Elastic hydrogel as a sensor for detection of mechanical stress generated by single cells grown in three-dimensional environment

Tissue geometry spatiotemporally drives bacterial infections

Epithelial tissues serve as the first line of host against bacterial infections. The self-organization of epithelial tissues continuously adapts to the architecture and mechanics of microenvironments, thereby dynamically impacting the initial niche of infections. However, the mechanism by which tissue geometry regulates bacterial infection remains poorly understood. Here, we showed geometry-guided infection patterns of bacteria in epithelial tissues using bioengineering strategies. We discovered that cellular traction forces play a crucial role in the regulation of bacterial invasive sites and marginal infection patterns in epithelial monolayers through triggering co-localization of mechanosensitive ion channel protein Piezo1 with bacteria. Further, we developed precise mechanobiology-based strategies to potentiate the antibacterial efficacy in animal models of wound and intestinal infection. Our findings demonstrate that tissue geometry exerts a key impact on mediating spatiotemporal infections of bacteria, which has important implications for the discovery and development of alternative strategies against bacterial infections.

Advanced Microarrays as Heterogeneous Force-Remodeling Coordinator to Orchestrate Nuclear Configuration and Force-Sensing Mechanotransduction in Stem Cells

Integrin and focal adhesion can regulate cytoskeleton distribution to govern actin-related force remodeling and play an important role in nuclear configuration and force-sensing mechanotransduction of stem cells. However, further exploration of the interaction between actinin complex and myosin, kinetics, and molecular mechanism of cytoskeleton structures to nucleate within the engineered stem cells is vague. An extensive comprehension of cell morphogenesis, force remodeling, and nuclear force-sensing mechanotransduction is essential to reveal the basic physical principles of cytoskeleton polymerization and force-related signaling delivery. Advanced microarrays are designed to determine heterogeneous cell morphology and cell adhesion behaviors in stem cells. The heterogeneity from the engineered microarrays is transferred into nuclei to regulate nuclear configuration and force-sensing mechanotransduction by the evaluation of Lamins, YAP, and BrdU expression. Tuning the activation of adhesion proteins and cytoskeleton nucleators to adjust heterogeneous cell mechanics may be the underlying mechanism to change nuclear force-sensing configuration in response to its physiological mechanotransduction in microarrayed stem cells.

Dynamic Stiffening Hydrogel with Instructive Stiffening Timing Modulates Stem Cell Fate In Vitro and Enhances Bone Remodeling In Vivo

Biomechanical stimuli derived from the extracellular matrix (ECM) extremely tune stem cell fate through 3D and spatiotemporal changes in vivo. The matrix stiffness is a crucial factor during bone tissue development. However, most in vitro models to study the osteogenesis of mesenchymal stem cells (MSCs) are static or stiffening in a 2D environment. Here, a dynamic and controllable stiffening 3D biomimetic model is created to regulate the osteogenic differentiation of MSCs with a dual-functional gelatin macromer that can generate a double-network hydrogel by sequential enzymatic and light-triggered crosslinking reactions. The findings show that these dynamic hydrogels allowed cells to spread and expand prior to the secondary crosslinking and to sense high stiffness after stiffening. The MSCs in the dynamic hydrogels, especially the hydrogel stiffened at the late period, present significantly elevated osteogenic ECM secretion, gene expression, and nuclear localization of Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ). In vivo evaluation of animal experiments further indicates that the enhancement of dynamic stiffening on osteogenesis of MSCs substantially promotes bone remodeling. Consequently, this work reveals that the 3D dynamic stiffening microenvironment as a critical biophysical cue not only mediates the stem cell fate in vitro, but also augments bone restoration in vivo.

