Epifluorescence-based three-dimensional traction force microscopy

Uncertainty-Aware Traction Force Microscopy

Traction Force Microscopy (TFM) is a versatile tool to quantify cell-exerted forces by imaging and tracking fiduciary markers embedded in elastic substrates. The computations involved in TFM are ill-conditioned, and data smoothing or regularization is required to avoid overfitting the noise in the tracked substrate displacements. Most TFM calculations depend critically on the heuristic selection of regularization (hyper)parameters affecting the balance between overfitting and smoothing. However, TFM methods rarely estimate or account for measurement errors in substrate deformation to adjust the regularization level accordingly. Moreover, there is a lack of tools to quantify how these errors propagate to the recovered traction stresses. These limitations make it difficult to interpret TFM readouts and hinder comparing different experiments. This manuscript presents an uncertainty-aware TFM technique that estimates the variability in the magnitude and direction of the traction stress vector recovered at each point in space and time of each experiment. In this technique, substrate deformation and its uncertainty are quantified using a non-parametric bootstrap PIV method by resampling the microscopy image pixels (PIV-UQ). This information is passed to a hierarchical Bayesian framework that automatically selects its hyperparameters to perform spatially adaptive regularization conditioned on image quality and propagates the uncertainty to the traction stress readouts (TFM-UQ). We validate the performance of PIV-UQ and TFM-UQ using synthetic datasets with prescribed image quality variations and demonstrate the application of PIV-UQ and TFM-UQ to experimental datasets. These studies show that TFM-UQ locally adapts the level of smoothing, outperforming traditional regularization methods. They also illustrate how uncertainty-aware TFM tools can be used to objectively choose key image analysis parameters like PIV-UQ interrogation window size. We anticipate that these tools will allow for decoupling biological heterogeneity from measurement variability and facilitate automating the analysis of large datasets by parameter-free, input data-based regularization.

Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH

The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding ability and evasion of the host immune response. In this study, we conducted extensive equilibrium microsecond-level all-atom molecular dynamics (MD) simulations of the HA protein to explore the influence of low pH on its conformational dynamics. Specifically, we investigated the impact of protonation on conserved histidine residues (His106 2 ) located in the hinge region of HA2. Our analysis encompassed comparisons between non-protonated (NP), partially protonated (1P, 2P), and fully-protonated (3P) conditions. Our findings reveal substantial pH-dependent conformational alterations in the HA protein, affecting its receptor-binding capability and immune evasion potential. Notably, the non-protonated form exhibits greater stability compared to protonated states. Conformational shifts in the central helices of HA2 involve outward movement, counterclockwise rotation of protonated helices, and fusion peptide release in protonated systems. Disruption of hydrogen bonds between the fusion peptide and central helices of HA2 drives this release. Moreover, HA1 separation is more likely in the fully-protonated system (3P) compared to non-protonated systems (NP), underscoring the influence of protonation. These insights shed light on influenza virus infection mechanisms and may inform the development of novel antiviral drugs targeting HA protein and pH-responsive drug delivery systems for influenza.

Zonal Patterning of Extracellular Matrix and Stromal Cell Populations Along a Perfusable Cellular Microchannel

The spatial organization of biophysical and biochemical cues in the extracellular matrix (ECM) in concert with reciprocal cell-cell signaling is vital to tissue patterning during development. However, elucidating the role an individual microenvironmental factor plays using existing in vivo models is difficult due to their inherent complexity. In this work, we have developed a microphysiological system to spatially pattern the biochemical, biophysical, and stromal cell composition of the ECM along an epithelialized 3D microchannel. This technique is adaptable to multiple hydrogel compositions and scalable to the number of zones patterned. We confirmed that the methodology to create distinct zones resulted in a continuous, annealed hydrogel with regional interfaces that did not hinder the transport of soluble molecules. Further, the interface between hydrogel regions did not disrupt microchannel structure, epithelial lumen formation, or media perfusion through an acellular or cellularized microchannel. Finally, we demonstrated spatially patterned tubulogenic sprouting of a continuous epithelial tube into the surrounding hydrogel confined to local regions with stromal cell populations, illustrating spatial control of cell-cell interactions and signaling gradients. This easy-to-use system has wide utility for modeling three-dimensional epithelial and endothelial tissue interactions with heterogeneous hydrogel compositions and/or stromal cell populations to investigate their mechanistic roles during development, homeostasis, or disease.

