Beyond the Rhythm: In Silico Identification of Key Genes and Therapeutic Targets in Atrial Fibrillation

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia worldwide and is characterized by a high risk of thromboembolism, ischemic stroke, and fatality. The precise molecular mechanisms of AF pathogenesis remain unclear. The purpose of this study was to use bioinformatics tools to identify novel key genes in AF, provide deeper insights into the molecular pathogenesis of AF, and uncover potential therapeutic targets. Four publicly available raw RNA-Seq datasets obtained through the ENA Browser, as well as proteomic analysis results, both derived from atrial tissues, were used in this analysis. Differential gene expression analysis was performed and cross-validated with proteomics results to identify common genes/proteins between them. A functional enrichment pathway analysis was performed. Cross-validation analysis revealed five differentially expressed genes, namely FGL2, IGFBP5, NNMT, PLA2G2A, and TNC, in patients with AF compared with those with sinus rhythm (SR). These genes play crucial roles in various cardiovascular functions and may be part of the molecular signature of AF. Furthermore, functional enrichment analysis revealed several pathways related to the extracellular matrix, inflammation, and structural remodeling. This study highlighted five key genes that constitute promising candidates for further experimental exploration as biomarkers as well as therapeutic targets for AF.

Janus electro-microenvironment membrane with surface-selective osteogenesis/gingival healing ability for guided bone regeneration

Guided bone regeneration is widely applied in clinical practice to treat alveolar bone defects. However, the rate of healing of severe alveolar bone defects is slow, and there is a high incidence of soft tissue wound dehiscence. In this study, we propose a barrier membrane with a Janus electro-microenvironment (JEM) to achieve side-selective bone regeneration and soft tissue healing. The JEM membrane was constructed using a polarized polyvinylidene fluoride ferroelectric membrane with different surface potentials on either side. It promoted osteogenic differentiation and bone regeneration on the negatively polarized side (JEM-) and soft tissue regeneration on the positively polarized side (JEM+). Further investigation revealed that the JEM-mediated promotion of bone formation was related to mitochondrial autophagy, as indicated by depolarization of the mitochondrial membrane potential and the expression of LC3, Pink I, and Parkin. Moreover, the gingival healing promoted by JEM+ was related to oxidative phosphorylation in mitochondria, as indicated by the upregulation of mitochondrial complexes I–V and an increase in ATP generation. The design concept of the JEM provides a new avenue for regulating tissue regeneration between different tissue interfaces.

Kappa-carrageenan-Functionalization of octacalcium phosphate-coated titanium Discs enhances pre-osteoblast behavior and osteogenic differentiation

Bioactive coatings are promising for improving osseointegration and the long-term success of titanium dental or orthopaedic implants. Biomimetic octacalcium phosphate (OCP) coating can be used as a carrier for osteoinductive agents. κ-Carrageenan, a highly hydrophilic and biocompatible seaweed-derived sulfated-polysaccharide, promotes pre-osteoblast activity required for bone regeneration. Whether κ-carrageenan can functionalize OCP-coating to enhance osseointegration of titanium implants is unclear. This study aimed to analyze carrageenan-functionalized biomimetic OCP-coated titanium structure, and effects of carrageenan functionalization on pre-osteoblast behavior and osteogenic differentiation. Titanium discs were coated with OCP/κ-carrageenan at 0.125-2 mg/ml OCP solution, and physicochemical and biological properties were investigated. κ-Carrageenan (2 mg/ml) in the OCP coating of titanium discs decreased the pore size in the sheet-like OCP crystal by 41.32%. None of the κ-carrageenan concentrations tested in the OCP-coating did affect hydrophilicity. However, κ-carrageenan (2 mg/ml) increased (1.26-fold) MC3T3-E1 pre-osteoblast spreading at 1 h i.e., κ-Carrageenan in the OCP-coating increased pre-osteoblast proliferation (max. 1.92-fold at 2 mg/ml, day 1), metabolic activity (max. 1.50-fold at 2 mg/ml, day 3), and alkaline phosphatase protein (max. 4.21-fold at 2 mg/ml, day 3), as well as matrix mineralization (max. 5.45-fold at 2 mg/ml, day 21). κ-Carrageenan (2 mg/ml) in the OCP-coating increased gene expression of Mepe (4.93-fold) at day 14, and Runx2 (2.94-fold), Opn (3.59-fold), Fgf2 (3.47-fold), Ocn (3.88-fold), and Dmp1 (4.59-fold) at day 21 in pre-osteoblasts. In conclusion, κ-carrageenan modified the morphology and microstructure of OCP-coating on titanium discs, and enhanced pre-osteoblast metabolic activity, proliferation, and osteogenic differentiation. This suggests that κ-carrageenan-functionalized OCP coating may be promising for in vivo improvement of titanium implant osseointegration.

