operates through catch bond dynamics, wherein the bond lifetime paradoxically increases with greater force. The mechanism sustaining the characteristic catch bond dynamics of α5β1-FN remains unclear. Leveraging molecular dynamics simulations, our approach unveils a pivot-clip mechanism. Two key binding sites on FN, namely the synergy site and the RGD (Arg-Gly-Asp) motif, act as active points for structural changes in α5β1 integrin. Conformational adaptations at these sites are induced by a series of hydrogen bond formations and breaks at the synergy site. We disrupt these adaptations through a double mutation on FN, known to reduce cell adhesion. A whole-cell finite-element model is employed to elucidate how the synergy site may promote dynamic α5β1-FN binding, resisting cell contraction. In summary, our study integrates molecular- and cellular-level modeling to propose that FN's synergy site reinforces cell adhesion through enhanced binding dynamics and a mechanosensitive pivot-clip mechanism. This work sheds light on the interplay between mechanical forces and cell-matrix interactions, contributing to our understanding of cellular behaviors in physiological and pathological contexts.
Collapse
Affiliation(s)
- Andre R Montes
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, Berkeley, California
| | - Anahi Barroso
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, Berkeley, California
| | - Wei Wang
- Berkeley City College, Berkeley, California; Berkeley Biomechanics Laboratory, Department of Mechanical Engineering, University of California, Berkeley, Berkeley, California
| | - Grace D O'Connell
- Berkeley Biomechanics Laboratory, Department of Mechanical Engineering, University of California, Berkeley, Berkeley, California
| | - Adrian B Tepole
- Tepole Mechanics and Mechanobiology Laboratory, School of Mechanical Engineering, Purdue University, West Lafayette, Indiana.
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, Berkeley, California; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California.
| |
Collapse
|
3
|
Kovács KD, Szittner Z, Magyaródi B, Péter B, Szabó B, Vörös A, Kanyó N, Székács I, Horvath R. Optical sensor reveals the hidden influence of cell dissociation on adhesion measurements. Sci Rep 2024; 14:11719. [PMID: 38778185 PMCID: PMC11111754 DOI: 10.1038/s41598-024-61485-6] [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: 12/15/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Cell adhesion experiments are important in tissue engineering and for testing new biologically active surfaces, prostheses, and medical devices. Additionally, the initial state of adhesion (referred to as nascent adhesion) plays a key role and is currently being intensively researched. A critical step in handling all adherent cell types is their dissociation from their substrates for further processing. Various cell dissociation methods and reagents are used in most tissue culture laboratories (here, cell dissociation from the culture surface, cell harvesting, and cell detachment are used interchangeably). Typically, the dissociated cells are re-adhered for specific measurements or applications. However, the impact of the choice of dissociation method on cell adhesion in subsequent measurements, especially when comparing the adhesivity of various surfaces, is not well clarified. In this study, we demonstrate that the application of a label-free optical sensor can precisely quantify the effect of cell dissociation methods on cell adhesivity, both at the single-cell and population levels. The optical measurements allow for high-resolution monitoring of cellular adhesion without interfering with the physiological state of the cells. We found that the choice of reagent significantly alters cell adhesion on various surfaces. Our results clearly demonstrate that biological conclusions about cellular adhesion when comparing various surfaces are highly dependent on the employed dissociation method. Neglecting the choice of cellular dissociation can lead to misleading conclusions when evaluating cell adhesion data from various sources and comparing the adhesivity of two different surfaces (i.e., determining which surface is more or less adhesive).
Collapse
Affiliation(s)
- Kinga Dóra Kovács
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary
- Department of Biological Physics, ELTE Eötvös University, Budapest, Hungary
| | - Zoltán Szittner
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary
| | - Beatrix Magyaródi
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary
- Chemical Engineering and Material Sciences Doctoral School, University of Pannonia, Veszprém, Hungary
| | - Beatrix Péter
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary
| | - Bálint Szabó
- Department of Biological Physics, ELTE Eötvös University, Budapest, Hungary
- Cellsorter Kft., Budapest, Hungary
| | - Alexa Vörös
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary
| | - Nicolett Kanyó
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary
| | - Inna Székács
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Laboratory, MFA, Centre for Energy Research, HUN-REN, Budapest, Hungary.
| |
Collapse
|
4
|
Hagelaars MJ, Nikolic M, Vermeulen M, Dekker S, Bouten CVC, Loerakker S. A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarization in renal epithelial cells. PLoS Comput Biol 2024; 20:e1012140. [PMID: 38768266 PMCID: PMC11142725 DOI: 10.1371/journal.pcbi.1012140] [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: 10/31/2023] [Revised: 05/31/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Apical-basal polarization in renal epithelial cells is crucial to renal function and an important trigger for tubule formation in kidney development. Loss of polarity can induce epithelial-to-mesenchymal transition (EMT), which can lead to kidney pathologies. Understanding the relative and combined roles of the involved proteins and their interactions that govern epithelial polarity may provide insights for controlling the process of polarization via chemical or mechanical manipulations in an in vitro or in vivo setting. Here, we developed a computational framework that integrates several known interactions between integrins, Rho-GTPases Rho, Rac and Cdc42, and polarity complexes Par and Scribble, to study their mutual roles in the emergence of polarization. The modeled protein interactions were shown to induce the emergence of polarized distributions of Rho-GTPases, which in turn led to the accumulation of apical and basal polarity complexes Par and Scribble at their respective poles, effectively recapitulating polarization. Our multiparametric sensitivity analysis suggested that polarization depends foremost on the mutual inhibition between Rac and Rho. Next, we used the computational framework to investigate the role of integrins and GTPases in the generation and disruption of polarization. We found that a minimum concentration of integrins is required to catalyze the process of polarization. Furthermore, loss of polarization was found to be only inducible via complete degradation of the Rho-GTPases Rho and Cdc42, suggesting that polarization is fairly stable once it is established. Comparison of our computational predictions against data from in vitro experiments in which we induced EMT in renal epithelial cells while quantifying the relative Rho-GTPase levels, displayed that EMT coincides with a large reduction in the Rho-GTPase Rho. Collectively, these results demonstrate the essential roles of integrins and Rho-GTPases in the establishment and disruption of apical-basal polarity and thereby provide handles for the in vitro or in vivo regulation of polarity.