Advanced Mechanical Testing Technologies at the Cellular Level: The Mechanisms and Application in Tissue Engineering

Mechanics, as a key physical factor which affects cell function and tissue regeneration, is attracting the attention of researchers in the fields of biomaterials, biomechanics, and tissue engineering. The macroscopic mechanical properties of tissue engineering scaffolds have been studied and optimized based on different applications. However, the mechanical properties of the overall scaffold materials are not enough to reveal the mechanical mechanism of the cell-matrix interaction. Hence, the mechanical detection of cell mechanics and cellular-scale microenvironments has become crucial for unraveling the mechanisms which underly cell activities and which are affected by physical factors. This review mainly focuses on the advanced technologies and applications of cell-scale mechanical detection. It summarizes the techniques used in micromechanical performance analysis, including atomic force microscope (AFM), optical tweezer (OT), magnetic tweezer (MT), and traction force microscope (TFM), and analyzes their testing mechanisms. In addition, the application of mechanical testing techniques to cell mechanics and tissue engineering scaffolds, such as hydrogels and porous scaffolds, is summarized and discussed. Finally, it highlights the challenges and prospects of this field. This review is believed to provide valuable insights into micromechanics in tissue engineering.

Extracellular Matrix Rigidities Regulate the Tricarboxylic Acid Cycle and Antibiotic Resistance of Three-Dimensionally Confined Bacterial Microcolonies

As a major cause of clinical chronic infection, microbial biofilms/microcolonies in host tissues essentially live in 3D-constrained microenvironments, which potentially modulate their spatial self-organization and morphodynamics. However, it still remains unclear whether and how mechanical cues of 3D confined microenvironments, for example, extracellular matrix (ECM) stiffness, exert an impact on antibiotic resistance of bacterial biofilms/microcolonies. With a high-throughput antibiotic sensitivity testing (AST) platform, it is revealed that 3D ECM rigidities greatly modulate their resistance to diverse antibiotics. The microcolonies in 3D ECM with human tissue-specific rigidities varying from 0.5 to 20 kPa show a ≈2-10 000-fold increase in minimum inhibitory concentration, depending on the types of antibiotics. The authors subsequently identified that the increase in 3D ECM rigidities leads to the downregulation of the tricarboxylic acid (TCA) cycle, which is responsible for enhanced antibiotic resistance. Further, it is shown that fumarate, as a potentiator of TCA cycle activity, can alleviate the elevated antibiotic resistance and thus remarkably improve the efficacy of antibiotics against bacterial microcolonies in 3D confined ECM, as confirmed in the chronic infection mice model. These findings suggest fumarate can be employed as an antibiotic adjuvant to effectively treat infections induced by bacterial biofilms/microcolonies in a 3D-confined environment.

Nanocomposite Hydrogels as Functional Extracellular Matrices

Over recent years, nano-engineered materials have become an important component of artificial extracellular matrices. On one hand, these materials enable static enhancement of the bulk properties of cell scaffolds, for instance, they can alter mechanical properties or electrical conductivity, in order to better mimic the in vivo cell environment. Yet, many nanomaterials also exhibit dynamic, remotely tunable optical, electrical, magnetic, or acoustic properties, and therefore, can be used to non-invasively deliver localized, dynamic stimuli to cells cultured in artificial ECMs in three dimensions. Vice versa, the same, functional nanomaterials, can also report changing environmental conditions-whether or not, as a result of a dynamically applied stimulus-and as such provide means for wireless, long-term monitoring of the cell status inside the culture. In this review article, we present an overview of the technological advances regarding the incorporation of functional nanomaterials in artificial extracellular matrices, highlighting both passive and dynamically tunable nano-engineered components.

Deep learning-based 3D cellular force reconstruction directly from volumetric images

The forces exerted by single cells in the three-dimensional (3D) environments play a crucial role in modulating cellular functions and behaviors closely related to physiological and pathological processes. Cellular force microscopy (CFM) provides a feasible solution for quantifying the mechanical interactions, which usually regains cellular forces from deformation information of extracellular matrices embedded with fluorescent beads. Owing to computational complexity, the traditional 3D-CFM is usually extremely time-consuming, which makes it challenging for efficient force recovery and large-scale sample analysis. With the aid of deep neural networks, this study puts forward a novel data-driven 3D-CFM to reconstruct 3D cellular force fields directly from volumetric images with random fluorescence patterns. The deep learning (DL)-based network is established through stacking deep convolutional neural network (DCNN) and specific function layers. Some necessary physical information associated with constitutive relation of extracellular matrix material is coupled to the data-driven network. The mini-batch stochastic gradient descent and back-propagation algorithms are introduced to ensure its convergence and training efficiency. The network not only have good generalization ability and robustness, but also can recover 3D cellular forces directly from the input fluorescence image pairs. Particularly, the computational efficiency of the DL-based network is at least one to two orders of magnitude higher than that of the traditional 3D-CFM. This study provides a novel scheme for developing high-performance 3D cellular force microscopy to quantitatively characterize mechanical interactions between single cells and surrounding extracellular matrices, which is of vital importance for quantitative investigations in biomechanics and mechanobiology.