Adhesive peptide and polymer density modulate 3D cell traction forces within synthetic hydrogels

Cell-extracellular matrix forces provide pivotal signals regulating diverse physiological and pathological processes. Although mechanobiology has been widely studied in two-dimensional configurations, limited research has been conducted in three-dimensional (3D) systems due to the complex nature of mechanics and cellular behaviors. In this study, we established a platform integrating a well-defined synthetic hydrogel system (PEG-4MAL) with 3D traction force microscopy (TFM) methodologies to evaluate deformation and force responses within synthetic microenvironments, providing insights that are not tractable using biological matrices because of the interdependence of biochemical and biophysical properties and complex mechanics. We dissected the contributions of adhesive peptide density and polymer density, which determines hydrogel stiffness, to 3D force generation for fibroblasts. A critical threshold of adhesive peptide density at a constant matrix elasticity is required for cells to generate 3D forces. Furthermore, matrix displacements and strains decreased with matrix stiffness whereas stresses, and tractions increased with matrix stiffness until reaching constant values at higher stiffness values. Finally, Rho-kinase-dependent contractility and vinculin expression are required to generate significant 3D forces in both collagen and synthetic hydrogels. This research establishes a tunable platform for the study of mechanobiology and provides new insights into how cells sense and transmit forces in 3D.

Actomyosin contractility and buckling of microtubules in nucleation, growth and disassembling of focal adhesions

Building up and maintenance of cytoskeletal structure in living cells are force-dependent processes involving a dynamic chain of polymerization and depolymerization events, which are also at the basis of cells’ remodelling and locomotion. All these phenomena develop by establishing cell–matrix interfaces made of protein complexes, known as focal adhesions, which govern mechanosensing and mechanotransduction mechanisms mediated by stress transmission between cell interior and external environment. Within this framework, by starting from a work by Cao et al. (Biophys J 109:1807–1817, 2015), we here investigate the role played by actomyosin contractility of stress fibres in nucleation, growth and disassembling of focal adhesions. In particular, we propose a tensegrity model of an adherent cell incorporating nonlinear elasticity and unstable behaviours, which provides a new kinematical interpretation of cellular contractile forces and describes how stress fibres, microtubules and adhesion plaques interact mechanobiologically. The results confirm some experimental evidences and suggest how the actomyosin contraction level could be exploited by cells to actively control their adhesion, eventually triggering cytoskeleton reconfigurations and migration processes observed in both physiological conditions and diseases.

In silico framework to inform the design of repair constructs for peripheral nerve injury repair

Peripheral nerve injuries affect millions of people per year and cause loss of sensation and muscle control alongside chronic pain. The most severe injuries are treated through a nerve autograft; however, donor site morbidity and poor outcomes mean alternatives are required. One option is to engineer nerve replacement tissues to provide a supportive microenvironment to encourage nerve regeneration as an alternative to nerve grafts. Currently, progress is hampered due to a lack of consensus on how to arrange materials and cells in space to maximize rate of regeneration. This is compounded by a reliance on experimental testing, which precludes extensive investigations of multiple parameters due to time and cost limitations. Here, a computational framework is proposed to simulate the growth of repairing neurites, captured using a random walk approach and parameterized against literature data. The framework is applied to a specific scenario where the engineered tissue comprises a collagen hydrogel with embedded biomaterial fibres. The size and number of fibres are optimized to maximize neurite regrowth, and the robustness of model predictions is tested through sensitivity analyses. The approach provides an in silico tool to inform the design of engineered replacement tissues, with the opportunity for further development to multi-cue environments.

A computational modeling of invadopodia protrusion into an extracellular matrix fiber network

Invadopodia are dynamic actin-rich membrane protrusions that have been implicated in cancer cell invasion and metastasis. In addition, invasiveness of cancer cells is strongly correlated with invadopodia formation, which are observed during extravasation and colonization of metastatic cancer cells at secondary sites. However, quantitative understanding of the interaction of invadopodia with extracellular matrix (ECM) is lacking, and how invadopodia protrusion speed is associated with the frequency of protrusion-retraction cycles remains unknown. Here, we present a computational framework for the characterization of invadopodia protrusions which allows two way interactions between intracellular branched actin network and ECM fibers network. We have applied this approach to predicting the invasiveness of cancer cells by computationally knocking out actin-crosslinking molecules, such as α-actinin, filamin and fascin. The resulting simulations reveal distinct invadopodia dynamics with cycles of protrusion and retraction. Specifically, we found that (1) increasing accumulation of MT1-MMP at tips of invadopodia as the duration of protrusive phase is increased, and (2) the movement of nucleus toward the leading edge of the cell becomes unstable as duration of the retractile phase (or myosin turnover time) is longer than 1 min.

