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Jafarinia H, Khalilimeybodi A, Barrasa-Fano J, Fraley SI, Rangamani P, Carlier A. Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction. NPJ Syst Biol Appl 2024; 10:90. [PMID: 39147782 PMCID: PMC11327324 DOI: 10.1038/s41540-024-00414-9] [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: 02/29/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024] Open
Abstract
YAP/TAZ signaling pathway is regulated by a multiplicity of feedback loops, crosstalk with other pathways, and both mechanical and biochemical stimuli. Computational modeling serves as a powerful tool to unravel how these different factors can regulate YAP/TAZ, emphasizing biophysical modeling as an indispensable tool for deciphering mechanotransduction and its regulation of cell fate. We provide a critical review of the current state-of-the-art of computational models focused on YAP/TAZ signaling.
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Affiliation(s)
- Hamidreza Jafarinia
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering, Maastricht University, Maastricht, The Netherlands
| | - Ali Khalilimeybodi
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA
| | - Jorge Barrasa-Fano
- Department of Mechanical Engineering, Biomechanics Section, KU Leuven, Leuven, Belgium
| | - Stephanie I Fraley
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093-0411, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA.
| | - Aurélie Carlier
- MERLN Institute for Technology-Inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering, Maastricht University, Maastricht, The Netherlands.
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2
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Xiao Z, Postma RJ, van Zonneveld AJ, van den Berg BM, Sol WM, White NA, van de Stadt HJ, Mirza A, Wen J, Bijkerk R, Rotmans JI. A bypass flow model to study endothelial cell mechanotransduction across diverse flow environments. Mater Today Bio 2024; 27:101121. [PMID: 38988818 PMCID: PMC11234155 DOI: 10.1016/j.mtbio.2024.101121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/07/2024] [Accepted: 06/08/2024] [Indexed: 07/12/2024] Open
Abstract
Disturbed flow is one of the pathological initiators of endothelial dysfunction in intimal hyperplasia (IH) which is commonly seen in vascular bypass grafts, and arteriovenous fistulas. Various in vitro disease models have been designed to simulate the hemodynamic conditions found in the vasculature. Nonetheless, prior investigations have encountered challenges in establishing a robust disturbed flow model, primarily attributed to the complex bifurcated geometries and distinctive flow dynamics. In the present study, we aim to address this gap by introducing an in vitro bypass flow model capable of inducing disturbed flow and other hemodynamics patterns through a pulsatile flow in the same model. To assess the model's validity, we employed computational fluid dynamics (CFD) to simulate hemodynamics and compared the morphology and functions of human umbilical venous endothelial cells (HUVECs) under disturbed flow conditions to those in physiological flow or stagnant conditions. CFD analysis revealed the generation of disturbed flow within the model, pinpointing the specific location in the channel where the effects of disturbed flow were observed. High-content screening, a single-cell morphological profile assessment, demonstrated that HUVECs in the disturbed flow area exhibited random orientation, and morphological features were significantly distinct compared to cells in the physiological flow or stagnant condition after a two days of flow exposure. Furthermore, HUVECs exposed to disturbed flow underwent extensive remodeling of the adherens junctions and expressed higher levels of endothelial cell activation markers compared to other hemodynamic conditions. In conclusion, our in vitro bypass flow model provides a robust platform for investigating the associations between disturbed flow pattern and vascular diseases.
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Affiliation(s)
- Zhuotao Xiao
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
- Department of Nephrology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China
| | - Rudmer J. Postma
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
| | - Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
| | - Bernard M. van den Berg
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
| | - Wendy M.P.J. Sol
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
| | - Nicholas A. White
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
- Department of BioMechanical Engineering, Delft University of Technology, Delft, 2628, CN, Netherlands
| | - Huybert J.F. van de Stadt
- Department of Medical Technology, Design & Prototyping, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
| | - Asad Mirza
- Department of Biomedical Engineering, Florida International University, Miami, FL, 33199, United States
| | - Jun Wen
- Department of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
| | - Joris I. Rotmans
- Department of Internal Medicine (Nephrology) and the Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, 2333, ZA, Netherlands
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3
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Lee CT, Bell M, Bonilla-Quintana M, Rangamani P. Biophysical Modeling of Synaptic Plasticity. Annu Rev Biophys 2024; 53:397-426. [PMID: 38382115 DOI: 10.1146/annurev-biophys-072123-124954] [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: 02/23/2024]
Abstract
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
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4
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Gekle M, Eckenstaler R, Braun H, Olgac A, Robaa D, Mildenberger S, Dubourg V, Schreier B, Sippl W, Benndorf R. Direct GPCR-EGFR interaction enables synergistic membrane-to-nucleus information transfer. Cell Mol Life Sci 2024; 81:272. [PMID: 38900158 DOI: 10.1007/s00018-024-05281-5] [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: 12/27/2023] [Revised: 04/12/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
We addressed the heteromerization of the epidermal growth factor receptor (EGFR) with G-protein coupled receptors (GPCR) on the basis of angiotensin-II-receptor-subtype-1(AT1R)-EGFR interaction as proof-of-concept and show its functional relevance during synergistic nuclear information transfer, beyond ligand-dependent EGFR transactivation. Following in silico modelling, we generated EGFR-interaction deficient AT1R-mutants and compared them to AT1R-wildtype. Receptor interaction was assessed by co-immunoprecipitation (CoIP), Förster resonance energy transfer (FRET) and fluorescence-lifetime imaging microscopy (FLIM). Changes in cell morphology, ERK1/2-phosphorylation (ppERK1/2), serum response factor (SRF)-activation and cFOS protein expression were determined by digital high content microscopy at the single cell level. FRET, FLIM and CoIP confirmed the physical interaction of AT1R-wildtype with EGFR that was strongly reduced for the AT1R-mutants. Responsiveness of cells transfected with AT1R-WT or -mutants to angiotensin II or EGF was similar regarding changes in cell circularity, ppERK1/2 (direct and by ligand-dependent EGFR-transactivation), cFOS-expression and SRF-activity. By contrast, the EGFR-AT1R-synergism regarding these parameters was completely absent for in the interaction-deficient AT1R mutants. The results show that AT1R-EGFR heteromerisation enables AT1R-EGFR-synergism on downstream gene expression regulation, modulating the intensity and the temporal pattern of nuclear AT1R/EGFR-information transfer. Furthermore, remote EGFR transactivation, via ligand release or cytosolic tyrosine kinases, is not sufficient for the complete synergistic control of gene expression.
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Affiliation(s)
- Michael Gekle
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, 06112, Halle (Saale), Germany.
| | - Robert Eckenstaler
- Institute of Pharmacy, Department of Clinical Pharmacy and Pharmacotherapy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Heike Braun
- Institute of Pharmacy, Department of Clinical Pharmacy and Pharmacotherapy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Abdurrahman Olgac
- Institute of Pharmacy, Department of Medical Chemistry, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dina Robaa
- Institute of Pharmacy, Department of Medical Chemistry, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Sigrid Mildenberger
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, 06112, Halle (Saale), Germany
| | - Virginie Dubourg
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, 06112, Halle (Saale), Germany
| | - Barbara Schreier
- Julius-Bernstein-Institute of Physiology, Martin Luther University Halle-Wittenberg, 06112, Halle (Saale), Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Department of Medical Chemistry, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ralf Benndorf
- Institute of Pharmacy, Department of Clinical Pharmacy and Pharmacotherapy, Martin Luther University Halle-Wittenberg, Halle, Germany
- Institute of Pharmacology and Toxicology, Ruhr-University Bochum, 44780, Bochum, Germany
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5
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Christoph E, Yu L, Newby SD, Rivera Orsini MA, Scroggins J, Keffer DJ, Harper DP, Dhar M. Novel Kraft Softwood Lignin-Derived Carbon Quantum Dots: Synthesis, Characterization, and In Vitro Cytocompatibility. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1029. [PMID: 38921905 PMCID: PMC11206522 DOI: 10.3390/nano14121029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/27/2024]
Abstract
Carbon quantum dots (CQDs) have been investigated for biomedical applications in medical imaging due to their fluorescent properties, overall long-term stability, and excellent cytocompatibility and biocompatibility. Lignin is an organic polymer in the tissues of woody plants. It is also considered a byproduct of the wood and pulp industries. Hence, it presents as a renewable source of carbon nanoparticles. In this study, we report the synthesis and material and biological characterization of two colloidal suspensions of CQDs in water derived from lignin-based carbon. One was the native form of CQDs derived from lignin carbon, and the second was doped with nitrogen to evaluate material differences. Material characterization was carried out using various commonly used techniques, including Fourier transform infrared spectroscopy (FTIR), emission and absorbance spectra, zeta potential, transmission electron microscopy (TEM), and scanning electron microscopy (SEM). Thin films of CQDs were formed on glass and silicon substrates to assess the in vitro cytocompatibility with human mesenchymal stem cells (hMSCs). Observations suggest that the two forms of CQDs promote cell attachment within 24 h and sustain it for at least 7 days. The overall structure and shape of cells suggest a lack of any adverse or toxic effects of CQDs. The data lay down the novel foundation to support the use of lignin-derived CQDs in tissue engineering applications.
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Affiliation(s)
- Eli Christoph
- Material Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA; (E.C.); (L.Y.); (J.S.); (D.J.K.)
- Tissue Engineering and Regenerative Medicine, Large Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA; (S.D.N.); (M.A.R.O.)
| | - Lu Yu
- Material Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA; (E.C.); (L.Y.); (J.S.); (D.J.K.)
| | - Steven D. Newby
- Tissue Engineering and Regenerative Medicine, Large Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA; (S.D.N.); (M.A.R.O.)
| | - Michael A. Rivera Orsini
- Tissue Engineering and Regenerative Medicine, Large Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA; (S.D.N.); (M.A.R.O.)
| | - Jakob Scroggins
- Material Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA; (E.C.); (L.Y.); (J.S.); (D.J.K.)
| | - David J. Keffer
- Material Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA; (E.C.); (L.Y.); (J.S.); (D.J.K.)
| | - David P. Harper
- Center for Renewable Carbon, School for Natural Resources, University of Tennessee, Knoxville, TN 37996, USA;
| | - Madhu Dhar
- Tissue Engineering and Regenerative Medicine, Large Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA; (S.D.N.); (M.A.R.O.)
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6
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Massidda MW, Ashirov D, Demkov A, Sices A, Baker AB. A Computational Model of Mechanical Stretching of Cultured Cells on a Flexible Membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597769. [PMID: 38895285 PMCID: PMC11185657 DOI: 10.1101/2024.06.06.597769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Mechanical forces applied to cells are known to regulate a wide variety of biological processes. Recent studies have supported that mechanical forces can cause nuclear deformation, leading to significant alterations in the gene expression and chromatin landscape of the cell. While the stresses and strains applied to cells is it is often known or controlled experimentally on a macroscopic length scale, it is often unclear what the actual forces and displacements are at the microscopic level of the cell. In this work, we created a model of cell deformation during application of mechanical stretch to cultured cells growth on a flexible membrane. This configuration is commonly used is in experimental studies as a means to apply controlled mechanical strains to adherent cultured cells. The parameters used in the study were used for application of strain to a mesenchymal stem cell stretched on a membrane. computational model was created to simulate the stresses and strains within the cell under a variety of stain amplitudes, waveforms and frequencies of mechanical loading with the range of commonly used experimental systems. The results demonstrate the connection between mechanical loading parameters applied through the flexible membrane and the resulting stresses and strains within the cell and nucleus. Using a viscoelastic model of chromatin, we connected the results provide to a rough model of resulting deformation within chromatin from the forces applied to the nucleus. Overall, the model is useful in providing insight between experimentally applied mechanical forces and the actual forces within the cell to better interpret the results of experimental studies. Statement of Significance In this work, we created a computational model of the mechanical stretching of cell on a flexible membrane under cyclic mechanical loading. This model provides insight into the forces and displacements inside of cell that result from that application of stretch. As many experiments use this set up, our work is relevant to interpreting many studies that use mechanical stretch to stimulate mechanotransduction.