3D Traction Force Microscopy in Biological Gels: From Single Cells to Multicellular Spheroids

Cell traction force plays a critical role in directing cellular functions, such as proliferation, migration, and differentiation. Current understanding of cell traction force is largely derived from 2D measurements where cells are plated on 2D substrates. However, 2D measurements do not recapitulate a vital aspect of living systems; that is, cells actively remodel their surrounding extracellular matrix (ECM), and the remodeled ECM, in return, can have a profound impact on cell phenotype and traction force generation. This reciprocal adaptivity of living systems is encoded in the material properties of biological gels. In this review, we summarize recent progress in measuring cell traction force for cells embedded within 3D biological gels, with an emphasis on cell-ECM cross talk. We also provide perspectives on tools and techniques that could be adapted to measure cell traction force in complex biochemical and biophysical environments.

JEasyTFM: an open-source software package for the analysis of large 2D TFM data within ImageJ

Motivation

Cells adhering to the extracellular matrix can sense and respond to a wide variety of chemical and physical features of the adhesive surface. Traction force microscopy (TFM) allows determining the tensile forces exerted by the cells on their substrate with high resolution.

Results

To allow broad access of this techniques to cell biology laboratories we developed JeasyTFM, an open-source ImageJ package able to process multi-color and multi-position time-lapse pictures thus suitable for the automatic analysis of large TFM data.

Availability and implementation

JEasyTFM is implemented as an ImageJ plugin and available at: http://questpharma.u-strasbg.fr/JEasyTFM.html.

2.5D Traction Force Microscopy: Imaging three-dimensional cell forces at interfaces and biological applications

The forces that cells, tissues, and organisms exert on the surface of a soft substrate can be measured using Traction Force Microscopy (TFM), an important and well-established technique in Mechanobiology. The usual TFM technique (two-dimensional, 2D TFM) treats only the in-plane component of the traction forces and omits the out-of-plane forces at the substrate interfaces (2.5D) that turn out to be important in many biological processes such as tissue migration and tumour invasion. Here, we review the imaging, material, and analytical tools to perform "2.5D TFM" and explain how they are different from 2D TFM. Challenges in 2.5D TFM arise primarily from the need to work with a lower imaging resolution in the z-direction, track fiducial markers in three-dimensions, and reliably and efficiently reconstruct mechanical stress from substrate deformation fields. We also discuss how 2.5D TFM can be used to image, map, and understand the complete force vectors in various important biological events of various length-scales happening at two-dimensional interfaces, including focal adhesions forces, cell diapedesis across tissue monolayers, the formation of three-dimensional tissue structures, and the locomotion of large multicellular organisms. We close with future perspectives including the use of new materials, imaging and machine learning techniques to continuously improve the 2.5D TFM in terms of imaging resolution, speed, and faithfulness of the force reconstruction procedure.