Isolation and culturing of primary mouse astrocytes for the analysis of focal adhesion dynamics

Primary astrocytes have gained attention as an important model for in vitro biological and biochemical research in the last decades. In this protocol, we describe a fast and cost-effective technique for isolating, culturing, and maintaining primary mouse astrocytes at ∼ 80% purity levels, which can be used in in vitro studies for migration and focal adhesion dynamics. In addition, we present an optimized transfection and manual quantification approach for focal adhesion analysis in fixed and living cells.

For complete details on the use and execution of this protocol, please refer to Kusuluri et al. (2021).

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High purity of primary mouse astrocyte isolation without commercial kits

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Isolated mouse primary astrocytes are functional for downstream applications

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Quantitative analysis of focal adhesion properties in fixed and living astrocytes

Additive manufacturing pertaining to bone: Hopes, reality and future challenges for clinical applications

For the past 20 years, the democratization of additive manufacturing (AM) technologies has made many of us dream of: low cost, waste-free, and on-demand production of functional parts; fully customized tools; designs limited by imagination only, etc. As every patient is unique, the potential of AM for the medical field is thought to be considerable: AM would allow the division of dedicated patient-specific healthcare solutions entirely adapted to the patients' clinical needs. Pertinently, this review offers an extensive overview of bone-related clinical applications of AM and ongoing research trends, from 3D anatomical models for patient and student education to ephemeral structures supporting and promoting bone regeneration. Today, AM has undoubtably improved patient care and should facilitate many more improvements in the near future. However, despite extensive research, AM-based strategies for bone regeneration remain the only bone-related field without compelling clinical proof of concept to date. This may be due to a lack of understanding of the biological mechanisms guiding and promoting bone formation and due to the traditional top-down strategies devised to solve clinical issues. Indeed, the integrated holistic approach recommended for the design of regenerative systems (i.e., fixation systems and scaffolds) has remained at the conceptual state. Challenged by these issues, a slower but incremental research dynamic has occurred for the last few years, and recent progress suggests notable improvement in the years to come, with in view the development of safe, robust and standardized patient-specific clinical solutions for the regeneration of large bone defects.

The Impact of Elastic Deformations of the Extracellular Matrix on Cell Migration

The mechanical properties of the extracellular matrix, in particular its stiffness, are known to impact cell migration. In this paper, we develop a mathematical model of a single cell migrating on an elastic matrix, which accounts for the deformation of the matrix induced by forces exerted by the cell, and investigate how the stiffness impacts the direction and speed of migration. We model a cell in 1D as a nucleus connected to a number of adhesion sites through elastic springs. The cell migrates by randomly updating the position of its adhesion sites. We start by investigating the case where the cell springs are constant, and then go on to assuming that they depend on the matrix stiffness, on matrices of both uniform stiffness as well as those with a stiffness gradient. We find that the assumption that cell springs depend on the substrate stiffness is necessary and sufficient for an efficient durotactic response. We compare simulations to recent experimental observations of human cancer cells exhibiting durotaxis, which show good qualitative agreement.

Cell migration: implications for repair and regeneration in joint disease

Connective tissues within the synovial joints are characterized by their dense extracellular matrix and sparse cellularity. With injury or disease, however, tissues commonly experience an influx of cells owing to proliferation and migration of endogenous mesenchymal cell populations, as well as invasion of the tissue by other cell types, including immune cells. Although this process is critical for successful wound healing, aberrant immune-mediated cell infiltration can lead to pathological inflammation of the joint. Importantly, cells of mesenchymal or haematopoietic origin use distinct modes of migration and thus might respond differently to similar biological cues and microenvironments. Furthermore, cell migration in the physiological microenvironment of musculoskeletal tissues differs considerably from migration in vitro. This Review addresses the complexities of cell migration in fibrous connective tissues from three separate but interdependent perspectives: physiology (including the cellular and extracellular factors affecting 3D cell migration), pathophysiology (cell migration in the context of synovial joint autoimmune disease and injury) and tissue engineering (cell migration in engineered biomaterials). Improved understanding of the fundamental mechanisms governing interstitial cell migration might lead to interventions that stop invasion processes that culminate in deleterious outcomes and/or that expedite migration to direct endogenous cell-mediated repair and regeneration of joint tissues.