Collapse
Affiliation(s)
- Maria J. Hagelaars
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, The Netherlands
| | - Milica Nikolic
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, The Netherlands
| | - Maud Vermeulen
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, The Netherlands
| | - Sylvia Dekker
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, The Netherlands
| | - Carlijn V. C. Bouten
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, The Netherlands
| | - Sandra Loerakker
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, The Netherlands
| |
Collapse
|
5
|
Blanchard AT. Can a bulky glycocalyx promote catch bonding in early integrin adhesion? Perhaps a bit. Biomech Model Mechanobiol 2024; 23:117-128. [PMID: 37704890 DOI: 10.1007/s10237-023-01762-x] [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: 03/23/2023] [Accepted: 07/30/2023] [Indexed: 09/15/2023]
Abstract
Many types of cancer cells overexpress bulky glycoproteins to form a thick glycocalyx layer. The glycocalyx physically separates the cell from its surroundings, but recent work has shown that the glycocalyx can paradoxically increase adhesion to soft tissues and therefore promote the metastasis of cancer cells. This surprising phenomenon occurs because the glycocalyx forces adhesion molecules (called integrins) on the cell's surface into clusters. These integrin clusters have cooperative effects that allow them to form stronger adhesions to surrounding tissues than would be possible with equivalent numbers of un-clustered integrins. These cooperative mechanisms have been intensely scrutinized in recent years. A more nuanced understanding of the biophysical underpinnings of glycocalyx-mediated adhesion could uncover therapeutic targets, deepen our general understanding of cancer metastasis, and elucidate general biophysical processes that extend far beyond the realm of cancer research. This work examines the hypothesis that the glycocalyx has the additional effect of increasing mechanical tension experienced by clustered integrins. Integrins function as mechanosensors that undergo catch bonding-meaning the application of moderate tension increases integrin bond lifetime relative to the lifetime of integrins experiencing low tension. In this work, a three-state chemomechanical catch bond model of integrin tension is used to investigate catch bonding in the presence of a bulky glycocalyx. A pseudo-steady-state approximation is applied, which relies on the assumption that integrin bond dynamics occur on a much faster timescale than the evolution of the full adhesion between the plasma membrane and the substrate. Force-dependent kinetic rate constants are used to calculate a steady-state distribution of integrin-ligand bonds for Gaussian-shaped adhesion geometries. The relationship between the energy of the system and adhesion geometry is then analyzed in the presence and absence of catch bonding in order to evaluate the extent to which catch bonding alters the energetics of adhesion formation. This modeling suggests that a bulky glycocalyx can lightly trigger catch bonding, increasing the bond lifetime of integrins at adhesion edges by up to 100%. The total number of integrin-ligand bonds within an adhesion is predicted to increase by up to ~ 60% for certain adhesion geometries. Catch bonding is predicted to decrease the activation energy of adhesion formation by ~ 1-4 kBT, which translates to a ~ 3-50 × increase in the kinetic rate of adhesion nucleation. This work reveals that integrin mechanics and clustering likely both contribute to glycocalyx-mediated metastasis.
Collapse
Affiliation(s)
- Aaron T Blanchard
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
- Duke Cancer Institute, Duke University, Durham, NC, 27708, USA.
| |
Collapse
|
6
|
Carney KR, Khan AM, Stam S, Samson SC, Mittal N, Han SJ, Bidone TC, Mendoza MC. Nascent adhesions shorten the period of lamellipodium protrusion through the Brownian ratchet mechanism. Mol Biol Cell 2023; 34:ar115. [PMID: 37672339 PMCID: PMC10846621 DOI: 10.1091/mbc.e23-08-0314] [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: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
Directional cell migration is driven by the conversion of oscillating edge motion into lasting periods of leading edge protrusion. Actin polymerization against the membrane and adhesions control edge motion, but the exact mechanisms that determine protrusion period remain elusive. We addressed this by developing a computational model in which polymerization of actin filaments against a deformable membrane and variable adhesion dynamics support edge motion. Consistent with previous reports, our model showed that actin polymerization and adhesion lifetime power protrusion velocity. However, increasing adhesion lifetime decreased the protrusion period. Measurements of adhesion lifetime and edge motion in migrating cells confirmed that adhesion lifetime is associated with and promotes protrusion velocity, but decreased duration. Our model showed that adhesions' control of protrusion persistence originates from the Brownian ratchet mechanism for actin filament polymerization. With longer adhesion lifetime or increased-adhesion density, the proportion of actin filaments tethered to the substrate increased, maintaining filaments against the cell membrane. The reduced filament-membrane distance generated pushing force for high edge velocity, but limited further polymerization needed for protrusion duration. We propose a mechanism for cell edge protrusion in which adhesion strength regulates actin filament polymerization to control the periods of leading edge protrusion.
Collapse
Affiliation(s)
- Keith R. Carney
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
- Huntsman Cancer Institute, Salt Lake City, UT 84112
| | - Akib M. Khan
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
- Huntsman Cancer Institute, Salt Lake City, UT 84112
| | - Samantha Stam
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
- Huntsman Cancer Institute, Salt Lake City, UT 84112
| | - Shiela C. Samson
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
- Huntsman Cancer Institute, Salt Lake City, UT 84112
| | - Nikhil Mittal
- Department of Biomedical Engineering, Michigan Technological University, Houghton, MI 49931
| | - Sangyoon J. Han
- Department of Biomedical Engineering, Michigan Technological University, Houghton, MI 49931
| | - Tamara C. Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112
- Scientific Computing and Imaging Institute, Salt Lake City, UT 84112
| | - Michelle C. Mendoza
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112
- Huntsman Cancer Institute, Salt Lake City, UT 84112
| |
Collapse
|
7
|
Wu P, Yanagi K, Yokota K, Hakamada M, Mabuchi M. Unusual effects of a nanoporous gold substrate on cell adhesion and differentiation because of independent multi-branch signaling of focal adhesions. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2023; 34:54. [PMID: 37884819 PMCID: PMC10602965 DOI: 10.1007/s10856-023-06760-0] [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: 03/22/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
A variety of cell behaviors, such as cell adhesion, motility, and fate, can be controlled by substrate characteristics such as surface topology and chemistry. In particular, the surface topology of substrates strongly affects cell behaviors, and the topological spacing is a critical factor in inducing cell responses. Various works have demonstrated that cell adhesion was enhanced with decreasing topological spacing although differentiation progressed slowly. However, there are exceptions, and thus, correlations between topological spacing and cell responses are still debated. We show that a nanoporous gold substrate affected cell adhesion while it neither affected osteogenic nor adipogenic differentiation. In addition, the cell adhesion was reduced with decreasing pore size. These do not agree with previous findings. A focal adhesion (FA) is an aggregate of modules comprising specific proteins such as FA kinase, talin, and vinculin. Therefore, it is suggested that because various extracellular signals can be independently branched off from the FA modules, the unusual effects of nanoporous gold substrates are related to the multi-branching of FAs.