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7
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Cai FF, Blanquer A, Costa MB, Schweiger L, Sarac B, Greer AL, Schroers J, Teichert C, Nogués C, Spieckermann F, Eckert J. Hierarchical Surface Pattern on Ni-Free Ti-Based Bulk Metallic Glass to Control Cell Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310364. [PMID: 38109153 DOI: 10.1002/smll.202310364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Ni-free Ti-based bulk metallic glasses (BMGs) are exciting materials for biomedical applications because of their outstanding biocompatibility and advantageous mechanical properties. The glassy nature of BMGs allows them to be shaped and patterned via thermoplastic forming (TPF). This work demonstrates the versatility of the TPF technique to create micro- and nano-patterns and hierarchical structures on Ti40Zr10Cu34Pd14Sn2 BMG. Particularly, a hierarchical structure fabricated by a two-step TPF process integrates 400 nm hexagonal close-packed protrusions on 2.5 µm square protuberances while preserving the advantageous mechanical properties from the as-cast material state. The correlations between thermal history, structure, and mechanical properties are explored. Regarding biocompatibility, Ti40Zr10Cu34Pd14Sn2 BMGs with four surface topographies (flat, micro-patterned, nano-patterned, and hierarchical-structured surfaces) are investigated using Saos-2 cell lines. Alamar Blue assay and live/dead analysis show that all tested surfaces have good cell proliferation and viability. Patterned surfaces are observed to promote the formation of longer filopodia on the edge of the cytoskeleton, leading to star-shaped and dendritic cell morphologies compared with the flat surface. In addition to potential implant applications, TPF-patterned Ti-BMGs enable a high level of order and design flexibility on the surface topography, expanding the available toolbox for studying cell behavior on rigid and ordered surfaces.
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Affiliation(s)
- Fei-Fan Cai
- Department of Materials Science, Chair of Materials Physics, Montanuniversität Leoben, Jahnstraße 12, Leoben, A-8700, Austria
- Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Jahnstraße 12, Leoben, A-8700, Austria
| | - Andreu Blanquer
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Miguel B Costa
- Department of Materials Science & Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Lukas Schweiger
- Department of Materials Science, Chair of Materials Physics, Montanuniversität Leoben, Jahnstraße 12, Leoben, A-8700, Austria
| | - Baran Sarac
- Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Jahnstraße 12, Leoben, A-8700, Austria
| | - A Lindsay Greer
- Department of Materials Science & Metallurgy, University of Cambridge, Cambridge, CB3 0FS, UK
| | - Jan Schroers
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT 06511, USA
| | - Christian Teichert
- Department Physics, Mechanics and Electrical Engineering, Chair of Physics, Montanuniversität Leoben, Franz-Josef-Strasse 18, Leoben, A-8700, Austria
| | - Carme Nogués
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Florian Spieckermann
- Department of Materials Science, Chair of Materials Physics, Montanuniversität Leoben, Jahnstraße 12, Leoben, A-8700, Austria
| | - Jürgen Eckert
- Department of Materials Science, Chair of Materials Physics, Montanuniversität Leoben, Jahnstraße 12, Leoben, A-8700, Austria
- Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Jahnstraße 12, Leoben, A-8700, Austria
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Raj P, Gupta H, Anantha P, Barman I. Cell-TIMP: Cellular Trajectory Inference based on Morphological Parameter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590109. [PMID: 38712120 PMCID: PMC11071304 DOI: 10.1101/2024.04.18.590109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cellular morphology, shaped by various genetic and environmental influences, is pivotal to studying experimental cell biology, necessitating precise measurement and analysis techniques. Traditional approaches, which rely on geometric metrics derived from stained images, encounter obstacles stemming from both the imaging and analytical domains. Staining processes can disrupt the cell's natural state and diminish accuracy due to photobleaching, while conventional analysis techniques, which categorize cells based on shape to discern pathophysiological conditions, often fail to capture the continuous and asynchronous nature of biological processes such as cell differentiation, immune responses, and cancer progression. In this work, we propose the use of quantitative phase imaging for morphological assessment due to its label-free nature. For analysis, we repurposed the genomic analysis toolbox to perform trajectory inference analysis purely based on morphology information. We applied the developed framework to study the progression of leukemia and breast cancer metastasis. Our approach revealed a clear pattern of morphological evolution tied to the diseases' advancement, highlighting the efficacy of our method in identifying functionally significant shape changes where conventional techniques falter. This advancement offers a fresh perspective on analyzing cellular morphology and holds significant potential for the broader research community, enabling a deeper understanding of complex biological dynamics.
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Affiliation(s)
- Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Himanshu Gupta
- Centre for Applied Autonomous Sensor Systems (AASS), Örebro University, Örebro, Sweden
| | - Pooja Anantha
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland, USA
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9
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Lin J, Zhang Q, Xie T, Wu Z, Hou Y, Song Y, Lin Y, Lin JM. Understanding Macrophage-Tumor Interactions: Insights from Single-Cell Behavior Monitoring in a Sessile Microdroplet System. SMALL METHODS 2024:e2301659. [PMID: 38623914 DOI: 10.1002/smtd.202301659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/25/2024] [Indexed: 04/17/2024]
Abstract
Interaction between tumor-associated macrophages and tumor cells is crucial for tumor development, metastasis, and the related immune process. However, the macrophages are highly heterogeneous spanning from anti-tumorigenic to pro-tumorigenic, which needs to be understood at the single-cell level. Herein, a sessile microdroplet system designed for monitoring cellular behavior and analyzing intercellular interaction, demonstrated with macrophage-tumor cell pairs is presented. An automatic procedure based on the inkjet printing method is utilized for the precise pairing and co-encapsulation of heterotypic cells within picoliter droplets. The sessile nature of microdroplets ensures controlled fusion and provides stable environments conducive to adherent cell culture. The nitric oxide generation and morphological changes over incubation are explored to reveal the complicated interactions from a single-cell perspective. The immune response of macrophages under distinct cellular microenvironments is recorded. The results demonstrate that the tumor microenvironment displays a modulating role in polarizing macrophages from anti-tumorigenic into pro-tumorigenic phenotype. The approach provides a versatile and compatible platform to investigate intercellular interaction at the single-cell level, showing promising potential for advancing single-cell behavior studies.
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Affiliation(s)
- Jiaxu Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Qiang Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Tianze Xie
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Zengnan Wu
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Ying Hou
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Yang Song
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Yongning Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
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10
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Mirzakhel Z, Reddy GA, Boman J, Manns B, Veer ST, Katira P. "Patchiness" in mechanical stiffness across a tumor as an early-stage marker for malignancy. BMC Ecol Evol 2024; 24:33. [PMID: 38486161 PMCID: PMC10938681 DOI: 10.1186/s12862-024-02221-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 03/03/2024] [Indexed: 03/17/2024] Open
Abstract
Mechanical phenotyping of tumors, either at an individual cell level or tumor cell population level is gaining traction as a diagnostic tool. However, the extent of diagnostic and prognostic information that can be gained through these measurements is still unclear. In this work, we focus on the heterogeneity in mechanical properties of cells obtained from a single source such as a tissue or tumor as a potential novel biomarker. We believe that this heterogeneity is a conventionally overlooked source of information in mechanical phenotyping data. We use mechanics-based in-silico models of cell-cell interactions and cell population dynamics within 3D environments to probe how heterogeneity in cell mechanics drives tissue and tumor dynamics. Our simulations show that the initial heterogeneity in the mechanical properties of individual cells and the arrangement of these heterogenous sub-populations within the environment can dictate overall cell population dynamics and cause a shift towards the growth of malignant cell phenotypes within healthy tissue environments. The overall heterogeneity in the cellular mechanotype and their spatial distributions is quantified by a "patchiness" index, which is the ratio of the global to local heterogeneity in cell populations. We observe that there exists a threshold value of the patchiness index beyond which an overall healthy population of cells will show a steady shift towards a more malignant phenotype. Based on these results, we propose that the "patchiness" of a tumor or tissue sample, can be an early indicator for malignant transformation and cancer occurrence in benign tumors or healthy tissues. Additionally, we suggest that tissue patchiness, measured either by biochemical or biophysical markers, can become an important metric in predicting tissue health and disease likelihood just as landscape patchiness is an important metric in ecology.
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Affiliation(s)
- Zibah Mirzakhel
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Gudur Ashrith Reddy
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Jennifer Boman
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Brianna Manns
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Savannah Ter Veer
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA.
- Computational Science Research Center, San Diego State University, San Diego, CA, USA.
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11
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Barbieri S, Gotta M. Order from chaos: cellular asymmetries explained with modelling. Trends Cell Biol 2024; 34:122-135. [PMID: 37574346 DOI: 10.1016/j.tcb.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 08/15/2023]
Abstract
Molecules inside cells are subject to physical forces and undergo biochemical interactions, continuously changing their physical properties and dynamics. Despite this, cells achieve highly ordered molecular patterns that are crucial to regulate various cellular functions and to specify cell fate. In the Caenorhabditis elegans one-cell embryo, protein asymmetries are established in the narrow time window of a cell division. What are the mechanisms that allow molecules to establish asymmetries, defying the randomness imposed by Brownian motion? Mathematical and computational models have paved the way to the understanding of protein dynamics up to the 'single-molecule level' when resolution represents an issue for precise experimental measurements. Here we review the models that interpret cortical and cytoplasmic asymmetries in the one-cell C. elegans embryo.
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Affiliation(s)
- Sofia Barbieri
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland.
| | - Monica Gotta
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
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12
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Venkatraman K, Lee CT, Garcia GC, Mahapatra A, Milshteyn D, Perkins G, Kim K, Pasolli HA, Phan S, Lippincott‐Schwartz J, Ellisman MH, Rangamani P, Budin I. Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome. EMBO J 2023; 42:e114054. [PMID: 37933600 PMCID: PMC10711667 DOI: 10.15252/embj.2023114054] [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: 03/19/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023] Open
Abstract
Cristae are high-curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous lipid-based mechanisms have yet to be elucidated. Here, we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the inner mitochondrial membrane against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. This model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that cardiolipin is essential in low-oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of cardiolipin is dependent on the surrounding lipid and protein components of the IMM.