Paxillin S273 Phosphorylation Regulates Adhesion Dynamics and Cell Migration through a Common Protein Complex with PAK1 and βPIX

Cell migration is an important biological phenomenon involved in many homeostatic and aberrant physiological processes. Phosphorylation of the focal adhesion adaptor protein, paxillin, on serine 273 (S273) has been implicated as a key regulator of cell migration. Here, it is shown that phosphorylation on paxillin S273 leads to highly migratory cells with small dynamic adhesions. Adhesions at protrusive edges of the cell were more dynamic than adhesions at retracting edges. Temporal image correlation microscopy revealed that these dynamic adhesions undergo rapid binding of paxillin, PAK1 and βPIX. We identified membrane proximal adhesion subdomains in protrusive regions of the cell that show rapid protein binding that is dependent on paxillin S273 phosphorylation, PAK1 kinase activity and phosphatases. These dynamic adhesion subdomains corresponded to regions of the adhesion that also show co-binding of paxillin/PAK1 and paxillin/βPIX complexes. It is likely that parts of individual adhesions are more dynamic while others are less dynamic due to their association with the actin cytoskeleton. Variable adhesion and binding dynamics are regulated via differential paxillin S273 phosphorylation across the cell and within adhesions and are required for regulated cell migration. Dysregulation through phosphomutants, PAK1-KD or βPIX mutants resulted in large stable adhesions, long protein binding times and slow cell migration. Dysregulation through phosphomimics or PAK1-CA led to small dynamic adhesions and rapid cell migration reminiscent of highly migratory cancer cells. Thus, phosphorylation of paxillin S273 is a key regulator of cell migration through recruitment of βPIX and PAK1 to sites of adhesion.

A Biophysical Model for Curvature-Guided Cell Migration

The latest experiments have shown that adherent cells can migrate according to cell-scale curvature variations via a process called curvotaxis. Despite identification of key cellular factors, a clear understanding of the mechanism is lacking. We employ a mechanical model featuring a detailed description of the cytoskeleton filament networks, the viscous cytosol, the cell adhesion dynamics, and the nucleus. We simulate cell adhesion and migration on sinusoidal substrates. We show that cell adhesion on three-dimensional curvatures induces a gradient of pressure inside the cell that triggers the internal motion of the nucleus. We propose that the resulting out-of-equilibrium position of the nucleus alters cell migration directionality, leading to cell motility toward concave regions of the substrate, resulting in lower potential energy states. Altogether, we propose a simple mechanism explaining how intracellular mechanics enable the cells to react to substratum curvature, induce a deterministic cell polarization, and break down cells basic persistent random walk, which correlates with latest experimental evidences.

Mathematical modelling of cell migration: stiffness dependent jump rates result in durotaxis

Durotaxis, the phenomena where cells migrate up a gradient in substrate stiffness, remains poorly understood. It has been proposed that durotaxis results from the reinforcement of focal adhesions on stiff substrates. In this paper we formulate a mathematical model of single cell migration on elastic substrates with spatially varying stiffness. We develop a stochastic model where the cell moves by updating the position of its adhesion sites at random times, and the rate of updates is determined by the local stiffness of the substrate. We investigate two physiologically motivated mechanisms of stiffness sensing. From the stochastic model of single cell migration we derive a population level description in the form of a partial differential equation for the time evolution of the density of cells. The equation is an advection–diffusion equation, where the advective velocity is proportional to the stiffness gradient. The model shows quantitative agreement with experimental results in which cells tend to cluster when seeded on a matrix with periodically varying stiffness.

Rhodoptilometrin, a Crinoid-Derived Anthraquinone, Induces Cell Regeneration by Promoting Wound Healing and Oxidative Phosphorylation in Human Gingival Fibroblast Cells

Gingival recession (GR) potentially leads to the exposure of tooth root to the oral cavity microenvironment and increases susceptibility to dental caries, dentin hypersensitivity, and other dental diseases. Even though many etiological factors were reported, the specific mechanism of GR is yet to be elucidated. Given the species richness concerning marine biodiversity, it could be a treasure trove for drug discovery. In this study, we demonstrate the effects of a marine compound, (+)-rhodoptilometrin from crinoid, on gingival cell migration, wound healing, and oxidative phosphorylation (OXPHOS). Experimental results showed that (+)-rhodoptilometrin can significantly increase wound healing, migration, and proliferation of human gingival fibroblast cells, and it does not have effects on oral mucosa fibroblast cells. In addition, (+)-rhodoptilometrin increases the gene and protein expression levels of focal adhesion kinase (FAK), fibronectin, and type I collagen, changes the intracellular distribution of FAK and F-actin, and increases OXPHOS and the expression levels of complexes I~V in the mitochondria. Based on our results, we believe that (+)-rhodoptilometrin might increase FAK expression and promote mitochondrial function to affect cell migration and promote gingival regeneration. Therefore, (+)-rhodoptilometrin may be a promising therapeutic agent for GR.