Collapse
Affiliation(s)
- Peizheng Wu
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan.
| | - Kazuya Yanagi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
| | - Kazuki Yokota
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
| | - Masataka Hakamada
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
| | - Mamoru Mabuchi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
| |
Collapse
|
8
|
Caillier A, Oleksyn D, Fowell DJ, Miller J, Oakes PW. T cells Use Focal Adhesions to Pull Themselves Through Confined Environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562587. [PMID: 37904911 PMCID: PMC10614902 DOI: 10.1101/2023.10.16.562587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Immune cells are highly dynamic and able to migrate through environments with diverse biochemical and mechanical composition. Their migration has classically been defined as amoeboid under the assumption that it is integrin-independent. Here we show that activated primary Th1 T cells require both confinement and extracellular matrix protein to migrate efficiently. This migration is mediated through small and dynamic focal adhesions that are composed of the same proteins associated with canonical mesenchymal focal adhesions, such as integrins, talin, and vinculin. These focal adhesions, furthermore, localize to sites of contractile traction stresses, enabling T cells to pull themselves through confined spaces. Finally, we show that Th1 T cell preferentially follows tracks of other T cells, suggesting that these adhesions are modifying the extracellular matrix to provide additional environmental guidance cues. These results demonstrate not only that the boundaries between amoeboid and mesenchymal migration modes are ambiguous, but that integrin-mediated adhesions play a key role in T cell motility.
Collapse
Affiliation(s)
- Alexia Caillier
- Department of Cell & Molecular Physiology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, USA
| | - David Oleksyn
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Deborah J Fowell
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jim Miller
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Patrick W Oakes
- Department of Cell & Molecular Physiology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, USA
| |
Collapse
|
9
|
Grudtsyna V, Packirisamy S, Bidone TC, Swaminathan V. Extracellular matrix sensing via modulation of orientational order of integrins and F-actin in focal adhesions. Life Sci Alliance 2023; 6:e202301898. [PMID: 37463754 PMCID: PMC10355215 DOI: 10.26508/lsa.202301898] [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: 01/04/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Specificity of cellular responses to distinct cues from the ECM requires precise and sensitive decoding of physical information. However, how known mechanisms of mechanosensing like force-dependent catch bonds and conformational changes in FA proteins can confer that this sensitivity is not known. Using polarization microscopy and computational modeling, we identify dynamic changes in an orientational order of FA proteins as a molecular organizational mechanism that can fine-tune cell sensitivity to the ECM. We find that αV integrins and F-actin show precise changes in the orientational order in an ECM-mediated integrin activation-dependent manner. These changes are sensitive to ECM density and are regulated independent of myosin-II activity though contractility can enhance this sensitivity. A molecular-clutch model demonstrates that the orientational order of integrin-ECM binding coupled to directional catch bonds can capture cellular responses to changes in ECM density. This mechanism also captures decoupling of ECM density sensing from stiffness sensing thus elucidating specificity. Taken together, our results suggest relative geometric organization of FA molecules as an important molecular architectural feature and regulator of mechanotransduction.
Collapse
Affiliation(s)
- Valeriia Grudtsyna
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Swathi Packirisamy
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Tamara C Bidone
- Department of Biomedical Engineering, The University of Utah, Salt Lake City, UT, USA
| | - Vinay Swaminathan
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
| |
Collapse
|
10
|
Venturini C, Sáez P. A multi-scale clutch model for adhesion complex mechanics. PLoS Comput Biol 2023; 19:e1011250. [PMID: 37450544 PMCID: PMC10393167 DOI: 10.1371/journal.pcbi.1011250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cell-matrix adhesion is a central mechanical function to a large number of phenomena in physiology and disease, including morphogenesis, wound healing, and tumor cell invasion. Today, how single cells respond to different extracellular cues has been comprehensively studied. However, how the mechanical behavior of the main individual molecules that form an adhesion complex cooperatively responds to force within the adhesion complex is still poorly understood. This is a key aspect of cell adhesion because how these cell adhesion molecules respond to force determines not only cell adhesion behavior but, ultimately, cell function. To answer this question, we develop a multi-scale computational model for adhesion complexes mechanics. We extend the classical clutch hypothesis to model individual adhesion chains made of a contractile actin network, a talin rod, and an integrin molecule that binds at individual adhesion sites on the extracellular matrix. We explore several scenarios of integrins dynamics and analyze the effects of diverse extracellular matrices on the behavior of the adhesion molecules and on the whole adhesion complex. Our results describe how every single component of the adhesion chain mechanically responds to the contractile actomyosin force and show how they control the traction forces exerted by the cell on the extracellular space. Importantly, our computational results agree with previous experimental data at the molecular and cellular levels. Our multi-scale clutch model presents a step forward not only to further understand adhesion complexes mechanics but also to impact, e.g., the engineering of biomimetic materials, tissue repairment, or strategies to arrest tumor progression.