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Affiliation(s)
- Kailash Venkatraman
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
| | - Christopher T Lee
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
| | - Guadalupe C Garcia
- Computational Neurobiology LaboratorySalk Institute for Biological StudiesLa JollaCAUSA
| | - Arijit Mahapatra
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
- Present address:
Applied Physical SciencesUniversity of North Carolina Chapel HillChapel HillNCUSA
| | - Daniel Milshteyn
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - Keun‐Young Kim
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - H Amalia Pasolli
- Howard Hughes Medical InstituteAshburnVAUSA
- Present address:
Electron Microscopy Resource CenterThe Rockefeller UniversityNew YorkNYUSA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | | | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological SystemsUniversity of California San DiegoLa JollaCAUSA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace EngineeringUniversity of California San DiegoLa JollaCAUSA
| | - Itay Budin
- Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaCAUSA
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13
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Xu SQ, Sie ZY, Hsu JI, Tan KT. Small Plasma Membrane-Targeted Fluorescent Dye for Long-Time Imaging and Protein Degradation Analyses. Anal Chem 2023; 95:15549-15555. [PMID: 37816133 DOI: 10.1021/acs.analchem.3c01980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Plasma membrane (PM)-targeted fluorescent dyes have become an important tool to visualize morphological and dynamic changes in the cell membrane. However, most of these PM dyes are either too large and thus might potentially perturb the membrane and affect its functions or exhibit a short retention time on the cell membrane. The rapid internalization problem is particularly severe for PM dyes based on cationic and neutral hydrophobic fluorescent dyes, which can be easily transported into the cells by transmembrane potential and passive diffusion mechanisms. In this paper, we report a small but highly specific PM fluorescent dye, PM-1, which exhibits a very long retention time on the plasma membrane with a half-life of approximately 15 h. For biological applications, we demonstrated that PM-1 can be used in combination with protein labeling probes to study ectodomain shedding and endocytosis processes of cell surface proteins and successfully demonstrated that native transmembrane human carbonic anhydrase IX (hCAIX) is degraded via the ectodomain shedding mechanism. In contrast, hCAIX undergoes endocytic degradation in the presence of sheddase inhibitors. We believe that PM-1 can be a versatile tool to provide detailed insights into the dynamic processes of the cell surface proteins.
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Affiliation(s)
- Shun-Qiang Xu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Zong-Yan Sie
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Jung-I Hsu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China
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14
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Srikanth S, Narayanan R. Heterogeneous off-target impact of ion-channel deletion on intrinsic properties of hippocampal model neurons that self-regulate calcium. Front Cell Neurosci 2023; 17:1241450. [PMID: 37904732 PMCID: PMC10613471 DOI: 10.3389/fncel.2023.1241450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/20/2023] [Indexed: 11/01/2023] Open
Abstract
How do neurons that implement cell-autonomous self-regulation of calcium react to knockout of individual ion-channel conductances? To address this question, we used a heterogeneous population of 78 conductance-based models of hippocampal pyramidal neurons that maintained cell-autonomous calcium homeostasis while receiving theta-frequency inputs. At calcium steady-state, we individually deleted each of the 11 active ion-channel conductances from each model. We measured the acute impact of deleting each conductance (one at a time) by comparing intrinsic electrophysiological properties before and immediately after channel deletion. The acute impact of deleting individual conductances on physiological properties (including calcium homeostasis) was heterogeneous, depending on the property, the specific model, and the deleted channel. The underlying many-to-many mapping between ion channels and properties pointed to ion-channel degeneracy. Next, we allowed the other conductances (barring the deleted conductance) to evolve towards achieving calcium homeostasis during theta-frequency activity. When calcium homeostasis was perturbed by ion-channel deletion, post-knockout plasticity in other conductances ensured resilience of calcium homeostasis to ion-channel deletion. These results demonstrate degeneracy in calcium homeostasis, as calcium homeostasis in knockout models was implemented in the absence of a channel that was earlier involved in the homeostatic process. Importantly, in reacquiring homeostasis, ion-channel conductances and physiological properties underwent heterogenous plasticity (dependent on the model, the property, and the deleted channel), even introducing changes in properties that were not directly connected to the deleted channel. Together, post-knockout plasticity geared towards maintaining homeostasis introduced heterogenous off-target effects on several channels and properties, suggesting that extreme caution be exercised in interpreting experimental outcomes involving channel knockouts.
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Affiliation(s)
- Sunandha Srikanth
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Undergraduate Program, Indian Institute of Science, Bangalore, India
| | - Rishikesh Narayanan
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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15
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Venkatraman K, Lee CT, Garcia GC, Mahapatra A, Milshteyn D, Perkins G, Kim KY, Pasolli HA, Phan S, Lippincott-Schwartz J, Ellisman MH, Rangamani P, Budin I. Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532310. [PMID: 36993370 PMCID: PMC10054968 DOI: 10.1101/2023.03.13.532310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Cristae are high curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous mechanisms for lipids have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the IMM against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. The model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that CL is essential in low oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of CL is dependent on the surrounding lipid and protein components of the IMM.
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Affiliation(s)
- Kailash Venkatraman
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093
| | - Guadalupe C Garcia
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla CA 92097
| | - Arijit Mahapatra
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093
| | - Daniel Milshteyn
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | - Keun-Young Kim
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | - H Amalia Pasolli
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn VA 20147
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | | | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Lead contact
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16
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Keto L, Manninen T. CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations. Neuroinformatics 2023; 21:483-500. [PMID: 37133688 PMCID: PMC10406679 DOI: 10.1007/s12021-023-09627-5] [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] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
Understanding functions of astrocytes can be greatly enhanced by building and simulating computational models that capture their morphological details. Novel computational tools enable utilization of existing morphological data of astrocytes and building models that have appropriate level of details for specific simulation purposes. In addition to analyzing existing computational tools for constructing, transforming, and assessing astrocyte morphologies, we present here the CellRemorph toolkit implemented as an add-on for Blender, a 3D modeling platform increasingly recognized for its utility for manipulating 3D biological data. To our knowledge, CellRemorph is the first toolkit for transforming astrocyte morphologies from polygonal surface meshes into adjustable surface point clouds and vice versa, precisely selecting nanoprocesses, and slicing morphologies into segments with equal surface areas or volumes. CellRemorph is an open-source toolkit under the GNU General Public License and easily accessible via an intuitive graphical user interface. CellRemorph will be a valuable addition to other Blender add-ons, providing novel functionality that facilitates the creation of realistic astrocyte morphologies for different types of morphologically detailed simulations elucidating the role of astrocytes both in health and disease.
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Affiliation(s)
- Laura Keto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Tiina Manninen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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17
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Zhou FY, Weems A, Gihana GM, Chen B, Chang BJ, Driscoll M, Danuser G. Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536640. [PMID: 37131779 PMCID: PMC10153113 DOI: 10.1101/2023.04.12.536640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have limited quantitative understanding of the processes implicated in the regulation of molecular signals at the whole cell scale. In particular, complex and transient cell surface morphologies challenge the complete sampling of cell geometry, membrane-associated molecular concentration and activity and the computing of meaningful parameters such as the cofluctuation between morphology and signals. Here, we introduce u-Unwrap3D, a framework to remap arbitrarily complex 3D cell surfaces and membrane-associated signals into equivalent lower dimensional representations. The mappings are bidirectional, allowing the application of image processing operations in the data representation best suited for the task and to subsequently present the results in any of the other representations, including the original 3D cell surface. Leveraging this surface-guided computing paradigm, we track segmented surface motifs in 2D to quantify the recruitment of Septin polymers by blebbing events; we quantify actin enrichment in peripheral ruffles; and we measure the speed of ruffle movement along topographically complex cell surfaces. Thus, u-Unwrap3D provides access to spatiotemporal analyses of cell biological parameters on unconstrained 3D surface geometries and signals.
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Affiliation(s)
- Felix Y. Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Weems
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gabriel M. Gihana
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bingying Chen
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meghan Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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18
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Zhou FY, Weems A, Gihana GM, Chen B, Chang BJ, Driscoll M, Danuser G. Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D. ARXIV 2023:arXiv:2304.06176v1. [PMID: 37090235 PMCID: PMC10120750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have limited quantitative understanding of the processes implicated in the regulation of molecular signals at the whole cell scale. In particular, complex and transient cell surface morphologies challenge the complete sampling of cell geometry, membrane-associated molecular concentration and activity and the computing of meaningful parameters such as the cofluctuation between morphology and signals. Here, we introduce u-Unwrap3D, a framework to remap arbitrarily complex 3D cell surfaces and membrane-associated signals into equivalent lower dimensional representations. The mappings are bidirectional, allowing the application of image processing operations in the data representation best suited for the task and to subsequently present the results in any of the other representations, including the original 3D cell surface. Leveraging this surface-guided computing paradigm, we track segmented surface motifs in 2D to quantify the recruitment of Septin polymers by blebbing events; we quantify actin enrichment in peripheral ruffles; and we measure the speed of ruffle movement along topographically complex cell surfaces. Thus, u-Unwrap3D provides access to spatiotemporal analyses of cell biological parameters on unconstrained 3D surface geometries and signals.
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Affiliation(s)
- Felix Y. Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Weems
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gabriel M. Gihana
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bingying Chen
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meghan Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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19
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Li JH, Trivedi V, Diz-Muñoz A. Understanding the interplay of membrane trafficking, cell surface mechanics, and stem cell differentiation. Semin Cell Dev Biol 2023; 133:123-134. [PMID: 35641408 PMCID: PMC9703995 DOI: 10.1016/j.semcdb.2022.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/08/2022] [Accepted: 05/14/2022] [Indexed: 01/17/2023]
Abstract
Stem cells can generate a diversity of cell types during development, regeneration and adult tissue homeostasis. Differentiation changes not only the cell fate in terms of gene expression but also the physical properties and functions of cells, e.g. the secretory activity, cell shape, or mechanics. Conversely, these activities and properties can also regulate differentiation itself. Membrane trafficking is known to modulate signal transduction and thus has the potential to control stem cell differentiation. On the other hand, membrane trafficking, particularly from and to the plasma membrane, depends on the mechanical properties of the cell surface such as tension within the plasma membrane or the cortex. Indeed, recent findings demonstrate that cell surface mechanics can also control cell fate. Here, we review the bidirectional relationships between these three fundamental cellular functions, i.e. membrane trafficking, cell surface mechanics, and stem cell differentiation. Furthermore, we discuss commonly used methods in each field and how combining them with new tools will enhance our understanding of their interplay. Understanding how membrane trafficking and cell surface mechanics can guide stem cell fate holds great potential as these concepts could be exploited for directed differentiation of stem cells for the fields of tissue engineering and regenerative medicine.
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Affiliation(s)
- Jia Hui Li
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Vikas Trivedi
- EMBL, PRBB, Dr. Aiguader, 88, Barcelona 08003, Spain,Developmental Biology Unit, EMBL, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg 69117, Germany.