Mechanochemical modeling of neutrophil migration based on four signaling layers, integrin dynamics, and substrate stiffness

Directional neutrophil migration during human immune responses is a highly coordinated process regulated by both biochemical and biomechanical environments. In this paper, we developed an integrative mathematical model of neutrophil migration using a lattice Boltzmann-particle method built in-house to solve the moving boundary problem with spatiotemporal regulation of biochemical components. The mechanical features of the cell cortex are modeled by a series of spring-connected nodes representing discrete cell-substrate adhesive sites. The intracellular signaling cascades responsible for cytoskeletal remodeling [e.g., small GTPases, phosphoinositide-3-kinase (PI3K), and phosphatase and tensin homolog] are built based on our previous four-layered signaling model centered on the bidirectional molecular transport mechanism and implemented as reaction-diffusion equations. Focal adhesion dynamics are determined by force-dependent integrin-ligand binding kinetics and integrin recycling and are thus integrated with cell motion. Using numerical simulations, the model reproduces the major features of cell migration in response to uniform and gradient biochemical stimuli based on the quantitative spatiotemporal regulation of signaling molecules, which agree with experimental observations. The existence of multiple types of integrins with different binding kinetics could act as an adaptation mechanism for substrate stiffness. Moreover, cells can perform reversal, U-turn, or lock-on behaviors depending on the steepness of the reversal biochemical signals received. Finally, this model is also applied to predict the responses of mutants in which PTEN is overexpressed or disrupted.

Role of the Nucleus as a Sensor of Cell Environment Topography

The proper integration of biophysical cues from the cell vicinity is crucial for cells to maintain homeostasis, cooperate with other cells within the tissues, and properly fulfill their biological function. It is therefore crucial to fully understand how cells integrate these extracellular signals for tissue engineering and regenerative medicine. Topography has emerged as a prominent component of the cellular microenvironment that has pleiotropic effects on cell behavior. This progress report focuses on the recent advances in the understanding of the topography sensing mechanism with a special emphasis on the role of the nucleus. Here, recent techniques developed for monitoring the nuclear mechanics are reviewed and the impact of various topographies and their consequences on nuclear organization, gene regulation, and stem cell fate is summarized. The role of the cell nucleus as a sensor of cell-scale topography is further discussed.

Computational modeling of single-cell mechanics and cytoskeletal mechanobiology

Cellular cytoskeletal mechanics plays a major role in many aspects of human health from organ development to wound healing, tissue homeostasis and cancer metastasis. We summarize the state-of-the-art techniques for mathematically modeling cellular stiffness and mechanics and the cytoskeletal components and factors that regulate them. We highlight key experiments that have assisted model parameterization and compare the advantages of different models that have been used to recapitulate these experiments. An overview of feed-forward mechanisms from signaling to cytoskeleton remodeling is provided, followed by a discussion of the rapidly growing niche of encapsulating feedback mechanisms from cytoskeletal and cell mechanics to signaling. We discuss broad areas of advancement that could accelerate research and understanding of cellular mechanobiology. A precise understanding of the molecular mechanisms that affect cell and tissue mechanics and function will underpin innovations in medical device technologies of the future. WIREs Syst Biol Med 2018, 10:e1407. doi: 10.1002/wsbm.1407 This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Physiology > Mammalian Physiology in Health and Disease Models of Systems Properties and Processes > Cellular Models.

Alternative SiO2 Surface Direct MDCK Epithelial Behavior

The mechanical interactions of cells are mediated through adhesive interactions. In this study, we examined the growth, cellular behavior, and adhesion of MDCK epithelial cells on three different SiO₂ substrates: amorphous glass coverslips and the silicon oxide layers that grow on ⟨111⟩ and ⟨100⟩ wafers. While compositionally all three substrates are almost similar, differences in surface energy result in dramatic differences in epithelial cell morphology, cell-cell adhesion, cell-substrate adhesion, actin organization, and extracellular matrix (ECM) protein expression. We also observe striking differences in ECM protein binding to the various substrates due to the hydrogen bond interactions. Our results demonstrate that MDCK cells have a robust response to differences in substrates that is not obviated by nanotopography or surface composition and that a cell's response may manifest through subtle differences in surface energies of the materials. This work strongly suggests that other properties of a material other than composition and topology should be considered when interpreting and controlling interactions of cells with a substrate, whether it is synthetic or natural.