Egr1 is a 3D matrix-specific mediator of mechanosensitive stem cell lineage commitment

While extracellular matrix (ECM) mechanics strongly regulate stem cell commitment, the field's mechanistic understanding of this phenomenon largely derives from simplified two-dimensional (2D) culture substrates. Here, we found a 3D matrix-specific mechanoresponsive mechanism for neural stem cell (NSC) differentiation. NSC lineage commitment in 3D is maximally stiffness sensitive in the range of 0.1 to 1.2 kPa, a narrower and more brain-mimetic range than we had previously identified in 2D (0.75 to 75 kPa). Transcriptomics revealed stiffness-dependent up-regulation of early growth response 1 (Egr1) in 3D but not in 2D. Egr1 knockdown enhanced neurogenesis in stiff ECMs by driving β-catenin nuclear localization and activity in 3D, but not in 2D. Mechanical modeling and experimental studies under osmotic pressure indicate that stiff 3D ECMs are likely to stimulate Egr1 via increases in confining stress during cell volumetric growth. To our knowledge, Egr1 represents the first 3D-specific stem cell mechanoregulatory factor.

Exosome‑derived lncRNA‑Ankrd26 promotes dental pulp restoration by regulating miR‑150‑TLR4 signaling

At present, retaining the biological function of dental pulp is an urgent requirement in the treatment of pulp disease; it has been recognized that application of dental pulp stem cells (DPSCs) in regenerating dental pulp and dentin complexes is expected to become a safe and effective treatment of pulp disease; meanwhile the role of DPSC‑derived exosomes in dental pulp regeneration and repair is gaining attention. However, the underlying mechanism of DPSCs in dental pulp regeneration and repair is still unclear. In the present study, a variety of in vitro biological experiments and an animal model, as well as next‑generation sequencing and bioinformatics analysis, demonstrated that DPSCs promoted migration and osteoblastic differentiation of mesenchymal stem cells (MSCs) via exosomes; this was induced by DPSC‑derived exosomal long non‑coding (lnc)RNA‑ankyrin repeat domain (Ankrd)26. Mechanistically, the effect of exosomal lncRNA‑Ankrd26 on migration and osteoblastic differentiation of MSCs was dependent on microRNA (miR)‑150/Toll‑like receptor (TLR)4 signaling; this was regulated by lncRNA‑Ankrd26. The present study demonstrated that exosomes‑derived lncRNA‑Ankrd26 from DPSCs promoted dental pulp restoration via regulating miR‑150‑TLR4 signaling in MSCs; these findings help to understand the mechanism of dental pulp repair, identify therapeutic targets in the development of pulpitis and develop clinical treatments.

Spontaneous formation and spatial self-organization of mechanically induced mesenchymal-like cells within geometrically confined cancer cell monolayers

There is spatiotemporal heterogeneity in cell phenotypes and mechanical properties in tumor tissues, which is associated with cancer invasion and metastasis. It is well-known that exogenous growth factors like transforming growth factor (TGF)-β, can induce epithelial-mesenchymal transition (EMT)-based phenotypic transformation and the formation of EMT patterning on geometrically confined monolayers with mechanics heterogeneity. In the absence of exogenous TGF-β stimulation, however, whether geometric confinement-caused mechanics heterogeneity of cancer cell monolayers alone can trigger the EMT-based phenotypic heterogeneity still remains mysterious. Here, we develop a micropattern-based cell monolayer model to investigate the regulation of mechanics heterogeneity on the cell phenotypic switch. We reveal that mechanics heterogeneity itself is enough to spontaneously induce the emergence of mesenchymal-like phenotype and asymmetrical activation of TGF-β-SMAD signaling. Spatiotemporal dynamics of patterned cell monolayers with mesenchymal-like phenotypes is essentially regulated by tissue-scale cell behaviors like proliferation, migration as well as heterogeneous cytoskeletal contraction. The inhibition of cell contraction abrogates the asymmetrical TGF-β-SMAD signaling activation level and the emergence of mesenchymal-like phenotype. Our work not only sheds light on the key regulation of mechanics heterogeneity caused by spatially geometric confinement on regional mesenchymal-like phenotype of cancer cell monolayers, but highlights the key role of biophysical/mechanical cues in triggering phenotypic switch.