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20
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Florczyk SJ, Hotaling NA, Simon M, Chalfoun J, Horenberg AL, Schaub NJ, Wang D, Szczypiński PM, DeFelice VL, Bajcsy P, Simon CG. Measuring dimensionality of cell-scaffold contacts of primary human bone marrow stromal cells cultured on electrospun fiber scaffolds. J Biomed Mater Res A 2023; 111:106-117. [PMID: 36194510 DOI: 10.1002/jbm.a.37449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
Abstract
The properties and structure of the cellular microenvironment can influence cell behavior. Sites of cell adhesion to the extracellular matrix (ECM) initiate intracellular signaling that directs cell functions such as proliferation, differentiation, and apoptosis. Electrospun fibers mimic the fibrous nature of native ECM proteins and cell culture in fibers affects cell shape and dimensionality, which can drive specific functions, such as the osteogenic differentiation of primary human bone marrow stromal cells (hBMSCs), by. In order to probe how scaffolds affect cell shape and behavior, cell-fiber contacts were imaged to assess their shape and dimensionality through a novel approach. Fluorescent polymeric fiber scaffolds were made so that they could be imaged by confocal fluorescence microscopy. Fluorescent polymer films were made as a planar control. hBSMCs were cultured on the fluorescent substrates and the cells and substrates were imaged. Two different image analysis approaches, one having geometrical assumptions and the other having statistical assumptions, were used to analyze the 3D structure of cell-scaffold contacts. The cells cultured in scaffolds contacted the fibers in multiple planes over the surface of the cell, while the cells cultured on films had contacts confined to the bottom surface of the cell. Shape metric analysis indicated that cell-fiber contacts had greater dimensionality and greater 3D character than the cell-film contacts. These results suggest that cell adhesion site-initiated signaling could emanate from multiple planes over the cell surface during culture in fibers, as opposed to emanating only from the cell's basal surface during culture on planar surfaces.
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Affiliation(s)
- Stephanie J Florczyk
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Nathan A Hotaling
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.,Axle Informatics, Rockville, Maryland, USA
| | - Mylene Simon
- Software and Systems Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Joe Chalfoun
- Software and Systems Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Allison L Horenberg
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Nicholas J Schaub
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.,Axle Informatics, Rockville, Maryland, USA
| | - Dongbo Wang
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | | | - Veronica L DeFelice
- Biochemistry and Molecular Biology Program, Georgetown University, Washington, District of Columbia, USA
| | - Peter Bajcsy
- Software and Systems Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Carl G Simon
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
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21
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Mobashir M, Turunen SP, Izhari MA, Ashankyty IM, Helleday T, Lehti K. An Approach for Systems-Level Understanding of Prostate Cancer from High-Throughput Data Integration to Pathway Modeling and Simulation. Cells 2022; 11:cells11244121. [PMID: 36552885 PMCID: PMC9777290 DOI: 10.3390/cells11244121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To understand complex diseases, high-throughput data are generated at large and multiple levels. However, extracting meaningful information from large datasets for comprehensive understanding of cell phenotypes and disease pathophysiology remains a major challenge. Despite tremendous advances in understanding molecular mechanisms of cancer and its progression, current knowledge appears discrete and fragmented. In order to render this wealth of data more integrated and thus informative, we have developed a GECIP toolbox to investigate the crosstalk and the responsible genes'/proteins' connectivity of enriched pathways from gene expression data. To implement this toolbox, we used mainly gene expression datasets of prostate cancer, and the three datasets were GSE17951, GSE8218, and GSE1431. The raw samples were processed for normalization, prediction of differentially expressed genes, and the prediction of enriched pathways for the differentially expressed genes. The enriched pathways have been processed for crosstalk degree calculations for which number connections per gene, the frequency of genes in the pathways, sharing frequency, and the connectivity have been used. For network prediction, protein-protein interaction network database FunCoup2.0 was used, and cytoscape software was used for the network visualization. In our results, we found that there were enriched pathways 27, 45, and 22 for GSE17951, GSE8218, and GSE1431, respectively, and 11 pathways in common between all of them. From the crosstalk results, we observe that focal adhesion and PI3K pathways, both experimentally proven central for cellular output upon perturbation of numerous individual/distinct signaling pathways, displayed highest crosstalk degree. Moreover, we also observe that there were more critical pathways which appear to be highly significant, and these pathways are HIF1a, hippo, AMPK, and Ras. In terms of the pathways' components, GSK3B, YWHAE, HIF1A, ATP1A3, and PRKCA are shared between the aforementioned pathways and have higher connectivity with the pathways and the other pathway components. Finally, we conclude that the focal adhesion and PI3K pathways are the most critical pathways, and since for many other pathways, high-rank enrichment did not translate to high crosstalk degree, the global impact of one pathway on others appears distinct from enrichment.
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Affiliation(s)
- Mohammad Mobashir
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, Solna 17165, Sweden
- Correspondence: ; Tel.: +46-70-872-3675
| | - S. Pauliina Turunen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, Solna 17165, Sweden
| | - Mohammad Asrar Izhari
- Faculty of Applied Medical Sciences, University of Al-Baha, Al-Baha 65528, Saudi Arabia
| | - Ibraheem Mohammed Ashankyty
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22233, Saudi Arabia
| | - Thomas Helleday
- SciLifeLab, Department of Oncology and Pathology, Karolinska Institutet, P.O. Box 1031, 17121 Stockholm, Sweden
| | - Kaisa Lehti
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, Solna 17165, Sweden
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22
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Haftbaradaran Esfahani P, Westergren J, Lindfors L, Knöll R. Frequency-dependent signaling in cardiac myocytes. Front Physiol 2022; 13:926422. [PMID: 36117711 PMCID: PMC9478484 DOI: 10.3389/fphys.2022.926422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Recent experimental data support the view that signaling activity at the membrane depends on its geometric parameters such as surface area and curvature. However, a mathematical, biophysical concept linking shape to receptor signaling is missing. The membranes of cardiomyocytes are constantly reshaped due to cycles of contraction and relaxation. According to constant-volume behavior of cardiomyocyte contraction, the length shortening is compensated by Z-disc myofilament lattice expansion and dynamic deformation of membrane between two adjacent Z-discs. Both morphological changes are strongly dependent on the frequency of contraction. Here, we developed the hypothesis that dynamic geometry of cardiomyocytes could be important for their plasticity and signaling. This effect may depend on the frequency of the beating heart and may represent a novel concept to explain how changes in frequency affect cardiac signaling. Methods: This hypothesis is almost impossible to answer with experiments, as the in-vitro cardiomyocytes are almost two-dimensional and flattened rather than being in their real in-vivo shape. Therefore, we designed a COMSOL multiphysics program to mathematically model the dynamic geometry of a human cardiomyocyte and explore whether the beating frequency can modulate membrane signal transduction. Src kinase is an important component of cardiac mechanotransduction. We first presented that Src mainly localizes at costameres. Then, the frequency-dependent signaling effect was studied mathematically by numerical simulation of Src-mediated PDGFR signaling pathway. The reaction-convection-diffusion partial differential equation was formulated to simulate PDGFR pathway in a contracting sarcomeric disc for a range of frequencies from 1 to 4 Hz. Results: Simulations exhibits higher concentration of phospho-Src when a cardiomyocyte beats with higher rates. The calculated phospho-Src concentration at 4, 2, and 1 Hz beat rates, comparing to 0 Hz, was 21.5%, 9.4%, and 4.7% higher, respectively. Conclusion: Here we provide mathematical evidence for a novel concept in biology. Cell shape directly translates into signaling, an effect of importance particularly for the myocardium, where cells continuously reshape their membranes. The concept of locality of surface-to-volume ratios is demonstrated to lead to changes in membrane-mediated signaling and may help to explain the remarkable plasticity of the myocardium in response to biomechanical stress.
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Affiliation(s)
| | | | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
| | - Ralph Knöll
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Heart and Vascular Theme, Karolinska Institute, Stockholm, Sweden
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
- *Correspondence: Ralph Knöll,
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23
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Khalil K, Eon A, Janody F. Cell Architecture-Dependent Constraints: Critical Safeguards to Carcinogenesis. Int J Mol Sci 2022; 23:ijms23158622. [PMID: 35955754 PMCID: PMC9369145 DOI: 10.3390/ijms23158622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Animal cells display great diversity in their shape. These morphological characteristics result from crosstalk between the plasma membrane and the force-generating capacities of the cytoskeleton macromolecules. Changes in cell shape are not merely byproducts of cell fate determinants, they also actively drive cell fate decisions, including proliferation and differentiation. Global and local changes in cell shape alter the transcriptional program by a multitude of mechanisms, including the regulation of physical links between the plasma membrane and the nuclear envelope and the mechanical modulation of cation channels and signalling molecules. It is therefore not surprising that anomalies in cell shape contribute to several diseases, including cancer. In this review, we discuss the possibility that the constraints imposed by cell shape determine the behaviour of normal and pro-tumour cells by organizing the whole interconnected regulatory network. In turn, cell behaviour might stabilize cells into discrete shapes. However, to progress towards a fully transformed phenotype and to acquire plasticity properties, pro-tumour cells might need to escape these cell shape restrictions. Thus, robust controls of the cell shape machinery may represent a critical safeguard against carcinogenesis.
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Affiliation(s)
- Komal Khalil
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Master Programme in Oncology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Alice Eon
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Magistère Européen de Génétique, Université Paris Cité, 5 Rue Thomas Mann, 75013 Paris, France
| | - Florence Janody
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Correspondence:
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24
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Abstract
Some dividing cells sense their shape by becoming polarized along their long axis. Cell polarity is controlled in part by polarity proteins, like Rho GTPases, cycling between active membrane-bound forms and inactive cytosolic forms, modeled as a "wave-pinning" reaction-diffusion process. Does shape sensing emerge from wave pinning? We show that wave pinning senses the cell's long axis. Simulating wave pinning on a curved surface, we find that high-activity domains migrate to peaks and troughs of the surface. For smooth surfaces, a simple rule of minimizing the domain perimeter while keeping its area fixed predicts the final position of the domain and its shape. However, when we introduce roughness to our surfaces, shape sensing can be disrupted, and high-activity domains can become localized to locations other than the global peaks and valleys of the surface. On rough surfaces, the domains of the wave-pinning model are more robust in finding the peaks and troughs than the minimization rule, although both can become trapped in steady states away from the peaks and valleys. We can control the robustness of shape sensing by altering the Rho GTPase diffusivity and the domain size. We also find that the shape-sensing properties of cell polarity models can explain how domains localize to curved regions of deformed cells. Our results help to understand the factors that allow cells to sense their shape-and the limits that membrane roughness can place on this process.
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25
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Bell MK, Holst MV, Lee CT, Rangamani P. Dendritic spine morphology regulates calcium-dependent synaptic weight change. J Gen Physiol 2022; 154:e202112980. [PMID: 35819365 PMCID: PMC9280073 DOI: 10.1085/jgp.202112980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 01/14/2023] Open
Abstract
Dendritic spines act as biochemical computational units and must adapt their responses according to their activation history. Calcium influx acts as the first signaling step during postsynaptic activation and is a determinant of synaptic weight change. Dendritic spines also come in a variety of sizes and shapes. To probe the relationship between calcium dynamics and spine morphology, we used a stochastic reaction-diffusion model of calcium dynamics in idealized and realistic geometries. We show that despite the stochastic nature of the various calcium channels, receptors, and pumps, spine size and shape can modulate calcium dynamics and subsequently synaptic weight updates in a deterministic manner. Through a series of exhaustive simulations and analyses, we found that the calcium dynamics and synaptic weight change depend on the volume-to-surface area of the spine. The relationships between calcium dynamics and spine morphology identified in idealized geometries also hold in realistic geometries, suggesting that there are geometrically determined deterministic relationships that may modulate synaptic weight change.