Collapse
Affiliation(s)
- Chiara Venturini
- Laboratori de Càlcul Numèric (LaCaN), Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Pablo Sáez
- Laboratori de Càlcul Numèric (LaCaN), Universitat Politècnica de Catalunya, Barcelona, Spain
- E.T.S. de Ingeniería de Caminos, Universitat Politècnica de Catalunya, Barcelona, Spain
- Institut de Matemàtiques de la UPC-BarcelonaTech (IMTech), Universitat Politècnica de Catalunya, Barcelona, Spain
| |
Collapse
|
11
|
Gaikwad HK, Jaswandkar SV, Katti KS, Haage A, Katti DR. Molecular basis of conformational changes and mechanics of integrins. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220243. [PMID: 37211038 DOI: 10.1098/rsta.2022.0243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/13/2023] [Indexed: 05/23/2023]
Abstract
Integrin, as a mechanotransducer, establishes the mechanical reciprocity between the extracellular matrix (ECM) and cells at integrin-mediated adhesion sites. This study used steered molecular dynamics (SMD) simulations to investigate the mechanical responses of integrin αvβ3 with and without 10th type III fibronectin (FnIII10) binding for tensile, bending and torsional loading conditions. The ligand-binding integrin confirmed the integrin activation during equilibration and altered the integrin dynamics by changing the interface interaction between β-tail, hybrid and epidermal growth factor domains during initial tensile loading. The tensile deformation in integrin molecules indicated that fibronectin ligand binding modulates its mechanical responses in the folded and unfolded conformation states. The bending deformation responses of extended integrin models reveal the change in behaviour of integrin molecules in the presence of Mn2+ ion and ligand based on the application of force in the folding and unfolding directions of integrin. Furthermore, these SMD simulation results were used to predict the mechanical properties of integrin underlying the mechanism of integrin-based adhesion. The evaluation of integrin mechanics provides new insights into understanding the mechanotransmission (force transmission) between cells and ECM and contributes to developing an accurate model for integrin-mediated adhesion. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
Collapse
Affiliation(s)
- Hanmant K Gaikwad
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
| | - Sharad V Jaswandkar
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
| | - Kalpana S Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
| | - Amanda Haage
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Dinesh R Katti
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, Fargo, ND 58105, USA
| |
Collapse
|
12
|
Campbell S, Mendoza MC, Rammohan A, McKenzie ME, Bidone TC. Computational model of integrin adhesion elongation under an actin fiber. PLoS Comput Biol 2023; 19:e1011237. [PMID: 37410718 DOI: 10.1371/journal.pcbi.1011237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
Cells create physical connections with the extracellular environment through adhesions. Nascent adhesions form at the leading edge of migrating cells and either undergo cycles of disassembly and reassembly, or elongate and stabilize at the end of actin fibers. How adhesions assemble has been addressed in several studies, but the exact role of actin fibers in the elongation and stabilization of nascent adhesions remains largely elusive. To address this question, here we extended our computational model of adhesion assembly by incorporating an actin fiber that locally promotes integrin activation. The model revealed that an actin fiber promotes adhesion stabilization and elongation. Actomyosin contractility from the fiber also promotes adhesion stabilization and elongation, by strengthening integrin-ligand interactions, but only up to a force threshold. Above this force threshold, most integrin-ligand bonds fail, and the adhesion disassembles. In the absence of contraction, actin fibers still support adhesions stabilization. Collectively, our results provide a picture in which myosin activity is dispensable for adhesion stabilization and elongation under an actin fiber, offering a framework for interpreting several previous experimental observations.
Collapse
Affiliation(s)
- Samuel Campbell
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, United States of America
| | - Michelle C Mendoza
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Aravind Rammohan
- Corning Life Sciences, Tewksburry, Massachusetts, United States of America
| | - Matthew E McKenzie
- Corning Research and Development Corporation, Corning, New York, United States of America
| | - Tamara C Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, United States of America
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, United States of America
| |
Collapse
|
13
|
Bidone TC, Odde DJ. Multiscale models of integrins and cellular adhesions. Curr Opin Struct Biol 2023; 80:102576. [PMID: 36947952 PMCID: PMC10238663 DOI: 10.1016/j.sbi.2023.102576] [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: 11/09/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Computational models of integrin-based adhesion complexes have revealed important insights into the mechanisms by which cells establish connections with their external environment. However, how changes in conformation and function of individual adhesion proteins regulate the dynamics of whole adhesion complexes remains largely elusive. This is because of the large separation in time and length scales between the dynamics of individual adhesion proteins (nanoseconds and nanometers) and the emergent dynamics of the whole adhesion complex (seconds and micrometers), and the limitations of molecular simulation approaches in extracting accurate free energies, conformational transitions, reaction mechanisms, and kinetic rates, that can inform mechanisms at the larger scales. In this review, we discuss models of integrin-based adhesion complexes and highlight their main findings regarding: (i) the conformational transitions of integrins at the molecular and macromolecular scales and (ii) the molecular clutch mechanism at the mesoscale. Lastly, we present unanswered questions in the field of modeling adhesions and propose new ideas for future exciting modeling opportunities.
Collapse
Affiliation(s)
- Tamara C Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA.
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA. https://twitter.com/davidodde
| |
Collapse
|
14
|
Blanchard A. Can a bulky glycocalyx promote catch bonding in early integrin adhesion? Perhaps a bit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532909. [PMID: 36993661 PMCID: PMC10055170 DOI: 10.1101/2023.03.16.532909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Many types of cancer overexpress bulky glycoproteins to form a thick glycocalyx layer. The glycocalyx physically separates the cell from its surroundings, but recent work has shown that the glycocalyx can paradoxically increase adhesion to soft tissues and therefore promote the metastasis of cancer cells. This surprising phenomenon occurs because the glycocalyx forces adhesion molecules (called integrins) on the cell's surface into clusters. These integrin clusters have cooperative effects that allow them to form stronger adhesions to surrounding tissues than would be possible with equivalent numbers of un-clustered integrins. These cooperative mechanisms have been intensely scrutinized in recent years; a more nuanced understanding of the biophysical underpinnings of glycocalyx-mediated adhesion could uncover therapeutic targets, deepen our general understanding of cancer metastasis, and elucidate general biophysical processes that extend far beyond the realm of cancer research. This work examines the hypothesis that the glycocalyx has the additional effect of increasing mechanical tension experienced by clustered integrins. Integrins function as mechanosensors that undergo catch bonding - meaning the application of moderate tension increases integrin bond lifetime relative to the lifetime of integrins experiencing low tension. In this work, a three-state chemomechanical catch bond model of integrin tension is used to investigate catch bonding in the presence of a bulky glycocalyx. This modeling suggests that a bulky glycocalyx can lightly trigger catch bonding, increasing the bond lifetime of integrins at adhesion edges by up to 100%. The total number of integrin-ligand bonds within an adhesion is predicted to increase by up to ~60% for certain adhesion geometries. Catch bonding is predicted to decrease the activation energy of adhesion formation by ~1-4 k B T, which translates to a ~3-50× increase in the kinetic rate of adhesion nucleation. This work reveals that integrin mechanic and clustering likely both contribute to glycocalyx-mediated metastasis.