Tuning the response of fluid filled hydrogel core-shell structures

Hydrogels are hydrophilic polymer networks that swell upon submersion in water. Thanks to their bio-compatibility, compliance, and ability to undergo large deformations, hydrogels can be used in a wide variety of applications such as in situ sensors for measuring cell-generated forces and drug delivery vehicles. In this work we investigate the equilibrium mechanical responses that can be achieved with hydrogel-based shells filled with a liquid core. Two types of gel shell geometries are considered - a cylinder and a spherical shell. Each shell is filled with either water or oil and subjected to compressive loading. We illustrate the influence of the shell geometry and the core composition on the mechanical response of the structure. We find that all core-shell structures stiffen under increasing compressive loading due to the load-induced expulsion of water molecules from the hydrogel shell. Furthermore, we show that cylindrical core-shell configurations are stiffer then their spherical equivalents. Interestingly, we demonstrate that the compression of a core-shell structure with an aqueous core leads to the transportation of water molecules from the core into the hydrogel. These results will guide the design of novel core-shell structures with tunable properties and mechanical responses.

Polyacrylamide Bead Sensors for in vivo Quantification of Cell-Scale Stress in Zebrafish Development

Mechanical stress exerted and experienced by cells during tissue morphogenesis and organ formation plays an important role in embryonic development. While techniques to quantify mechanical stresses in vitro are available, few methods exist for studying stresses in living organisms. Here, we describe and characterize cell-like polyacrylamide (PAAm) bead sensors with well-defined elastic properties and size for in vivo quantification of cell-scale stresses. The beads were injected into developing zebrafish embryos and their deformations were computationally analyzed to delineate spatio-temporal local acting stresses. With this computational analysis-based cell-scale stress sensing (COMPAX) we are able to detect pulsatile pressure propagation in the developing neural rod potentially originating from polarized midline cell divisions and continuous tissue flow. COMPAX is expected to provide novel spatio-temporal insight into developmental processes at the local tissue level and to facilitate quantitative investigation and a better understanding of morphogenetic processes.

SUMO-modified bone marrow mesenchymal stem cells promoted the repair of articular cartilage in rats

Articular cartilage damage can lead to joint deformity, pain, and severe dysfunction. However, due to the lack of blood vessels and nerves in articular cartilage, the self-healing capacity of damaged cartilage is limited. In this study, we overexpressed small ubiquitin-like modifier (SUMO)1, SUMO2/3, and SUMO1/2/3 in bone marrow mesenchymal stem cells (BMSCs). Then, these cells were inoculated on surfaces of different hardness, and their differentiation into chondrocytes, hypoxic tolerance ability, and inflammatory response was detected. Finally, BMSCs were transplanted into the injured knee joint cavity of the rats, and the repair was evaluated. We found that BMSCs overexpressing SUMO1 were more likely to differentiate into articular cartilage along with the hardness of the surface, while BMSCs overexpressing SUMO2/3 could reduce inflammation response and improve the damaged cartilage microenvironment. In the rat model, BMSCs overexpressing SUMO1/2/3 transplanted on injured articular cartilage surface showed better survival, less inflammatory response, and improved tissue repair capability. In conclusion, BMSCs overexpressing SUMO are more tolerant to hypoxia conditions, and have stronger repair ability for damaged chondrocytes in vitro and for articular cartilage injury model in rats, and are excellent seed cells for repairing articular cartilage.

Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function

In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.

Reengineering the Physical Microenvironment of Tumors to Improve Drug Delivery and Efficacy: From Mathematical Modeling to Bench to Bedside

Physical forces have a crucial role in tumor progression and cancer treatment. The application of principles of engineering and physical sciences to oncology has provided powerful insights into the mechanisms by which these forces affect tumor progression and confer resistance to delivery and efficacy of molecular, nano-, cellular, and immuno-medicines. Here, we discuss the mechanics of the solid and fluid components of a tumor, with a focus on how they impede the transport of therapeutic agents and create an abnormal tumor microenvironment (TME) that fuels tumor progression and treatment resistance. We also present strategies to reengineer the TME by normalizing the tumor vasculature and the extracellular matrix (ECM) to improve cancer treatment. Finally, we summarize various mathematical models that have provided insights into the physical barriers to cancer treatment and revealed new strategies to overcome these barriers.