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Affiliation(s)
- Miriam K. Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
| | - Maven V. Holst
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
| | - Christopher T. Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
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26
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Wang ZJ, Thomson M. Localization of signaling receptors maximizes cellular information acquisition in spatially structured natural environments. Cell Syst 2022; 13:530-546.e12. [PMID: 35679857 DOI: 10.1016/j.cels.2022.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/08/2022] [Accepted: 05/12/2022] [Indexed: 01/25/2023]
Abstract
Cells in natural environments, such as tissue or soil, sense and respond to extracellular ligands with intricately structured and non-monotonic spatial distributions, sculpted by processes such as fluid flow and substrate adhesion. In this work, we show that spatial sensing and navigation can be optimized by adapting the spatial organization of signaling pathways to the spatial structure of the environment. We develop an information-theoretic framework for computing the optimal spatial organization of a sensing system for a given signaling environment. We find that receptor localization previously observed in cells maximizes information acquisition in simulated natural contexts, including tissue and soil. Specifically, information acquisition is maximized when receptors form localized patches at regions of maximal ligand concentration. Receptor localization extends naturally to produce a dynamic protocol for continuously redistributing signaling receptors, which when implemented using simple feedback, boosts cell navigation efficiency by 30-fold.
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Affiliation(s)
- Zitong Jerry Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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27
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Reddy GA, Katira P. Differences in cell death and division rules can alter tissue rigidity and fluidization. SOFT MATTER 2022; 18:3713-3724. [PMID: 35502875 DOI: 10.1039/d2sm00174h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tissue mechanical properties such as rigidity and fluidity, and changes in these properties driven by jamming-unjamming transitions (UJT), have come under recent highlight as mechanical markers of health and disease in various biological processes including cancer. However, most analyses of these mechanical properties and UJT have sidestepped the effect of cellular death and division in these systems. Cellular apoptosis (programmed cell death) and mitosis (cell division) can drive significant changes in tissue properties. The balance between the two is crucial in maintaining tissue function, and an imbalance between the two is seen in situations such as cancer progression, wound healing and necrosis. In this work we investigate the impact of cell death and division on tissue mechanical properties, by incorporating specific mechanosensitive triggers of cell death and division based on the size and geometry of the cell within in silico models of tissue dynamics. Specifically, we look at cell migration, tissue response to external stress, tissue extrusion propensity and self-organization of different cell types within the tissue, as a function of cell death and division and the rules that trigger these events. We find that not only do cell death and division events significantly alter tissue mechanics when compared to systems without these events, but that the choice of triggers driving these cell death and division events also alters the predicted tissue mechanics and overall system behavior.
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Affiliation(s)
- Gudur Ashrith Reddy
- Mechanical Engineering Department, San Diego State University, San Diego, CA, USA.
- Department of Bioengineering, University of California - San Diego, San Diego, CA, USA
| | - Parag Katira
- Mechanical Engineering Department, San Diego State University, San Diego, CA, USA.
- Computational Science Research Center, San Diego State University, San Diego, CA, USA
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28
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Rajagopal V, Arumugam S, Hunter PJ, Khadangi A, Chung J, Pan M. The Cell Physiome: What Do We Need in a Computational Physiology Framework for Predicting Single-Cell Biology? Annu Rev Biomed Data Sci 2022; 5:341-366. [PMID: 35576556 DOI: 10.1146/annurev-biodatasci-072018-021246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modern biology and biomedicine are undergoing a big data explosion, needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome project: a framework and approach for creating, sharing, and using biophysics-based computational models of single-cell physiology. Using examples in calcium signaling, bioenergetics, and endosomal trafficking, we highlight the need for spatially detailed, biophysics-based computational models to uncover new mechanisms underlying cell biology. We review progress and challenges to date toward creating cell physiome models. We then introduce bond graphs as an efficient way to create cell physiome models that integrate chemical, mechanical, electromagnetic, and thermal processes while maintaining mass and energy balance. Bond graphs enhance modularization and reusability of computational models of cells at scale. We conclude with a look forward at steps that will help fully realize this exciting new field of mechanistic biomedical data science. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Vijay Rajagopal
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia;
| | - Senthil Arumugam
- Cellular Physiology Lab, Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences; European Molecular Biological Laboratory (EMBL) Australia; and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton/Melbourne, Victoria, Australia
| | - Peter J Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Afshin Khadangi
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia;
| | - Joshua Chung
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia;
| | - Michael Pan
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
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29
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Chi YH, Wang WP, Hung MC, Liou GG, Wang JY, Chao PHG. Deformation of the nucleus by TGFβ1 via the remodeling of nuclear envelope and histone isoforms. Epigenetics Chromatin 2022; 15:1. [PMID: 34983624 PMCID: PMC8725468 DOI: 10.1186/s13072-021-00434-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022] Open
Abstract
The cause of nuclear shape abnormalities which are often seen in pre-neoplastic and malignant tissues is not clear. In this study we report that deformation of the nucleus can be induced by TGFβ1 stimulation in several cell lines including Huh7. In our results, the upregulated histone H3.3 expression downstream of SMAD signaling contributed to TGFβ1-induced nuclear deformation, a process of which requires incorporation of the nuclear envelope (NE) proteins lamin B1 and SUN1. During this process, the NE constitutively ruptured and reformed. Contrast to lamin B1 which was relatively stationary around the nucleus, the upregulated lamin A was highly mobile, clustering at the nuclear periphery and reintegrating into the nucleoplasm. The chromatin regions that lost NE coverage formed a supra-nucleosomal structure characterized by elevated histone H3K27me3 and histone H1, the formation of which depended on the presence of lamin A. These results provide evidence that shape of the nucleus can be modulated through TGFβ1-induced compositional changes in the chromatin and nuclear lamina.
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Affiliation(s)
- Ya-Hui Chi
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan. .,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan.
| | - Wan-Ping Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan
| | - Ming-Chun Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan
| | - Gunn-Guang Liou
- National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Jing-Ya Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan
| | - Pen-Hsiu Grace Chao
- Department of Biomedical Engineering, School of Medicine and School of Engineering, National Taiwan University, Taipei, 10617, Taiwan
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30
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Qu C, Roth R, Puapatanakul P, Loitman C, Hammad D, Genin GM, Miner JH, Suleiman HY. Three-Dimensional Visualization of the Podocyte Actin Network Using Integrated Membrane Extraction, Electron Microscopy, and Machine Learning. J Am Soc Nephrol 2022; 33:155-173. [PMID: 34758982 PMCID: PMC8763187 DOI: 10.1681/asn.2021020182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 10/19/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Actin stress fibers are abundant in cultured cells, but little is known about them in vivo. In podocytes, much evidence suggests that mechanobiologic mechanisms underlie podocyte shape and adhesion in health and in injury, with structural changes to actin stress fibers potentially responsible for pathologic changes to cell morphology. However, this hypothesis is difficult to rigorously test in vivo due to challenges with visualization. A technology to image the actin cytoskeleton at high resolution is needed to better understand the role of structures such as actin stress fibers in podocytes. METHODS We developed the first visualization technique capable of resolving the three-dimensional cytoskeletal network in mouse podocytes in detail, while definitively identifying the proteins that comprise this network. This technique integrates membrane extraction, focused ion-beam scanning electron microscopy, and machine learning image segmentation. RESULTS Using isolated mouse glomeruli from healthy animals, we observed actin cables and intermediate filaments linking the interdigitated podocyte foot processes to newly described contractile actin structures, located at the periphery of the podocyte cell body. Actin cables within foot processes formed a continuous, mesh-like, electron-dense sheet that incorporated the slit diaphragms. CONCLUSIONS Our new technique revealed, for the first time, the detailed three-dimensional organization of actin networks in healthy podocytes. In addition to being consistent with the gel compression hypothesis, which posits that foot processes connected by slit diaphragms act together to counterbalance the hydrodynamic forces across the glomerular filtration barrier, our data provide insight into how podocytes respond to mechanical cues from their surrounding environment.
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Affiliation(s)
- Chengqing Qu
- Department of Mechanical Engineering, National Science Foundation Science and Technology Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri
| | - Robyn Roth
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
| | | | - Charles Loitman
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Dina Hammad
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Guy M. Genin
- Department of Mechanical Engineering, National Science Foundation Science and Technology Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri
| | - Jeffrey H. Miner
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri,Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
| | - Hani Y. Suleiman
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri
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31
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Stochasticity and positive feedback enable enzyme kinetics at the membrane to sense reaction size. Proc Natl Acad Sci U S A 2021; 118:2103626118. [PMID: 34789575 PMCID: PMC8617498 DOI: 10.1073/pnas.2103626118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2021] [Indexed: 12/27/2022] Open
Abstract
Cellular membranes span a wide range of spatial dimensions, from the plasma membrane with a scale of microns to vesicles on the nanometer scale. The work presented here identifies a molecular mechanism, based on common features of cellular signaling enzymes, that causes the average enzymatic catalytic rate to exhibit reaction size dependency. This effect stems from stochastic variation, but the final results can be essentially deterministic. In competitive enzymatic reaction cycles, the final product can depend on the size of the reaction system. The simplicity of the mechanism suggests that size-dependent reaction rates may be widespread among signaling enzymes and thus enable reaction size to be an important factor in signal regulation at the membrane. Here, we present detailed kinetic analyses of a panel of soluble lipid kinases and phosphatases, as well as Ras activating proteins, acting on their respective membrane surface substrates. The results reveal that the mean catalytic rate of such interfacial enzymes can exhibit a strong dependence on the size of the reaction system—in this case membrane area. Experimental measurements and kinetic modeling reveal how stochastic effects stemming from low molecular copy numbers of the enzymes alter reaction kinetics based on mechanistic characteristics of the enzyme, such as positive feedback. For the competitive enzymatic cycles studied here, the final product—consisting of a specific lipid composition or Ras activity state—depends on the size of the reaction system. Furthermore, we demonstrate how these reaction size dependencies can be controlled by engineering feedback mechanisms into the enzymes.
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32
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Khang A, Lejeune E, Abbaspour A, Howsmon DP, Sacks MS. On the Three-Dimensional Correlation Between Myofibroblast Shape and Contraction. J Biomech Eng 2021; 143:094503. [PMID: 33876206 PMCID: PMC8299802 DOI: 10.1115/1.4050915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/02/2021] [Indexed: 01/05/2023]
Abstract
Myofibroblasts are responsible for wound healing and tissue repair across all organ systems. In periods of growth and disease, myofibroblasts can undergo a phenotypic transition characterized by an increase in extracellular matrix (ECM) deposition rate, changes in various protein expression (e.g., alpha-smooth muscle actin (αSMA)), and elevated contractility. Cell shape is known to correlate closely with stress-fiber geometry and function and is thus a critical feature of cell biophysical state. However, the relationship between myofibroblast shape and contraction is complex, even as well in regards to steady-state contractile level (basal tonus). At present, the relationship between myofibroblast shape and basal tonus in three-dimensional (3D) environments is poorly understood. Herein, we utilize the aortic valve interstitial cell (AVIC) as a representative myofibroblast to investigate the relationship between basal tonus and overall cell shape. AVICs were embedded within 3D poly(ethylene glycol) (PEG) hydrogels containing degradable peptide crosslinkers, adhesive peptide sequences, and submicron fluorescent microspheres to track the local displacement field. We then developed a methodology to evaluate the correlation between overall AVIC shape and basal tonus induced contraction. We computed a volume averaged stretch tensor ⟨U⟩ for the volume occupied by the AVIC, which had three distinct eigenvalues (λ1,2,3=1.08,0.99, and 0.89), suggesting that AVIC shape is a result of anisotropic contraction. Furthermore, the direction of maximum contraction correlated closely with the longest axis of a bounding ellipsoid enclosing the AVIC. As gel-imbedded AVICs are known to be in a stable state by 3 days of incubation used herein, this finding suggests that the overall quiescent AVIC shape is driven by the underlying stress-fiber directional structure and potentially contraction level.