Collapse
Affiliation(s)
- Aaron Blanchard
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708 United States
- Duke Cancer Institute, Duke University, Durham, NC, 27708, United States
| |
Collapse
|
15
|
Shen SC, Khare E, Lee NA, Saad MK, Kaplan DL, Buehler MJ. Computational Design and Manufacturing of Sustainable Materials through First-Principles and Materiomics. Chem Rev 2023; 123:2242-2275. [PMID: 36603542 DOI: 10.1021/acs.chemrev.2c00479] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Engineered materials are ubiquitous throughout society and are critical to the development of modern technology, yet many current material systems are inexorably tied to widespread deterioration of ecological processes. Next-generation material systems can address goals of environmental sustainability by providing alternatives to fossil fuel-based materials and by reducing destructive extraction processes, energy costs, and accumulation of solid waste. However, development of sustainable materials faces several key challenges including investigation, processing, and architecting of new feedstocks that are often relatively mechanically weak, complex, and difficult to characterize or standardize. In this review paper, we outline a framework for examining sustainability in material systems and discuss how recent developments in modeling, machine learning, and other computational tools can aid the discovery of novel sustainable materials. We consider these through the lens of materiomics, an approach that considers material systems holistically by incorporating perspectives of all relevant scales, beginning with first-principles approaches and extending through the macroscale to consider sustainable material design from the bottom-up. We follow with an examination of how computational methods are currently applied to select examples of sustainable material development, with particular emphasis on bioinspired and biobased materials, and conclude with perspectives on opportunities and open challenges.
Collapse
Affiliation(s)
- Sabrina C Shen
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue 1-165, Cambridge, Massachusetts 02139, United States.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eesha Khare
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue 1-165, Cambridge, Massachusetts 02139, United States.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nicolas A Lee
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue 1-165, Cambridge, Massachusetts 02139, United States.,School of Architecture and Planning, Media Lab, Massachusetts Institute of Technology, 75 Amherst Street, Cambridge, Massachusetts 02139, United States
| | - Michael K Saad
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue 1-165, Cambridge, Massachusetts 02139, United States.,Center for Computational Science and Engineering, Schwarzman College of Computing, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
16
|
Tong D, Soley N, Kolasangiani R, Schwartz MA, Bidone TC. Integrin α IIbβ 3 intermediates: From molecular dynamics to adhesion assembly. Biophys J 2023; 122:533-543. [PMID: 36566352 PMCID: PMC9941721 DOI: 10.1016/j.bpj.2022.12.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/14/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
The platelet integrin αIIbβ3 undergoes long-range conformational transitions associated with its functional conversion from inactive (low-affinity) to active (high-affinity) during hemostasis. Although new conformations that are intermediate between the well-characterized bent and extended states have been identified, their molecular dynamic properties and functions in the assembly of adhesions remain largely unexplored. In this study, we evaluated the properties of intermediate conformations of integrin αIIbβ3 and characterized their effects on the assembly of adhesions by combining all-atom simulations, principal component analysis, and mesoscale modeling. Our results show that in the low-affinity, bent conformation, the integrin ectodomain tends to pivot around the legs; in intermediate conformations, the headpiece becomes partially extended, away from the lower legs. In the fully open, active state, αIIbβ3 is flexible, and the motions between headpiece and lower legs are accompanied by fluctuations of the transmembrane helices. At the mesoscale, bent integrins form only unstable adhesions, but intermediate or open conformations stabilize the adhesions. These studies reveal a mechanism by which small variations in ligand binding affinity and enhancement of the ligand-bound lifetime in the presence of actin retrograde flow stabilize αIIbβ3 integrin adhesions.
Collapse
Affiliation(s)
- Dudu Tong
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Nidhi Soley
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Reza Kolasangiani
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Martin A Schwartz
- Yale Cardiovascular Research Center, Department of Internal Medicine (Cardiology), Yale University, New Haven, Connecticut; Department of Cell Biology, Yale University, New Haven, Connecticut; Department of Biomedical Engineering, School of Engineering and Applied Science, Yale University, New Haven, Connecticut
| | - Tamara C Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah; Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah; Department of Biochemistry, University of Utah, Salt Lake City, Utah; Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, Utah.
| |
Collapse
|
17
|
Blanchard AT, Piranej S, Pan V, Salaita K. Adhesive Dynamics Simulations of Highly Polyvalent DNA Motors. J Phys Chem B 2022; 126:7495-7509. [PMID: 36137248 DOI: 10.1021/acs.jpcb.2c01897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular motors, such as myosin and kinesin, perform diverse tasks ranging from vesical transport to bulk muscle contraction. Synthetic molecular motors may eventually be harnessed to perform similar tasks in versatile synthetic systems. The most promising type of synthetic molecular motor, the DNA walker, can undergo processive motion but generally exhibits low speeds and virtually no capacity for force generation. However, we recently showed that highly polyvalent DNA motors (HPDMs) can rival biological motors by translocating at micrometer per minute speeds and generating 100+ pN of force. Accordingly, DNA nanotechnology-based designs may hold promise for the creation of synthetic, force-generating nanomotors. However, the dependencies of HPDM speed and force on tunable design parameters are poorly understood and difficult to characterize experimentally. To overcome this challenge, we present RoloSim, an adhesive dynamics software package for fine-grained simulations of HPDM translocation. RoloSim uses biophysical models for DNA duplex formation and dissociation kinetics to explicitly model tens of thousands of molecular scale interactions. These molecular interactions are then used to calculate the nano- and microscale motions of the motor. We use RoloSim to uncover how motor force and speed scale with several tunable motor properties such as motor size and DNA duplex length. Our results support our previously defined hypothesis that force scales linearly with polyvalency. We also demonstrate that HPDMs can be steered with external force, and we provide design parameters for novel HPDM-based molecular sensor and nanomachine designs.