Cellular mechanosensing of the biophysical microenvironment: A review of mathematical models of biophysical regulation of cell responses

Cells in vivo reside within complex microenvironments composed of both biochemical and biophysical cues. The dynamic feedback between cells and their microenvironments hinges upon biophysical cues that regulate critical cellular behaviors. Understanding this regulation from sensing to reaction to feedback is therefore critical, and a large effort is afoot to identify and mathematically model the fundamental mechanobiological mechanisms underlying this regulation. This review provides a critical perspective on recent progress in mathematical models for the responses of cells to the biophysical cues in their microenvironments, including dynamic strain, osmotic shock, fluid shear stress, mechanical force, matrix rigidity, porosity, and matrix shape. The review highlights key successes and failings of existing models, and discusses future opportunities and challenges in the field.

Growth of hollow cell spheroids in microbead templated chambers

Cells form hollow, spheroidal structures during the development of many tissues, including the ocular lens, inner ear, and many glands. Therefore, techniques for in vitro formation of hollow spheroids are valued for studying developmental and disease processes. Current in vitro methods require cells to self-organize into hollow morphologies; we explored an alternative strategy based on cell growth in predefined, spherical scaffolds. Our method uses sacrificial, gelatin microbeads to simultaneously template spherical chambers within a hydrogel and deliver cells into the chambers. We use mouse lens epithelial cells to demonstrate that cells can populate the internal surfaces of the chambers within a week to create numerous hollow spheroids. The platform supports manipulation of matrix mechanics, curvature, and biochemical composition to mimic in vivo microenvironments. It also provides a starting point for engineering organoids of tissues that develop from hollow spheroids.

Stem cell mechanical behaviour modelling: substrate's curvature influence during adhesion

Recent experiments hint that adherent cells are sensitive to their substrate curvature. It is already well known that cells behaviour can be regulated by the mechanical properties of their environment. However, no mechanisms have been established regarding the influence of cell-scale curvature of the substrate. Using a numerical cell model, based on tensegrity structures theory and the non-smooth contact dynamics method, we propose to investigate the mechanical state of adherent cells on concave and convex hemispheres. Our mechanical cell model features a geometrical description of intracellular components, including the cell membrane, the focal adhesions, the cytoskeleton filament networks, the stress fibres, the microtubules, the nucleus membrane and the nucleoskeleton. The cell model has enabled us to analyse the evolution of the mechanical behaviour of intracellular components with varying curvature radii and with the removal of part of these components. We have observed the influence of the convexity of the substrate on the cell shape, the cytoskeletal force networks as well as on the nucleus strains. The more convex the substrate, the more tensed the stress fibres and the cell membrane, the more compressed the cytosol and the microtubules, leading to a stiffer cell. Furthermore, the more concave the substrate, the more stable and rounder the nucleus. These findings achieved using a verified virtual testing methodology, in particular regarding the nucleus stability, might be of significant importance with respect to the division and differentiation of mesenchymal stem cells. These results can also bring some hindsights on cell migration on curved substrates.

Surface coupling strength of gold nanoparticles affects cytotoxicity towards neurons

Weakly bound gold nanoparticles reveal awful toxicity towards neurons.

Single-Cell Migration in Complex Microenvironments: Mechanics and Signaling Dynamics

Cells are highly dynamic and mechanical automata powered by molecular motors that respond to external cues. Intracellular signaling pathways, either chemical or mechanical, can be activated and spatially coordinated to induce polarized cell states and directional migration. Physiologically, cells navigate through complex microenvironments, typically in three-dimensional (3D) fibrillar networks. In diseases, such as metastatic cancer, they invade across physiological barriers and remodel their local environments through force, matrix degradation, synthesis, and reorganization. Important external factors such as dimensionality, confinement, topographical cues, stiffness, and flow impact the behavior of migrating cells and can each regulate motility. Here, we review recent progress in our understanding of single-cell migration in complex microenvironments.