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Affiliation(s)
- Alex Khang
- James T. Willerson Center for Cardiovascular Modeling and Simulation, The Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Emma Lejeune
- James T. Willerson Center for Cardiovascular Modeling and Simulation, The Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712; Department of Mechanical Engineering, Boston University, Boston, MA 02215
| | - Ali Abbaspour
- James T. Willerson Center for Cardiovascular Modeling and Simulation, The Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Daniel P. Howsmon
- James T. Willerson Center for Cardiovascular Modeling and Simulation, The Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Michael S. Sacks
- James T. Willerson Center for Cardiovascular Modeling and Simulation, The Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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33
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Savage NS. Describing the movement of molecules in reduced-dimension models. Commun Biol 2021; 4:689. [PMID: 34099856 PMCID: PMC8184792 DOI: 10.1038/s42003-021-02200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/10/2021] [Indexed: 12/05/2022] Open
Abstract
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is restricted to the reduced dimension, changing the nature of molecular movement. This change in molecular movement can lead to quantitatively and even qualitatively different results in the full and reduced systems. Within this manuscript we discuss the condition under which restricted molecular movement in reduced-dimension models accurately approximates molecular movement in the full system. For those systems which do not satisfy the condition, we present a general method for approximating unrestricted molecular movement in reduced-dimension models. We will derive a mathematically robust, finite difference method for solving the 2D diffusion equation within a 1D reduced-dimension model. The methods described here can be used to improve the accuracy of many reduced-dimension models while retaining benefits of system simplification.
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34
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Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape. NPJ Syst Biol Appl 2021; 7:26. [PMID: 34078916 PMCID: PMC8172538 DOI: 10.1038/s41540-021-00185-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Spatiotemporal compartmentation of calcium dynamics is critical for neuronal function, particularly in postsynaptic spines. This exquisite level of Ca2+ compartmentalization is achieved through the storage and release of Ca2+ from various intracellular organelles particularly the endoplasmic reticulum (ER) and the mitochondria. Mitochondria and ER are established storage organelles controlling Ca2+ dynamics in neurons. Mitochondria also generate a majority of energy used within postsynaptic spines to support the downstream events associated with neuronal stimulus. Recently, high resolution microscopy has unveiled direct contact sites between the ER and the mitochondria (MERCs), which directly channel Ca2+ release from the ER into the mitochondrial membrane. In this study, we develop a computational 3D reaction-diffusion model to investigate the role of MERCs in regulating Ca2+ and ATP dynamics. This spatiotemporal model accounts for Ca2+ oscillations initiated by glutamate stimulus of metabotropic and ionotropic glutamate receptors and Ca2+ changes in four different compartments: cytosol, ER, mitochondria, and the MERC microdomain. Our simulations predict that the organization of these organelles and inter-organellar contact sites play a key role in modulating Ca2+ and ATP dynamics. We further show that the crosstalk between geometry (mitochondria and MERC) and metabolic parameters (cytosolic ATP hydrolysis, ATP generation) influences the neuronal energy state. Our findings shed light on the importance of organelle interactions in predicting Ca2+ dynamics in synaptic signaling. Overall, our model predicts that a combination of MERC linkage and mitochondria size is necessary for optimal ATP production in the cytosol.
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35
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Junyent S, Reeves JC, Szczerkowski JLA, Garcin CL, Trieu TJ, Wilson M, Lundie-Brown J, Habib SJ. Wnt- and glutamate-receptors orchestrate stem cell dynamics and asymmetric cell division. eLife 2021; 10:59791. [PMID: 34028355 PMCID: PMC8177892 DOI: 10.7554/elife.59791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
The Wnt-pathway is part of a signalling network that regulates many aspects of cell biology. Recently, we discovered crosstalk between AMPA/Kainate-type ionotropic glutamate receptors (iGluRs) and the Wnt-pathway during the initial Wnt3a-interaction at the cytonemes of mouse embryonic stem cells (ESCs). Here, we demonstrate that this crosstalk persists throughout the Wnt3a-response in ESCs. Both AMPA and Kainate receptors regulate early Wnt3a-recruitment, dynamics on the cell membrane, and orientation of the spindle towards a Wnt3a-source at mitosis. AMPA receptors specifically are required for segregating cell fate components during Wnt3a-mediated asymmetric cell division (ACD). Using Wnt-pathway component knockout lines, we determine that Wnt co-receptor Lrp6 has particular functionality over Lrp5 in cytoneme formation, and in facilitating ACD. Both Lrp5 and 6, alongside pathway effector β-catenin act in concert to mediate the positioning of the dynamic interaction with, and spindle orientation to, a localised Wnt3a-source. Wnt-iGluR crosstalk may prove pervasive throughout embryonic and adult stem cell signalling.
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Affiliation(s)
- Sergi Junyent
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Joshua C Reeves
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - James LA Szczerkowski
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Clare L Garcin
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Tung-Jui Trieu
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Matthew Wilson
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Jethro Lundie-Brown
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Shukry J Habib
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
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A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes. Proc Natl Acad Sci U S A 2021; 118:2021571118. [PMID: 33990464 DOI: 10.1073/pnas.2021571118] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
YAP/TAZ is a master regulator of mechanotransduction whose functions rely on translocation from the cytoplasm to the nucleus in response to diverse physical cues. Substrate stiffness, substrate dimensionality, and cell shape are all input signals for YAP/TAZ, and through this pathway, regulate critical cellular functions and tissue homeostasis. Yet, the relative contributions of each biophysical signal and the mechanisms by which they synergistically regulate YAP/TAZ in realistic tissue microenvironments that provide multiplexed input signals remain unclear. For example, in simple two-dimensional culture, YAP/TAZ nuclear localization correlates strongly with substrate stiffness, while in three-dimensional (3D) environments, YAP/TAZ translocation can increase with stiffness, decrease with stiffness, or remain unchanged. Here, we develop a spatial model of YAP/TAZ translocation to enable quantitative analysis of the relationships between substrate stiffness, substrate dimensionality, and cell shape. Our model couples cytosolic stiffness to nuclear mechanics to replicate existing experimental trends, and extends beyond current data to predict that increasing substrate activation area through changes in culture dimensionality, while conserving cell volume, forces distinct shape changes that result in nonlinear effect on YAP/TAZ nuclear localization. Moreover, differences in substrate activation area versus total membrane area can account for counterintuitive trends in YAP/TAZ nuclear localization in 3D culture. Based on this multiscale investigation of the different system features of YAP/TAZ nuclear translocation, we predict that how a cell reads its environment is a complex information transfer function of multiple mechanical and biochemical factors. These predictions reveal a few design principles of cellular and tissue engineering for YAP/TAZ mechanotransduction.
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Bhushan V, Heitz MP, Baker GA, Pandey S. Ionic Liquid-Controlled Shape Transformation of Spherical to Nonspherical Polymersomes via Hierarchical Self-Assembly of a Diblock Copolymer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5081-5088. [PMID: 33845575 DOI: 10.1021/acs.langmuir.1c00821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here, we report the self-assembly of poly(ethylene glycol) methyl ether-block-poly(ε-caprolactone) (PEG-b-PCL) copolymer in three ionic liquids (ILs) possessing different cations with common bis(trifluoromethylsulfonyl)imide anion. The observed polymeric nanostructures in ILs were directly visualized by room temperature conventional transmission and field emission scanning electron microscopy and were further examined for their size and shape by dynamic light scattering technique. The results show that through changes in the concentration of PEG-b-PCL and/or changing the solvent by using a different IL, we can effectively induce shape transformation of self-assembled PEG-b-PCL nanostructures in order to generate nonspherical polymersomes, such as worm-like aggregates, stomatocytes, nanotubes, large hexagonal and tubular-shaped polymersomes. These findings provide a promising platform for the design of biodegradable soft dynamic systems in the micro-/nano-motor field for cancer-targeted delivery, diagnosis and imaging-guided therapy, and controlled release of therapeutic drugs for treatment of many diseases. Non-spherical polymersome-based vaccines may be taken up more efficiently, especially against viruses for pulmonary drug delivery than the spherical polymersomes-based.
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Affiliation(s)
- Vidiksha Bhushan
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Mark P Heitz
- Department of Chemistry and Biochemistry, State University of New York at Brockport, Brockport, New York, New York 14420, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Siddharth Pandey
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Zakirov B, Charalambous G, Thuret R, Aspalter IM, Van-Vuuren K, Mead T, Harrington K, Regan ER, Herbert SP, Bentley K. Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190753. [PMID: 33550953 PMCID: PMC7934951 DOI: 10.1098/rstb.2019.0753] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
How do cells make efficient collective decisions during tissue morphogenesis? Humans and other organisms use feedback between movement and sensing known as 'sensorimotor coordination' or 'active perception' to inform behaviour, but active perception has not before been investigated at a cellular level within organs. Here we provide the first proof of concept in silico/in vivo study demonstrating that filopodia (actin-rich, dynamic, finger-like cell membrane protrusions) play an unexpected role in speeding up collective endothelial decisions during the time-constrained process of 'tip cell' selection during blood vessel formation (angiogenesis). We first validate simulation predictions in vivo with live imaging of zebrafish intersegmental vessel growth. Further simulation studies then indicate the effect is due to the coupled positive feedback between movement and sensing on filopodia conferring a bistable switch-like property to Notch lateral inhibition, ensuring tip selection is a rapid and robust process. We then employ measures from computational neuroscience to assess whether filopodia function as a primitive (basal) form of active perception and find evidence in support. By viewing cell behaviour through the 'basal cognitive lens' we acquire a fresh perspective on the tip cell selection process, revealing a hidden, yet vital time-keeping role for filopodia. Finally, we discuss a myriad of new and exciting research directions stemming from our conceptual approach to interpreting cell behaviour. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Bahti Zakirov
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
| | - Georgios Charalambous
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Raphael Thuret
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Irene M. Aspalter
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
| | - Kelvin Van-Vuuren
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
| | - Thomas Mead
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
| | - Kyle Harrington
- Virtual Technology and Design, University of Idaho, Moscow, ID, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Erzsébet Ravasz Regan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Biology, The College of Wooster, Wooster, OH, USA
| | - Shane Paul Herbert
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Katie Bentley
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
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Gavriljuk K, Scocozza B, Ghasemalizadeh F, Seidel H, Nandan AP, Campos-Medina M, Schmick M, Koseska A, Bastiaens PIH. A self-organized synthetic morphogenic liposome responds with shape changes to local light cues. Nat Commun 2021; 12:1548. [PMID: 33750780 PMCID: PMC7943604 DOI: 10.1038/s41467-021-21679-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2021] [Indexed: 12/02/2022] Open
Abstract
Reconstituting artificial proto-cells capable of transducing extracellular signals into cytoskeletal changes can reveal fundamental principles of how non-equilibrium phenomena in cellular signal transduction affect morphogenesis. Here, we generated a Synthetic Morphogenic Membrane System (SynMMS) by encapsulating a dynamic microtubule (MT) aster and a light-inducible signaling system driven by GTP/ATP chemical potential into cell-sized liposomes. Responding to light cues in analogy to morphogens, this biomimetic design embodies basic principles of localized Rho-GTPase signal transduction that generate an intracellular MT-regulator signaling gradient. Light-induced signaling promotes membrane-deforming growth of MT-filaments by dynamically elevating the membrane-proximal tubulin concentration. The resulting membrane deformations enable recursive coupling of the MT-aster with the signaling system, which generates global self-organized morphologies that reorganize towards local external cues in dependence on prior shape. SynMMS thereby signifies a step towards bio-inspired engineering of self-organized cellular morphogenesis. The authors generated a Synthetic Morphogenic Membrane System by encapsulating a dynamic microtubule aster and a light-inducible signaling system driven by GTP/ATP chemical potential into cell-sized liposomes. This reconstitution of artificial proto-cells reveals how non-equilibrium phenomena affect cellular information processing in morphogenesis.