Collapse
Affiliation(s)
- Aaron T Blanchard
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Selma Piranej
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Victor Pan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States.,Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
18
|
Stirnemann G. Recent Advances and Emerging Challenges in the Molecular Modeling of Mechanobiological Processes. J Phys Chem B 2022; 126:1365-1374. [PMID: 35143190 DOI: 10.1021/acs.jpcb.1c10715] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many biological processes result from the effect of mechanical forces on macromolecular structures and on their interactions. In particular, the cell shape, motion, and differentiation directly depend on mechanical stimuli from the extracellular matrix or from neighboring cells. The development of experimental techniques that can measure and characterize the tiny forces acting at the cellular scale and down to the single-molecule, biomolecular level has enabled access to unprecedented details about the involved mechanisms. However, because the experimental observables often do not provide a direct atomistic picture of the corresponding phenomena, particle-based simulations performed at various scales are instrumental in complementing these experiments and in providing a molecular interpretation. Here, we will review the recent key achievements in the field, and we will highlight and discuss the many technical challenges these simulations are facing, as well as suggest future directions for improvement.
Collapse
Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|
19
|
Transcriptome-Wide Analysis Reveals a Role for Extracellular Matrix and Integrin Receptor Genes in Otic Neurosensory Differentiation from Human iPSCs. Int J Mol Sci 2021; 22:ijms221910849. [PMID: 34639189 PMCID: PMC8509699 DOI: 10.3390/ijms221910849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 12/27/2022] Open
Abstract
We analyzed transcriptomic data from otic sensory cells differentiated from human induced pluripotent stem cells (hiPSCs) by a previously described method to gain new insights into the early human otic neurosensory lineage. We identified genes and biological networks not previously described to occur in the human otic sensory developmental cell lineage. These analyses identified and ranked genes known to be part of the otic sensory lineage program (SIX1, EYA1, GATA3, etc.), in addition to a number of novel genes encoding extracellular matrix (ECM) (COL3A1, COL5A2, DCN, etc.) and integrin (ITG) receptors (ITGAV, ITGA4, ITGA) for ECM molecules. The results were confirmed by quantitative PCR analysis of a comprehensive panel of genes differentially expressed during the time course of hiPSC differentiation in vitro. Immunocytochemistry validated results for select otic and ECM/ITG gene markers in the in vivo human fetal inner ear. Our screen shows ECM and ITG gene expression changes coincident with hiPSC differentiation towards human otic neurosensory cells. Our findings suggest a critical role of ECM-ITG interactions with otic neurosensory lineage genes in early neurosensory development and cell fate determination in the human fetal inner ear.
Collapse
|
20
|
Blanchard AT. Burnt bridge ratchet motor force scales linearly with polyvalency: a computational study. SOFT MATTER 2021; 17:6056-6062. [PMID: 34151336 DOI: 10.1039/d1sm00676b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nano- and micro-scale burnt bridge ratchet motors, which translocate via "guide" molecules that bind to and degrade a field of "fuel" molecules, have recently emerged in several biological and engineering contexts. The capacity of these motors to generate mechanical forces remains an open question. Here, chemomechanical modeling suggests that BBR force scales linearly with the steady-state number of guide-fuel bonds.
Collapse
Affiliation(s)
- Aaron T Blanchard
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA and Michigan Society of Fellows, University of Michigan, Ann Arbor, Michigan 48109, USA.
| |
Collapse
|
21
|
Yeoman B, Shatkin G, Beri P, Banisadr A, Katira P, Engler AJ. Adhesion strength and contractility enable metastatic cells to become adurotactic. Cell Rep 2021; 34:108816. [PMID: 33691109 PMCID: PMC7997775 DOI: 10.1016/j.celrep.2021.108816] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/10/2021] [Accepted: 02/10/2021] [Indexed: 11/05/2022] Open
Abstract
Significant changes in cell stiffness, contractility, and adhesion, i.e., mechanotype, are observed during a variety of biological processes. Whether cell mechanics merely change as a side effect of or driver for biological processes is still unclear. Here, we sort genotypically similar metastatic cancer cells into strongly adherent (SA) versus weakly adherent (WA) phenotypes to study how contractility and adhesion differences alter the ability of cells to sense and respond to gradients in material stiffness. We observe that SA cells migrate up a stiffness gradient, or durotax, while WA cells largely ignore the gradient, i.e., adurotax. Biophysical modeling and experimental validation suggest that differences in cell migration and durotaxis between weakly and strongly adherent cells are driven by differences in intra-cellular actomyosin activity. These results provide a direct relationship between cell phenotype and durotaxis and suggest how, unlike other senescent cells, metastatic cancer cells navigate against stiffness gradients.
Collapse
Affiliation(s)
- Benjamin Yeoman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Gabriel Shatkin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pranjali Beri
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Afsheen Banisadr
- Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA; Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA.
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
22
|
Antonova OY, Kochetkova OY, Shlyapnikov YM. ECM-Mimetic Nylon Nanofiber Scaffolds for Neurite Growth Guidance. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:516. [PMID: 33670540 PMCID: PMC7922859 DOI: 10.3390/nano11020516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/19/2022]
Abstract
Numerous nanostructured synthetic scaffolds mimicking the architecture of the natural extracellular matrix (ECM) have been described, but the polymeric nanofibers comprising the scaffold were substantially thicker than the natural collagen nanofibers of neural ECM. Here, we report neuron growth on electrospun scaffolds of nylon-4,6 fibers with an average diameter of 60 nm, which closely matches the diameter of collagen nanofibers of neural ECM, and compare their properties with the scaffolds of thicker 300 nm nanofibers. Previously unmodified nylon was not regarded as an independent nanostructured matrix for guided growth of neural cells; however, it is particularly useful for ultrathin nanofiber production. We demonstrate that, while both types of fibers stimulate directed growth of neuronal processes, ultrathin fibers are more efficient in promoting and accelerating neurite elongation. Both types of scaffolds also improved synaptogenesis and the formation of connections between hippocampal neurons; however, the mechanisms of interaction of neurites with the scaffolds were substantially different. While ultrathin fibers formed numerous weak immature β1-integrin-positive focal contacts localized over the entire cell surface, scaffolds of submicron fibers formed β1-integrin focal adhesions only on the cell soma. This indicates that the scaffold nanotopology can influence focal adhesion assembly involving various integrin subunits. The fabricated nanostructured scaffolds demonstrated high stability and resistance to biodegradation, as well as absence of toxic compound release after 1 month of incubation with live cells in vitro. Our results demonstrate the high potential of this novel type of nanofibers for clinical application as substrates facilitating regeneration of nervous tissue.