Direct Imaging of Protein Stability and Folding Kinetics in Hydrogels

We apply fast relaxation imaging (FReI) as a novel technique for investigating the folding stability and dynamics of proteins within polyacrylamide hydrogels, which have diverse and widespread uses in biotechnology. FReI detects protein unfolding in situ by imaging changes in fluorescence resonance energy transfer (FRET) after temperature jump perturbations. Unlike bulk measurements, diffraction-limited epifluorescence imaging combined with fast temperature perturbations reveals the impact of local environment effects on protein-biomaterial compatibility. Our experiments investigated a crowding sensor protein (CrH2) and phosphoglycerate kinase (PGK), which undergoes cooperative unfolding. The crowding sensor quantifies the confinement effect of the cross-linked hydrogel: the 4% polyacrylamide hydrogel is similar to aqueous solution (no confinement), while the 10% hydrogel is strongly confining. FRAP measurements and protein concentration gradients in the 4% and 10% hydrogels further support this observation. PGK reveals that noncovalent interactions of the protein with the polymer surface are more important than confinement for determining protein properties in the gel: the mere presence of hydrogel increases protein stability, speeds up folding relaxation, and promotes irreversible binding to the polymer even at the solution-gel interface, whereas the difference between the 4% and the 10% hydrogels is negligible despite their large difference in confinement. The imaging capabilities of FReI, demonstrated to be diffraction limited, further revealed spatially homogeneous protein unfolding across the hydrogels at 500 nm length scales and revealed differences in protein properties at the gel-solution boundary.

Mechanochemical mechanism of integrin clustering modulated by nanoscale ligand spacing and rigidity of extracellular substrates

Experimental findings indicate that cell function and behavior such as cell growth, division, migration and differentiation, are subtly regulated via integrin-dependent cell adhesion. Cell adhesion is influenced by nanoscale ligand spacing and rigidity of extracellular substrates, as cell adhesion drops greatly when the ligand spacing is larger than ~60nm, and cell adhesion is stronger on stiff than soft substrates. However, how nanoscale ligand spacing and substrate stiffness jointly affect integrin clustering and hence nascent cell adhesion remains to be elucidated. To quantitatively investigate the phenomena and the underlying mechanochemical mechanism of integrin clustering modulated by ligand spacing and substrate stiffness, we introduced Monte Carlo simulations varying the values of ligand spacing and substrate stiffness. Moreover, the effects of integrin number, integrin binding free energy, integrin association free energy, and local ligand spacing were investigated. The simulation results showed that integrin clustering decreased sharply, when ligand spacing was relatively large such as d_L>60nm in the current simulations, regardless of substrate rigidities, though with close spacing, the clustering increased with the substrate stiffness. The investigation contributes to the goals of understanding and predicting experimental phenomena, directing and optimizing biomaterial design, and manipulating integrin-dependent cell-substrate adhesion in tissue engineering.

Photoinitiator-free 3D scaffolds fabricated by excimer laser photocuring

Photoinitiator-free fabrication of poly(ethylene glycol) diacrylate (PEGDA) scaffolds is achieved using a novel three-dimensional (3D) printing method called mask projected excimer laser stereolithography (MPExSL). The spatial resolution of photoinitiator-free curing is suitable for 3D layer-by-layer fabrication with a single layer thickness well controllable at tens to hundreds of microns using 248 nm wavelength for the irradiation. The photoinitiator-free scaffolds are superior compared to their counterparts fabricated by using photoinitiator molecules, showing a higher level of biocompatibility. A release of toxic chemicals from the photoinitiator containing scaffolds is proven by cell proliferation tests. In contrast, no toxic release is found from the photoinitiator-free scaffolds, resulting in the very same level of cell proliferation as the control sample. The demonstration of photoinitiator-free PEGDA scaffolds enables the fabrication of 3D scaffolds with the highest level of biocompatibility for both in vitro and in vivo applications.