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Affiliation(s)
- Konstantin Gavriljuk
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Bruno Scocozza
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Farid Ghasemalizadeh
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Hans Seidel
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Akhilesh P Nandan
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany.,Cellular Computations and Learning, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - Manuel Campos-Medina
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Malte Schmick
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Aneta Koseska
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany.,Cellular Computations and Learning, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, TU Dortmund, Dortmund, Germany.
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40
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Xu XF, Zhu RM, Pan CY, You YZ, Zhang WJ, Hong CY. Polymerization-Induced Self-Assembly Driven by the Synergistic Effects of Aromatic and Solvophobic Interactions. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02882] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xiao-Fei Xu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ren-Man Zhu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Cai-Yuan Pan
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ye-Zi You
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wen-Jian Zhang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chun-Yan Hong
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
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41
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Baker EA, Fleischer MM, Vara AD, Salisbury MR, Baker KC, Fortin PT, Friedrich CR. Local and Systemic In Vivo Responses to Osseointegrative Titanium Nanotube Surfaces. NANOMATERIALS 2021; 11:nano11030583. [PMID: 33652733 PMCID: PMC7996927 DOI: 10.3390/nano11030583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 01/25/2023]
Abstract
Orthopedic implants requiring osseointegration are often surface modified; however, implants may shed these coatings and generate wear debris leading to complications. Titanium nanotubes (TiNT), a new surface treatment, may promote osseointegration. In this study, in vitro (rat marrow-derived bone marrow cell attachment and morphology) and in vivo (rat model of intramedullary fixation) experiments characterized local and systemic responses of two TiNT surface morphologies, aligned and trabecular, via animal and remote organ weight, metal ion, hematologic, and nondecalcified histologic analyses. In vitro experiments showed total adherent cells on trabecular and aligned TiNT surfaces were greater than control at 30 min and 4 h, and cells were smaller in diameter and more eccentric. Control animals gained more weight, on average; however, no animals met the institutional trigger for weight loss. No hematologic parameters (complete blood count with differential) were significantly different for TiNT groups vs. control. Inductively coupled plasma mass spectrometry (ICP-MS) showed greater aluminum levels in the lungs of the trabecular TiNT group than in those of the controls. Histologic analysis demonstrated no inflammatory infiltrate, cytotoxic, or necrotic conditions in proximity of K-wires. There were significantly fewer eosinophils/basophils and neutrophils in the distal region of trabecular TiNT-implanted femora; and, in the midshaft of aligned TiNT-implanted femora, there were significantly fewer foreign body giant/multinucleated cells and neutrophils, indicating a decreased immune response in aligned TiNT-implanted femora compared to controls.
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Affiliation(s)
- Erin A. Baker
- Departments of Orthopaedic Research and Surgery, Beaumont Health, Royal Oak, MI 48073, USA; (M.M.F.); (A.D.V.); (M.R.S.); (K.C.B.); (P.T.F.)
- Department of Mechanical Engineering-Engineering Mechanics, Michigan Technological University, Houghton, MI 49931, USA;
- Department of Orthopaedic Surgery, Oakland University William Beaumont School of Medicine, Rochester, MI 48309, USA
- Correspondence:
| | - Mackenzie M. Fleischer
- Departments of Orthopaedic Research and Surgery, Beaumont Health, Royal Oak, MI 48073, USA; (M.M.F.); (A.D.V.); (M.R.S.); (K.C.B.); (P.T.F.)
| | - Alexander D. Vara
- Departments of Orthopaedic Research and Surgery, Beaumont Health, Royal Oak, MI 48073, USA; (M.M.F.); (A.D.V.); (M.R.S.); (K.C.B.); (P.T.F.)
| | - Meagan R. Salisbury
- Departments of Orthopaedic Research and Surgery, Beaumont Health, Royal Oak, MI 48073, USA; (M.M.F.); (A.D.V.); (M.R.S.); (K.C.B.); (P.T.F.)
| | - Kevin C. Baker
- Departments of Orthopaedic Research and Surgery, Beaumont Health, Royal Oak, MI 48073, USA; (M.M.F.); (A.D.V.); (M.R.S.); (K.C.B.); (P.T.F.)
- Department of Orthopaedic Surgery, Oakland University William Beaumont School of Medicine, Rochester, MI 48309, USA
| | - Paul T. Fortin
- Departments of Orthopaedic Research and Surgery, Beaumont Health, Royal Oak, MI 48073, USA; (M.M.F.); (A.D.V.); (M.R.S.); (K.C.B.); (P.T.F.)
- Department of Orthopaedic Surgery, Oakland University William Beaumont School of Medicine, Rochester, MI 48309, USA
| | - Craig R. Friedrich
- Department of Mechanical Engineering-Engineering Mechanics, Michigan Technological University, Houghton, MI 49931, USA;
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The nuclear import of the transcription factor MyoD is reduced in mesenchymal stem cells grown in a 3D micro-engineered niche. Sci Rep 2021; 11:3021. [PMID: 33542304 PMCID: PMC7862644 DOI: 10.1038/s41598-021-81920-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/11/2021] [Indexed: 12/21/2022] Open
Abstract
Smart biomaterials are increasingly being used to control stem cell fate in vitro by the recapitulation of the native niche microenvironment. By integrating experimental measurements with numerical models, we show that in mesenchymal stem cells grown inside a 3D synthetic niche both nuclear transport of a myogenic factor and the passive nuclear diffusion of a smaller inert protein are reduced. Our results also suggest that cell morphology modulates nuclear proteins import through a partition of the nuclear envelope surface, which is a thin but extremely permeable annular portion in cells cultured on 2D substrates. Therefore, our results support the hypothesis that in stem cell differentiation, the nuclear import of gene-regulating transcription factors is controlled by a strain-dependent nuclear envelope permeability, probably related to the reorganization of stretch-activated nuclear pore complexes.
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43
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Singh AV, Maharjan RS, Kanase A, Siewert K, Rosenkranz D, Singh R, Laux P, Luch A. Machine-Learning-Based Approach to Decode the Influence of Nanomaterial Properties on Their Interaction with Cells. ACS APPLIED MATERIALS & INTERFACES 2021; 13:1943-1955. [PMID: 33373205 DOI: 10.1021/acsami.0c18470] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In an in vitro nanotoxicity system, cell-nanoparticle (NP) interaction leads to the surface adsorption, uptake, and changes into nuclei/cell phenotype and chemistry, as an indicator of oxidative stress, genotoxicity, and carcinogenicity. Different types of nanomaterials and their chemical composition or "corona" have been widely studied in context with nanotoxicology. However, rare reports are available, which delineate the details of the cell shape index (CSI) and nuclear area factors (NAFs) as a descriptor of the type of nanomaterials. In this paper, we propose a machine-learning-based graph modeling and correlation-establishing approach using tight junction protein ZO-1-mediated alteration in the cell/nuclei phenotype to quantify and propose it as indices of cell-NP interactions. We believe that the phenotypic variation (CSI and NAF) in the epithelial cell is governed by the physicochemical descriptors (e.g., shape, size, zeta potential, concentration, diffusion coefficients, polydispersity, and so on) of the different classes of nanomaterials, which critically determines the intracellular uptake or cell membrane interactions when exposed to the epithelial cells at sub-lethal concentrations. The intrinsic and extrinsic physicochemical properties of the representative nanomaterials (NMs) were measured using optical (dynamic light scattering, NP tracking analysis) methods to create a set of nanodescriptors contributing to cell-NM interactions via phenotype adjustments. We used correlation function as a machine-learning algorithm to successfully predict cell and nuclei shapes and polarity functions as phenotypic markers for five different classes of nanomaterials studied herein this report. The CSI and NAF as nanodescriptors can be used as intuitive cell phenotypic parameters to define the safety of nanomaterials extensively used in consumer products and nanomedicine.
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Affiliation(s)
- Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Romi-Singh Maharjan
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Anurag Kanase
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Katherina Siewert
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Daniel Rosenkranz
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Rishabh Singh
- Rajarshi Shahu College of Engineering, 411007 Pune, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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Gavazzo P, Viti F, Donnelly H, Oliva MAG, Salmeron-Sanchez M, Dalby MJ, Vassalli M. Biophysical phenotyping of mesenchymal stem cells along the osteogenic differentiation pathway. Cell Biol Toxicol 2021; 37:915-933. [PMID: 33420657 DOI: 10.1007/s10565-020-09569-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022]
Abstract
Mesenchymal stem cells represent an important resource, for bone regenerative medicine and therapeutic applications. This review focuses on new advancements and biophysical tools which exploit different physical and chemical markers of mesenchymal stem cell populations, to finely characterize phenotype changes along their osteogenic differentiation process. Special attention is paid to recently developed label-free methods, which allow monitoring cell populations with minimal invasiveness. Among them, quantitative phase imaging, suitable for single-cell morphometric analysis, and nanoindentation, functional to cellular biomechanics investigation. Moreover, the pool of ion channels expressed in cells during differentiation is discussed, with particular interest for calcium homoeostasis.Altogether, a biophysical perspective of osteogenesis is proposed, offering a valuable tool for the assessment of the cell stage, but also suggesting potential physiological links between apparently independent phenomena.
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Affiliation(s)
- Paola Gavazzo
- Institute of Biophysics, National Research Council, Genoa, Italy
| | - Federica Viti
- Institute of Biophysics, National Research Council, Genoa, Italy.
| | - Hannah Donnelly
- Centre for the Cellular Microenvironment, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mariana Azevedo Gonzalez Oliva
- Centre for the Cellular Microenvironment, Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | - Manuel Salmeron-Sanchez
- Centre for the Cellular Microenvironment, Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | - Matthew J Dalby
- Centre for the Cellular Microenvironment, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Massimo Vassalli
- Centre for the Cellular Microenvironment, Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
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45
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DiNapoli KT, Robinson DN, Iglesias PA. Tools for computational analysis of moving boundary problems in cellular mechanobiology. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 13:e1514. [PMID: 33305503 DOI: 10.1002/wsbm.1514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/08/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022]
Abstract
A cell's ability to change shape is one of the most fundamental biological processes and is essential for maintaining healthy organisms. When the ability to control shape goes awry, it often results in a diseased system. As such, it is important to understand the mechanisms that allow a cell to sense and respond to its environment so as to maintain cellular shape homeostasis. Because of the inherent complexity of the system, computational models that are based on sound theoretical understanding of the biochemistry and biomechanics and that use experimentally measured parameters are an essential tool. These models involve an inherent feedback, whereby shape is determined by the action of regulatory signals whose spatial distribution depends on the shape. To carry out computational simulations of these moving boundary problems requires special computational techniques. A variety of alternative approaches, depending on the type and scale of question being asked, have been used to simulate various biological processes, including cell motility, division, mechanosensation, and cell engulfment. In general, these models consider the forces that act on the system (both internally generated, or externally imposed) and the mechanical properties of the cell that resist these forces. Moving forward, making these techniques more accessible to the non-expert will help improve interdisciplinary research thereby providing new insight into important biological processes that affect human health. This article is categorized under: Cancer > Cancer>Computational Models Cancer > Cancer>Molecular and Cellular Physiology.