Collapse
Affiliation(s)
- Olga Y. Antonova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia; (O.Y.K.); (Y.M.S.)
| | | | | |
Collapse
|
23
|
Karagöz Z, Rijns L, Dankers PY, van Griensven M, Carlier A. Towards understanding the messengers of extracellular space: Computational models of outside-in integrin reaction networks. Comput Struct Biotechnol J 2020; 19:303-314. [PMID: 33425258 PMCID: PMC7779863 DOI: 10.1016/j.csbj.2020.12.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The interactions between cells and their extracellular matrix (ECM) are critically important for homeostatic control of cell growth, proliferation, differentiation and apoptosis. Transmembrane integrin molecules facilitate the communication between ECM and the cell. Since the characterization of integrins in the late 1980s, there has been great advancement in understanding the function of integrins at different subcellular levels. However, the versatility in molecular pathways integrins are involved in, the high diversity in their interaction partners both outside and inside the cell as well as on the cell membrane and the short lifetime of events happening at the cell-ECM interface make it difficult to elucidate all the details regarding integrin function experimentally. To overcome the experimental challenges and advance the understanding of integrin biology, computational modeling tools have been used extensively. In this review, we summarize the computational models of integrin signaling while we explain the function of integrins at three main subcellular levels (outside the cell, cell membrane, cytosol). We also discuss how these computational modeling efforts can be helpful in other disciplines such as biomaterial design. As such, this review is a didactic modeling summary for biomaterial researchers interested in complementing their experimental work with computational tools or for seasoned computational scientists that would like to advance current in silico integrin models.
Collapse
Affiliation(s)
- Zeynep Karagöz
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| | - Laura Rijns
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands
| | - Patricia Y.W. Dankers
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands
| | - Martijn van Griensven
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| | - Aurélie Carlier
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| |
Collapse
|
24
|
Henning Stumpf B, Ambriović-Ristov A, Radenovic A, Smith AS. Recent Advances and Prospects in the Research of Nascent Adhesions. Front Physiol 2020; 11:574371. [PMID: 33343382 PMCID: PMC7746844 DOI: 10.3389/fphys.2020.574371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
Nascent adhesions are submicron transient structures promoting the early adhesion of cells to the extracellular matrix. Nascent adhesions typically consist of several tens of integrins, and serve as platforms for the recruitment and activation of proteins to build mature focal adhesions. They are also associated with early stage signaling and the mechanoresponse. Despite their crucial role in sampling the local extracellular matrix, very little is known about the mechanism of their formation. Consequently, there is a strong scientific activity focused on elucidating the physical and biochemical foundation of their development and function. Precisely the results of this effort will be summarized in this article.
Collapse
Affiliation(s)
- Bernd Henning Stumpf
- PULS Group, Institute for Theoretical Physics, Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreja Ambriović-Ristov
- Laboratory for Cell Biology and Signalling, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ana-Sunčana Smith
- PULS Group, Institute for Theoretical Physics, Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| |
Collapse
|
25
|
Massaro EK, Goswami I, Verbridge SS, von Spakovsky MR. Electro-chemo-mechanical model to investigate multi-pulse electric-field-driven integrin clustering. Bioelectrochemistry 2020; 137:107638. [PMID: 33160180 DOI: 10.1016/j.bioelechem.2020.107638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022]
Abstract
The effect of pulsed electric fields (PEFs) on transmembrane proteins is not fully understood; how do chemo-mechanical cues in the microenvironment mediate the electric field sensing by these proteins? To answer this key gap in knowledge, we have developed a kinetic Monte Carlo statistical model of the integrin proteins that integrates three components of the morphogenetic field (i.e., chemical, mechanical, and electrical cues). Specifically, the model incorporates the mechanical stiffness of the cell membrane, the ligand density of the extracellular environment, the glycocalyx stiffness, thermal Brownian motion, and electric field induced diffusion. The effects of both steady-state electric fields and transient PEF pulse trains on integrin clustering are studied. Our results reveal that electric-field-driven integrin clustering is mediated by membrane stiffness and ligand density. In addition, we explore the effects of PEF pulse-train parameters (amplitude, polarity, and pulse-width) on integrin clustering. In summary, we demonstrate a computational methodology to incorporate experimental data and simulate integrin clustering when exposed to PEFs for time-scales comparable to experiments (seconds-minutes). Thus, we propose a blueprint for understanding PEF/electric field effects on protein induced signaling and highlight key impediments to incorporating experimental values into computational models such as the kinetic Monte Carlo method.
Collapse
Affiliation(s)
- Evan K Massaro
- Center for Computational Science and Engineering, Massachusetts Institute of Technology, MA, USA
| | - Ishan Goswami
- California Institute for Quantitative Biosciences, University of California Berkeley, CA, USA.
| | - Scott S Verbridge
- Department of Biomedical Engineering and Applied Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Michael R von Spakovsky
- Department of Mechanical Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| |
Collapse
|
26
|
Popowski E, Kohl B, Schneider T, Jankowski J, Schulze-Tanzil G. Uremic Toxins and Ciprofloxacin Affect Human Tenocytes In Vitro. Int J Mol Sci 2020; 21:ijms21124241. [PMID: 32545914 PMCID: PMC7353042 DOI: 10.3390/ijms21124241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
Tendinopathy is a rare but serious complication of quinolone therapy. Risk factors associated with quinolone-induced tendon disorders include chronic kidney disease accompanied by the accumulation of uremic toxins. Hence, the present study explored the effects of the representative uremic toxins phenylacetic acid (PAA) and quinolinic acid (QA), both alone and in combination with ciprofloxacin (CPX), on human tenocytes in vitro. Tenocytes incubated with uremic toxins +/- CPX were investigated for metabolic activity, vitality, expression of the dominant extracellular tendon matrix (ECM) protein type I collagen, cell-matrix receptor β1-integrin, proinflammatory interleukin (IL)-1β, and the ECM-degrading enzyme matrix metalloproteinase (MMP)-1. CPX, when administered at high concentrations (100 mM), suppressed tenocyte metabolism after 8 h exposure and at therapeutic concentrations after 72 h exposure. PAA reduced tenocyte metabolism only after 72 h exposure to very high doses and when combined with CPX. QA, when administered alone, led to scarcely any cytotoxic effect. Combinations of CPX with PAA or QA did not cause greater cytotoxicity than incubation with CPX alone. Gene expression of the pro-inflammatory cytokine IL-1β was reduced by CPX but up-regulated by PAA and QA. Protein levels of type I collagen decreased in response to high CPX doses, whereas PAA and QA did not affect its synthesis significantly. MMP-1 mRNA levels were increased by CPX. This effect became more pronounced in the form of a synergism following exposure to a combination of CPX and PAA. CPX was more tenotoxic than the uremic toxins PAA and QA, which showed only distinct suppressive effects.