Mechanosensitive traction force generation is regulated by the neutrophil activation state

The generation of traction forces by neutrophils regulates many crucial effector functions responsible for host defense, such as attachment, spreading, migration, phagocytosis, and NETosis. The activation state of the cell is a strong determinant of the functional efficacy of the neutrophil; however, the effect of activation on traction force production has not yet been determined experimentally. Previously, the mapping of cellular-generated forces produced by human neutrophils via a Traction Force Microscopy (TFM) method has required a three-dimensional imaging modality to capture out-of-plane forces, such as confocal or multiphoton techniques. A method newly developed in our laboratories can capture out-of-plane forces using only a two-dimensional imaging modality. This novel technique-combined with a topology-based single particle tracking algorithm and finite element method calculations-can construct high spatial frequency three-dimensional traction fields, allowing for traction forces in-plane and out-of-plane to the substrate to now be differentially visualized and quantified with a standard epifluorescence microscope. Here we apply this technology to determine the effect of neutrophil activation on force generation. Sepsis is a systemic inflammatory response that causes dysregulated neutrophil activation in vivo. We found that neutrophils from septic patients produced greater total forces than neutrophils from healthy donors and that the majority of this dysregulation occurred in-plane to the substrate. Ex vivo activation of neutrophils from healthy donors showed differential consequences depending on activation stimuli with mechanosensitive force decreases observed in some cases. These findings demonstrate the feasibility of epifluorescence-based microscopy in mapping traction forces to ask biologically significant questions regarding neutrophil function.

Trends in mechanobiology guided tissue engineering and tools to study cell-substrate interactions: a brief review

Sensing the mechanical properties of the substrates or the matrix by the cells and the tissues, the subsequent downstream responses at the cellular, nuclear and epigenetic levels and the outcomes are beginning to get unraveled more recently. There have been various instances where researchers have established the underlying connection between the cellular mechanosignalling pathways and cellular physiology, cellular differentiation, and also tissue pathology. It has been now accepted that mechanosignalling, alone or in combination with classical pathways, could play a significant role in fate determination, development, and organization of cells and tissues. Furthermore, as mechanobiology is gaining traction, so do the various techniques to ponder and gain insights into the still unraveled pathways. This review would briefly discuss some of the interesting works wherein it has been shown that specific alteration of the mechanical properties of the substrates would lead to fate determination of stem cells into various differentiated cells such as osteoblasts, adipocytes, tenocytes, cardiomyocytes, and neurons, and how these properties are being utilized for the development of organoids. This review would also cover various techniques that have been developed and employed to explore the effects of mechanosignalling, including imaging of mechanosensing proteins, atomic force microscopy (AFM), quartz crystal microbalance with dissipation measurements (QCMD), traction force microscopy (TFM), microdevice arrays, Spatio-temporal image analysis, optical tweezer force measurements, mechanoscanning ion conductance microscopy (mSICM), acoustofluidic interferometric device (AID) and so forth. This review would provide insights to the researchers who work on exploiting various mechanical properties of substrates to control the cellular and tissue functions for tissue engineering and regenerative applications, and also will shed light on the advancements of various techniques that could be utilized to unravel the unknown in the field of cellular mechanobiology.

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.

A review on the recent progress, opportunities, and challenges of 4D printing and bioprinting in regenerative medicine

Four-dimensional (4 D) printing is a novel emerging technology, which can be defined as the ability of 3 D printed materials to change their form and functions. The term 'time' is added to 3 D printing as the fourth dimension, in which materials can respond to a stimulus after finishing the manufacturing process. 4 D printing provides more versatility in terms of size, shape, and structure after printing the construct. Complex material programmability, multi-material printing, and precise structure design are the essential requirements of 4 D printing systems. The utilization of stimuli-responsive polymers has increasingly taken the place of cell traction force-dependent methods and manual folding, offering a more advanced technique to affect a construct's adjusted shape transformation. The present review highlights the concept of 4 D printing and the responsive bioinks used in 4 D printing, such as water-responsive, pH-responsive, thermo-responsive, and light-responsive materials used in tissue regeneration. Cell traction force methods are described as well. Finally, this paper aims to introduce the limitations and future trends of 4 D printing in biomedical applications based on selected key references from the last decade.

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.