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Affiliation(s)
- Kathleen T DiNapoli
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Douglas N Robinson
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Pablo A Iglesias
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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46
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Nguyen TNT, Sasaki K, Kino-Oka M. Development of a kinetic model expressing anomalous phenomena in human induced pluripotent stem cell culture. J Biosci Bioeng 2020; 131:305-313. [PMID: 33262019 DOI: 10.1016/j.jbiosc.2020.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022]
Abstract
During culture with feeder cells, deviation from the undifferentiated state of human induced pluripotent stem cells (hiPSCs) occurs at a very low frequency. Anomalous cell migration in central and peripheral regions of hiPSC colonies has been suggested to be the trigger for this phenomenon. To confirm this hypothesis, sequential cell migration prior to deviation must be demonstrated. This has been difficult using in vitro methods. We therefore developed a kinetic model with a proposed definition of anomalous cell migration as continuous relatively fast or slow cell migration. The developed model was validated via in silico reproduction of deviation phenomenon observed in vitro, such as the positions of deviated cells in a colony and the frequency of deviation in culture. This model suggests that anomalous cell migration-driven hiPSC deviation can be explained by two factors: a mechanical stimulus, represented by cell migration, and duration of the mechanical stimulus. The factor "duration of mechanical stimulus" sets our model apart from others, and helps to realize the ultra-rare trigger (approximately 10-5) of deviation from the undifferentiated state in hiPSC culture.
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Affiliation(s)
- Thi Nhu Trang Nguyen
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kei Sasaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Požgajová M, Navrátilová A, Šebová E, Kovár M, Kačániová M. Cadmium-Induced Cell Homeostasis Impairment is Suppressed by the Tor1 Deficiency in Fission Yeast. Int J Mol Sci 2020; 21:ijms21217847. [PMID: 33105893 PMCID: PMC7660220 DOI: 10.3390/ijms21217847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/10/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Cadmium has no known physiological function in the body; however, its adverse effects are associated with cancer and many types of organ system damage. Although much has been shown about Cd toxicity, the underlying mechanisms of its responses to the organism remain unclear. In this study, the role of Tor1, a catalytic subunit of the target of rapamycin complex 2 (TORC2), in Cd-mediated effects on cell proliferation, the antioxidant system, morphology, and ionome balance was investigated in the eukaryotic model organism Schizosaccharomyces pombe. Surprisingly, spectrophotometric and biochemical analyses revealed that the growth rate conditions and antioxidant defense mechanisms are considerably better in cells lacking the Tor1 signaling. The malondialdehyde (MDA) content of Tor1-deficient cells upon Cd treatment represents approximately half of the wild-type content. The microscopic determination of the cell morphological parameters indicates the role for Tor1 in cell shape maintenance. The ion content, determined by inductively coupled plasma optical emission spectroscopy (ICP-OES), showed that the Cd uptake potency was markedly lower in Tor1-depleted compared to wild-type cells. Conclusively, we show that the cadmium-mediated cell impairments in the fission yeast significantly depend on the Tor1 signaling. Additionally, the data presented here suggest the yet-undefined role of Tor1 in the transport of ions.
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Affiliation(s)
- Miroslava Požgajová
- AgroBioTech Research Centre, Slovak University of Agriculture in Nitra, 949 76 Nitra, Slovakia
- Correspondence: ; Tel.: +421-37-641-4919
| | - Alica Navrátilová
- Department of Genetics and Breeding Biology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, 94976 Nitra, Slovakia;
| | - Eva Šebová
- Institute of Experimental Medicine, Czech Academy of Science, 14220 Prague, Czech Republic;
| | - Marek Kovár
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, 94976 Nitra, Slovakia;
| | - Miroslava Kačániová
- Department of Fruit Science, Viticulture and Enology, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture in Nitra, 94976 Nitra, Slovakia;
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszow, 35-601 Rzeszow, Poland
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48
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Calizo RC, Bell MK, Ron A, Hu M, Bhattacharya S, Wong NJ, Janssen WGM, Perumal G, Pederson P, Scarlata S, Hone J, Azeloglu EU, Rangamani P, Iyengar R. Cell shape regulates subcellular organelle location to control early Ca 2+ signal dynamics in vascular smooth muscle cells. Sci Rep 2020; 10:17866. [PMID: 33082406 PMCID: PMC7576209 DOI: 10.1038/s41598-020-74700-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/05/2020] [Indexed: 12/23/2022] Open
Abstract
The shape of the cell is connected to its function; however, we do not fully understand underlying mechanisms by which global shape regulates a cell's functional capabilities. Using theory, experiments and simulation, we investigated how physiologically relevant cell shape changes affect subcellular organization, and consequently intracellular signaling, to control information flow needed for phenotypic function. Vascular smooth muscle cells going from a proliferative and motile circular shape to a contractile fusiform shape show changes in the location of the sarcoplasmic reticulum, inter-organelle distances, and differential distribution of receptors in the plasma membrane. These factors together lead to the modulation of signals transduced by the M3 muscarinic receptor/Gq/PLCβ pathway at the plasma membrane, amplifying Ca2+ dynamics in the cytoplasm, and the nucleus resulting in phenotypic changes, as determined by increased activity of myosin light chain kinase in the cytoplasm and enhanced nuclear localization of the transcription factor NFAT. Taken together, our observations show a systems level phenomenon whereby global cell shape affects subcellular organization to modulate signaling that enables phenotypic changes.
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Affiliation(s)
- R C Calizo
- Department of Pharmacological Sciences, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY, 10029, USA
| | - M K Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - A Ron
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| | - M Hu
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| | - S Bhattacharya
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - N J Wong
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - W G M Janssen
- Department of Pharmacological Sciences, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY, 10029, USA
| | - G Perumal
- Carl Zeiss Microscopy LLC, White Plains, NY, 10601, USA
| | - P Pederson
- Carl Zeiss Microscopy LLC, White Plains, NY, 10601, USA
| | - S Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - J Hone
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, USA
| | - E U Azeloglu
- Department of Pharmacological Sciences, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY, 10029, USA
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - P Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
| | - R Iyengar
- Department of Pharmacological Sciences, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY, 10029, USA.
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49
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Shahriyari F, Janmaleki M, Sharifi S, Hesar ME, Hoshian S, Taghiabadi R, Razaghian A, Ghadiri M, Peirovi A, Mahmoudi M, Nezhad AS, Khademhosseini A. Effect of cell imprinting on viability and drug susceptibility of breast cancer cells to doxorubicin. Acta Biomater 2020; 113:119-129. [PMID: 32525052 DOI: 10.1016/j.actbio.2020.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023]
Abstract
This study demonstrates the effect of substrate's geometrical cues on viability and the efficacy of an anti-cancer drug, doxorubicin (DOX), on breast cancer cells. It is hypothesized that the surface topographical properties can mediate the cellular drug intake. Pseudo-three dimensional (3D) platforms were fabricated using imprinting technique from polydimethylsiloxane (PDMS) and gelatin methacryloyl (GelMA) hydrogel to recapitulate topography of cells' membranes. The cells exhibited higher viability on the cell-imprinted platforms for both PDMS and GelMA materials compared to the plain/flat counterparts. For instance, MCF7 cells showed a higher metabolic activity (11.9%) on MCF7-imprinted PDMS substrate than plain PDMS. The increased metabolic activity for the imprinted GelMA was about 44.2% compared to plain hydrogel. The DOX response of cells was monitored for 24 h. Although imprinted substrates demonstrated enhanced biocompatibility, the cultured cells were more susceptible to the drug compared to the plain substrates. In particular, MCF7 cells on imprinted PDMS and GelMA substrates showed 37% and 50% higher in cell death compared to the corresponding plain PDMS and GelMA, respectively. Interestingly, the drug susceptibility of the cells on the imprinted hydrogel was about 70% higher than the cells cultured on imprinted PDMS substrates. Having MCF7 cell-imprinted substrates, DOX responses of two other breast cancer cell lines, SKBR3 and ZR-75-1, were also evaluated. The results support that cell membrane curvature developed by multiscale topography is able to mediate intracellular signaling and drug intake. STATEMENT OF SIGNIFICANCE: Research in biological sciences and drug discovery mostly rely on two dimensional (2D) cell culture techniques which cannot provide a reliable physiologically relevant environment. Lack of extracellular matrix and a large shift in physicochemical properties of conventional 2D substrates can induce aberrant cellular behaviors. While chemical composition, topographical, and mechanical properties of substrates have remarkable impacts on drug susceptibility, gene expression, and protein synthesis, the most cell culture plates are from rigid and plain substrates. A number of (bio)polymeric 3D-platforms have been introduced to resemble innate cell microenvironment. However, their intricate culture protocols restrain their applications in demanding high-throughput drug screening. To address the above concerns, in the present study, a hydrogel-based pseudo-3D substrate with imprinted cell features has been introduced.
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Balakin S, Yun YS, Lee J, Kang EH, Spohn J, Yun IS, Opitz J, Cuniberti G, Yeo JS. In vitro characterization of osteoblast cells on polyelectrolyte multilayers containing detonation nanodiamonds. ACTA ACUST UNITED AC 2020; 15:055026. [PMID: 32526712 DOI: 10.1088/1748-605x/ab9baf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Nanoparticle-enhanced coatings of bone implants are a promising method to facilitate sustainable wound healing, leading to an increase in patient well-being. This article describes the in vitro characterization of osteoblast cells interacting with polyelectrolyte multilayers, which contain detonation nanodiamonds (NDs), as a novel class of carbon-based coating material, which presents a unique combination of photoluminescence and drug-binding properties. The cationic polyelectrolyte, namely polydiallyldimethylammonium chloride (PDDA), has been used to immobilize NDs on silica glass. The height of ND-PDDA multilayers varies from a minimum of 10 nm for one bilayer to a maximum of 90 nm for five bilayers of NDs and PDDA. Human fetal osteoblasts (hFOBs) cultured on ND-PDDA multilayers show a large number of focal adhesions, which were studied via quantitative fluorescence imaging analysis. The influence of the surface roughness on the filopodia formation was assessed via scanning electron microscopy and atomic force microscopy. The nano-rough surface of five bilayers constrained the filopodia formation. The hFOBs grown on NDs tend to show not only a similar cell morphology compared to cells cultured on extracellular matrix protein-coated silica glass substrates, but also increased cell viability by about 40%. The high biocompatibility of the ND-PDDA multilayers, indicated via high cell proliferation and sound cell adhesion, shows their potential for biomedical applications such as drug-eluting coatings and biomaterials in general.
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Affiliation(s)
- Sascha Balakin
- Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, Dresden, Germany. Bio- and Nanotechnology, Fraunhofer Institute for Ceramic Technologies and Systems IKTS Material Diagnostics, Dresden, Germany. Both authors contributed equally to this manuscript
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