Endothelial cell sensing, restructuring, and invasion in collagen hydrogel structures

Experimental tools to model cell-tissue interactions will likely lead to new ways to both understand and treat cancer. While the mechanical properties and regulation of invasion have been recently studied for tumor cells, they have received less attention in the context of tumor vascular dynamics. In this article, we have investigated the interaction between the surfaces of structures encountered by endothelial cells invading their surrounding extracellular matrix (ECM) during angiogenesis. For this purpose, we have fabricated round and sharp geometries with various curvature and sharpness indices in collagen hydrogel over a wide range of stiffness to mimic different microenvironments varying from normal to tumor tissues. We have then cultured endothelial cells on these structures to investigate the bi-directional interaction between the cells and ECM. We have observed that cell invasion frequency is higher from the structures with the highest sharpness and curvature index, while interestingly the dependence of invasion on the local micro-geometry is strongest for the highest density matrices. Notably, structures with the highest invasion length are linked with higher deformation of side structures, which may be related to traction force-activated signaling suggesting further investigation. We have noted that round structures are more favorable for cell adhesion and in some cases round structures drive cell invasion faster than sharp ones. These results highlight the ability of endothelial cells to sense small variations in ECM geometry, and respond with a balance of matrix invasion as well as deformation, with potential implications for feedback mechanisms that may enhance vascular abnormality in response to tumor-induced ECM alterations.

Modeling the mechanics of cells in the cell-spreading process driven by traction forces

Mechanical properties of cells and their mechanical interaction with the extracellular environments are main factors influencing cellular function, thus indicating the progression of cells in different disease states. By considering the mechanical interactions between cell adhesion molecules and the extracellular environment, we developed a cell mechanical model that can characterize the mechanical changes in cells during cell spreading. A cell model was established that consisted of various main subcellular components, including cortical cytoskeleton, nuclear envelope, actin filaments, intermediate filaments, and microtubules. We demonstrated the structural changes in subcellular components and the changes in spreading areas during cell spreading driven by traction forces. The simulation of nanoindentation tests was conducted by integrating the indenting force to the cell model. The force-indentation curve of the cells at different spreading states was simulated, and the results showed that cell stiffness increased with increasing traction forces, which were consistent with the experimental results. The proposed cell mechanical model provides a strategy to investigate the mechanical interactions of cells with the extracellular environments through the adhesion molecules and to reveal the cell mechanical properties at the subcellular level as cells shift from the suspended state to the adherent state.

Cell Invasion Dynamics into a Three Dimensional Extracellular Matrix Fibre Network

The dynamics of filopodia interacting with the surrounding extracellular matrix (ECM) play a key role in various cell-ECM interactions, but their mechanisms of interaction with the ECM in 3D environment remain poorly understood. Based on first principles, here we construct an individual-based, force-based computational model integrating four modules of 1) filopodia penetration dynamics; 2) intracellular mechanics of cellular and nuclear membranes, contractile actin stress fibers, and focal adhesion dynamics; 3) structural mechanics of ECM fiber networks; and 4) reaction-diffusion mass transfers of seven biochemical concentrations in related with chemotaxis, proteolysis, haptotaxis, and degradation in ECM to predict dynamic behaviors of filopodia that penetrate into a 3D ECM fiber network. The tip of each filopodium crawls along ECM fibers, tugs the surrounding fibers, and contracts or retracts depending on the strength of the binding and the ECM stiffness and pore size. This filopodium-ECM interaction is modeled as a stochastic process based on binding kinetics between integrins along the filopodial shaft and the ligands on the surrounding ECM fibers. This filopodia stochastic model is integrated into migratory dynamics of a whole cell in order to predict the cell invasion into 3D ECM in response to chemotaxis, haptotaxis, and durotaxis cues. Predicted average filopodia speed and that of the cell membrane advance agreed with experiments of 3D HUVEC migration at r(2) > 0.95 for diverse ECMs with different pore sizes and stiffness.

Multiscale mechanobiology: computational models for integrating molecules to multicellular systems

Mechanical signals exist throughout the biological landscape. Across all scales, these signals, in the form of force, stiffness, and deformations, are generated and processed, resulting in an active mechanobiological circuit that controls many fundamental aspects of life, from protein unfolding and cytoskeletal remodeling to collective cell motions. The multiple scales and complex feedback involved present a challenge for fully understanding the nature of this circuit, particularly in development and disease in which it has been implicated. Computational models that accurately predict and are based on experimental data enable a means to integrate basic principles and explore fine details of mechanosensing and mechanotransduction in and across all levels of biological systems. Here we review recent advances in these models along with supporting and emerging experimental findings.