May the force be with your (immune) cells: an introduction to traction force microscopy in Immunology

For more than a couple of decades now, “force” has been recognized as an important physical parameter that cells employ to adapt to their microenvironment. Whether it is externally applied, or internally generated, cells use force to modulate their various actions, from adhesion and migration to differentiation and immune function. T lymphocytes use such mechano-sensitivity to decipher signals when recognizing cognate antigens presented on the surface of antigen presenting cells (APCs), a critical process in the adaptive immune response. As such, many techniques have been developed and used to measure the forces felt/exerted by these small, solitary and extremely reactive cells to decipher their influence on diverse T cell functions, primarily activation. Here, we focus on traction force microscopy (TFM), in which a deformable substrate, coated with the appropriate molecules, acts as a force sensor on the cellular scale. This technique has recently become a center of interest for many groups in the “ImmunoBiophysics” community and, as a consequence, has been subjected to refinements for its application to immune cells. Here, we present an overview of TFM, the precautions and pitfalls, and the most recent developments in the context of T cell immunology.

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.

Light-Sheet Scattering Microscopy to Visualize Long-Term Interactions Between Cells and Extracellular Matrix

Visualizing interactions between cells and the extracellular matrix (ECM) mesh is important to understand cell behavior and regulatory mechanisms by the extracellular environment. However, long term visualization of three-dimensional (3D) matrix structures remains challenging mainly due to photobleaching or blind spots perpendicular to the imaging plane. Here, we combine label-free light-sheet scattering microcopy (LSSM) and fluorescence microscopy to solve these problems. We verified that LSSM can reliably visualize structures of collagen matrices from different origin including bovine, human and rat tail. The quality and intensity of collagen structure images acquired by LSSM did not decline with time. LSSM offers abundant wavelength choice to visualize matrix structures, maximizing combination possibilities with fluorescently-labelled cells, allowing visualizing of long-term ECM-cell interactions in 3D. Interestingly, we observed ultrathin thread-like structures between cells and matrix using LSSM, which were not observed by normal fluorescence microscopy. Transient local alignment of matrix by cell-applied forces can be observed. In summary, LSSM provides a powerful and robust approach to investigate the complex interplay between cells and ECM.

Physics and Physiology of Cell Spreading in Two and Three Dimensions

Cells spread on surfaces and within three-dimensional (3-D) matrixes as they grow, divide, and move. Both chemical and physical signals orchestrate spreading during normal development, wound healing, and pathological states such as fibrosis and tumor growth. Diverse molecular mechanisms drive different forms of cell spreading. This article discusses mechanisms by which cells spread in 2-D and 3-D and illustrates new directions in studies of this aspect of cell function.

Traction force microscopy - Measuring the forces exerted by cells

Cells generate mechanical forces (traction forces, TFs) while interacting with the extracellular matrix or neighbouring cells. Forces are generated by both cells and extracellular matrix (ECM) and transmitted within the cell-ECM or cell-cell contacts involving focal adhesions or adherens junctions. Within more than two decades, substantial progress has been achieved in techniques that measure TFs. One of the techniques is traction force microscopy (TFM). This review discusses the TFM and its advances in measuring TFs exerted by cells (single cells and multicellular systems) at cell-ECM and cell-cell junctional intracellular interfaces. The answers to how cells sense, adapt and respond to mechanical forces unravel their role in controlling and regulating cell behaviour in normal and pathological conditions.

Imaging methods in mechanosensing: a historical perspective and visions for the future

Over the past three decades, as mechanobiology has become a distinct area of study, researchers have developed novel imaging tools to discover the pathways of biomechanical signaling. Early work with substrate engineering and particle tracking demonstrated the importance of cell–extracellular matrix interactions on the cell cycle as well as the mechanical flux of the intracellular environment. Most recently, tension sensor approaches allowed directly measuring tension in cell–cell and cell–substrate interactions. We retrospectively analyze how these various optical techniques progressed the field and suggest our vision forward for a unified theory of cell mechanics, mapping cellular mechanosensing, and novel biomedical applications for mechanobiology.