Collapse
Affiliation(s)
- Erman Popowski
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany; (E.P.); (B.K.); (T.S.)
| | - Benjamin Kohl
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany; (E.P.); (B.K.); (T.S.)
| | - Tobias Schneider
- Department of Traumatology and Reconstructive Surgery, Campus Benjamin Franklin, Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany; (E.P.); (B.K.); (T.S.)
- Institute of Anatomy, Paracelsus Private Medical University, Nuremberg and Salzburg, Nuremberg, Prof. Ernst Nathan Str. 1, 90419 Nuremberg, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany;
- Experimental Vascular Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Gundula Schulze-Tanzil
- Experimental Vascular Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 HX Maastricht, The Netherlands
- Correspondence: ; Tel.: +49-(0)911-398-6772
| |
Collapse
|
27
|
A Multiscale Model to Predict Neuronal Cell Deformation with Varying Extracellular Matrix Stiffness and Topography. Cell Mol Bioeng 2020; 13:229-245. [PMID: 32426060 DOI: 10.1007/s12195-020-00615-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/11/2020] [Indexed: 02/07/2023] Open
Abstract
Introduction Neuronal cells are sensitive to mechanical properties of extracellular matrix (ECM) such as stiffness and topography. Cells contract and exert a force on ECM to detect the microenvironment, which activates the signaling pathway to influence the cell functions such as differentiation, migration, and proliferation. There are numerous transmembrane proteins that transmit signals; however, integrin and neural cellular adhesion molecules (NCAM) play an important role in sensing the ECM mechanical properties. Mechanotransduction of cell-ECM is the key to understand the influence of ECM stiffness and topography; therefore, in this study, we develop a multiscale computational model to investigate these properties. Methods This model couples the molecular behavior of integrin and NCAM to microscale interactions of neuronal cell and the ECM. We analyze the atomistic/molecular behavior of integrin and NCAM due to mechanical stimuli using steered molecular dynamics. The microscale properties of the neuronal cell and the ECM are simulated using non-linear finite element analysis by applying cell contractility. Results We predict that by increasing the ECM stiffness, a neuronal cell exerts greater stress on the ECM. However, this stress reaches a saturation value for a threshold stiffness of ECM, and the saturation value is affected by the ECM thickness, topography, and clustering of integrin and NCAMs. Further, the ECM topography leads to asymmetric stress and deformation in the neuronal cell. Predicted stress distribution in neuronal cell and ECM are consistent with experimental results from the literature. Conclusion The multiscale computational model will guide in selecting the optimal ECM stiffness and topography range for in vitro studies.
Collapse
|
28
|
Cantini M, Donnelly H, Dalby MJ, Salmeron‐Sanchez M. The Plot Thickens: The Emerging Role of Matrix Viscosity in Cell Mechanotransduction. Adv Healthc Mater 2020; 9:e1901259. [PMID: 31815372 DOI: 10.1002/adhm.201901259] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/26/2019] [Indexed: 12/21/2022]
Abstract
Cell mechanotransduction is an area of intense research focus. Until now, very limited tools have existed to study how cells respond to changes in the extracellular matrix beyond, for example, mechanical deformation studies and twisting cytometry. However, emerging are a range of elastic, viscoelastic and even purely viscous materials that deform and dissipate on cellular length and timescales. This article reviews developments in these materials, typically translating from 2D model surfaces to 3D microenvironments and explores how cells interact with them. Specifically, it focuses on emerging concepts such as the molecular clutch model, how different extracellular matrix proteins engage the clutch under viscoelastic-stress relaxation conditions, and how mechanotransduction can drive transcriptional control through regulators such as YAP/TAZ.
Collapse
Affiliation(s)
- Marco Cantini
- Centre for the Cellular MicroenvironmentUniversity of Glasgow Glasgow G12 8QQ UK
| | - Hannah Donnelly
- Centre for the Cellular MicroenvironmentUniversity of Glasgow Glasgow G12 8QQ UK
| | - Matthew J. Dalby
- Centre for the Cellular MicroenvironmentUniversity of Glasgow Glasgow G12 8QQ UK
| | | |
Collapse
|
29
|
Franz F, Daday C, Gräter F. Advances in molecular simulations of protein mechanical properties and function. Curr Opin Struct Biol 2020; 61:132-138. [PMID: 31954324 DOI: 10.1016/j.sbi.2019.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 01/05/2023]
Abstract
Single-molecule force spectroscopy and classical molecular dynamics are natural allies. Recent advances in both experiments and simulations have increasingly facilitated a direct comparison of SMFS and MD data, most importantly by closing the gap between time scales, which has been traditionally at least 5 orders of magnitudes wide. In this review, we will explore these advances chiefly on the computational side. We focus on protein dynamics under force and highlight recent studies that showcase how lower loading rates and more statistics help to better interpret previous experiments and to also motivate new ones. At the same time, steadily increasing system sizes are used to mimic more closely the mechanical environment in the biological context. We showcase some of these advances on atomistic and coarse-grained scale, from asymmetric membrane tension to larger (multidomain/multimeric) protein assemblies under force.
Collapse
Affiliation(s)
- Florian Franz
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, 69120 Heidelberg, Germany
| | - Csaba Daday
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Frauke Gräter
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, 69120 Heidelberg, Germany.
| |
Collapse
|