Microfluidic perfusion culture system for multilayer artery tissue models

We described an assembly technique and perfusion culture system for constructing artery tissue models. This technique differed from previous studies in that it does not require a solid biodegradable scaffold; therefore, using sheet-like tissues, this technique allowed the facile fabrication of tubular tissues can be used as model. The fabricated artery tissue models had a multilayer structure. The assembly technique and perfusion culture system were applicable to many different sizes of fabricated arteries. The shape of the fabricated artery tissue models was maintained by the perfusion culture system; furthermore, the system reproduced the in vivo environment and allowed mechanical stimulation of the arteries. The multilayer structure of the artery tissue model was observed using fluorescent dyes. The equivalent Young's modulus was measured by applying internal pressure to the multilayer tubular tissues. The aim of this study was to determine whether fabricated artery tissue models maintained their mechanical properties with developing. We demonstrated both the rapid fabrication of multilayer tubular tissues that can be used as model arteries and the measurement of their equivalent Young's modulus in a suitable perfusion culture environment.

Podosomes revealed by advanced bioimaging: what did we learn?

Podosomes are micrometer-sized, circular adhesions formed by cells such as osteoclasts, macrophages, dendritic cells, and endothelial cells. Because of their small size and the lack of methods to visualize individual proteins and protein complexes, podosomes have long been considered a simple two-module structure with a protrusive actin core and a surrounding adhesive ring composed of integrins and cytoskeletal adaptor proteins such as vinculin and talin. In the past decade, the applications of fluorescence based techniques that circumvent the diffraction limit of conventional light microscopy took a major leap forward. Podosomes have been imaged by a variety of these super-resolution methods, and in this concise review we discuss how these super-resolution data have increased our understanding of the podosome ultra-structure and function.

Mechanical decision trees for investigating and modulating single-cell cancer invasion dynamics

Physical cues exist across all biological scales, from the geometries of molecules to the shapes of complex organisms. While their roles have been identified across a range of scales, i.e. the arrangements of biomolecules and the form and function of tissues, less is known in some intermediate lengths. Particularly, at the cell scale, there is emerging evidence demonstrating the impact of mechanical signals, such as substrate stiffness and confinement, on many critical biological processes and malignancies, especially cancer dissemination. In the context of cell invasion, it is currently unclear how cells select from accessible mechanical paths that result in migratory patterns observed in physiological environments. Here, we devise microchannel decision trees to explore how fundamental and ubiquitous mechanical factors, specifically dimensionality and directionality, affect migratory cell decision making. We then implement strategies based purely on mechanical asymmetries to induce repetitive, non-disseminating motions, in a phenomenon we call iteratio ad nauseam.

Actin in action: imaging approaches to study cytoskeleton structure and function

The cytoskeleton plays several fundamental roles in the cell, including organizing the spatial arrangement of subcellular organelles, regulating cell dynamics and motility, providing a platform for interaction with neighboring cells, and ultimately defining overall cell shape. Fluorescence imaging has proved to be vital in furthering our understanding of the cytoskeleton, and is now a mainstay technique used widely by cell biologists. In this review we provide an introduction to various imaging modalities used to study focal adhesions and the actin cytoskeleton, and using specific examples we highlight a number of recent studies in animal cells that have advanced our knowledge of cytoskeletal behavior.

Dynamic modeling of cell migration and spreading behaviors on fibronectin coated planar substrates and micropatterned geometries

An integrative cell migration model incorporating focal adhesion (FA) dynamics, cytoskeleton and nucleus remodeling, actin motor activity, and lamellipodia protrusion is developed for predicting cell spreading and migration behaviors. This work is motivated by two experimental works: (1) cell migration on 2-D substrates under various fibronectin concentrations and (2) cell spreading on 2-D micropatterned geometries. These works suggest (1) cell migration speed takes a maximum at a particular ligand density (∼1140 molecules/µm(2)) and (2) that strong traction forces at the corners of the patterns may exist due to combined effects exerted by actin stress fibers (SFs). The integrative model of this paper successfully reproduced these experimental results and indicates the mechanism of cell migration and spreading. In this paper, the mechanical structure of the cell is modeled as having two elastic membranes: an outer cell membrane and an inner nuclear membrane. The two elastic membranes are connected by SFs, which are extended from focal adhesions on the cortical surface to the nuclear membrane. In addition, the model also includes ventral SFs bridging two focal adhesions on the cell surface. The cell deforms and gains traction as transmembrane integrins distributed over the outer cell membrane bond to ligands on the ECM surface, activate SFs, and form focal adhesions. The relationship between the cell migration speed and fibronectin concentration agrees with existing experimental data for Chinese hamster ovary (CHO) cell migrations on fibronectin coated surfaces. In addition, the integrated model is validated by showing persistent high stress concentrations at sharp geometrically patterned edges. This model will be used as a predictive model to assist in design and data processing of upcoming microfluidic cell migration assays.