Biology subjects

Barrasa-Fano, J.

Publications and source records attributed to Barrasa-Fano, J..

7 recordsLinked to original sources

bioRxiv2025

Data-driven traction force microscopy in 3D collagen hydrogels

Quantitative measurements of cell-generated forces in fibrillar hydrogels have traditionally modeled the extracellular matrix as a continuum. Here we present a data-driven 3D traction force microscopy (DD-TFM) approach that reconstructs discrete collagen fiber networks from second-harmonic generation images and assigns fiber mechanics calibrated by shear rheology. In silico tests confirm the robustness of an inverse force-recovery method, and application to cells in collagen reveals pulling patterns and fiber-level stress distributions.

biophysics↗

bioRxiv2025

Osteoarthritis leads to more contractile and protrusive chondrocytes when cultured in 3D degradable hydrogels

Osteoarthritis (OA) induces phenotypic changes in chondrocytes as well as alterations in matrix composition and mechanics. Yet, its impact on active cell-generated forces, a key indicator of cell-matrix interaction, remains poorly characterized. In this study, we systematically compared the force generation capacity and associated proteins of interest between human OA and non-OA articular chondrocytes and how they are affected by cell culture dimensionality (2D versus 3D) and matrix degradability. Using traction force microscopy (TFM) combined with high-resolution immunostainings we show that OA alters the expression and organization of proteins involved in force exertion and transmission across both 2D and 3D cultures, but only in a 3D degradable hydrogel environment do these changes translate into higher cell-generated contractile forces This increased force generation correlates with elevated protrusive activity, higher actomyosin content and engagement, as well as altered localization of adhesion and matrix proteins, all of which could contribute to increased cell-matrix interaction in OA chondrocytes. In contrast, OA chondrocytes display no increase in cell tractions when cultured on 2D hydrogel substrates. These findings demonstrate that the detection and interpretation of OA-related alterations in chondrocyte mechanobiology are strongly dependent on the dimensionality and degradable properties of the culture system. Our results highlight the critical role of 3D degradable environments in revealing disease-associated changes in chondrocyte force generation and emphasize the necessity of carefully selecting model systems when investigating OA mechanobiology.

bioengineering↗

bioRxiv2025

Inverse modeling of heterogeneous ECM mechanical properties in nonlinear 3DTFM

Accurate characterization of cellular tractions is crucial for understanding cell-extracellular matrix (ECM) mechanical interactions and their implications in pathology-related situations, yet their direct measurement in experimental setups remains challenging. Traction Force Microscopy (TFM) has emerged as a key methodology to reconstruct traction fields from displacement data obtained via microscopic imaging techniques. While traditional TFM methods assume homogeneous and static ECM properties, the dynamic nature of the ECM through processes such as enzyme-induced collagen degradation or cellmediated collagen deposition i.e. ECM remodeling, requires approaches that account for spatio-temporal evolution of ECM stiffness heterogeneity and other mechanical properties. In this context, we present a novel inverse methodology for 3DTFM, capable of reconstructing spatially heterogeneous distributions of the ECMs stiffness. Our approach formulates the problem as a PDE-constrained inverse method which searches for both displacement and the stiffness map featured in the selected constitutive law. The elaborated numerical algorithm is integrated then into an iterative Newton-Raphson/Finite Element Method (NR/FEM) framework, bypassing the need for external iterative solvers. We validate our methodology using in silico 3DTFM cases based on real cell geometries, modeled within a nonlinear hyperelastic framework suitable for collagen hydrogels. The performance of our approach is evaluated across different noise levels, and compared versus the commonly used iterative L-BFGS algorithm. Besides the novelty of our formulation, we demonstrate the efficacy of our approach both in terms of accuracy and CPU time efficiency.

biophysics↗

bioRxiv2025

Linking Molecular Tension and Cellular Tractions: A Multiscale Approach to Focal Adhesion Mechanics

Focal adhesions (FAs) are mechanosensitive structures that mediate force transmission between cells and the extracellular matrix. While Traction Force Microscopy (TFM) quantifies cellular tractions exerted on deformable substrates, Forster Resonance Energy Transfer (FRET)-based tension probes, such as Vinculin Tension Sensors (VinTS), measure molecular-scale forces within FA proteins. Despite their potential synergy, these methods have rarely been combined to explore the interplay between molecular tension and cellular tractions. Here, we introduce a framework integrating TFM and VinTS to investigate FA mechanics across scales. At cell level, tractions and vinculin tension increased with substrate stiffness. At FA level, vinculin tension correlated with vinculin density, while tractions scaled with FA area, total vinculin content and vinculin density. Direct comparison of tractions to tension revealed a complex, heterogenous relationship between these forces, possibly linked to diverse cell and FA maturation states. Sub-FA analysis revealed conserved spatial patterns, with tension and traction increasing towards the cell periphery. This multiscale approach provides insights into the multiscale dynamics of FA mechanotransduction, bridging the gap between molecular forces and cellular mechanics.j

biophysics↗

bioRxiv2022

Traction force reconstruction assessment on real three-dimensional matrices and cellular morphologies

Traction force microscopy (TFM) allows to estimate tractions on the surface of cells when they mechanically interact with hydrogel substrates that mimic the extracellular matrix (ECM). The field of mechanobiology has a strong interest in using TFM in 3D in vitro models. However, there are a number of challenges that hamper the accuracy of 3D TFM and that are often bypassed. In this study, the computational efficiency and accuracy of TFM, referred to traction reconstruction from synthetically generated (control) ground truth solutions, are assessed from four different perspectives: magnitude of cellular pulling force (and hence strain level achieved in the hydrogel), effect of the complexity of the cellular morphology, accuracy and computational efficiency of forward vs inverse traction recovery methods, and the effect of incorrectly selecting a constitutive model that describes the behavior of the ECM (i.e. linear/nonlinear). The main results showed: (i) traction reconstruction is more challenging for complex cell morphologies, (ii) there is no significant impact of the magnitude of cellular pulling force on the overall reconstruction accuracy, and (iii) modeling a nonlinear hydrogel with a linear constitutive model leads to non-negligible errors (up to 80% and 30% for forward and inverse methodologies, respectively) in traction reconstruction. This study expands the characterization of the accuracy and efficiency of 3D TFM, highlighting important factors to be considered in future 3D TFM in vitro applications.

cell biology↗

bioRxiv2022

Synthetic fibrous hydrogels as a platform to decipher cell-matrix mechanical interactions

The interactions between cells and their direct environment are crucial for cell fate but biochemically and mechanically highly complex, and therefore, poorly understood. Despite recent advances that exposed the impact of a range of different factors, real progress remains challenging, since appropriate controllable matrices and quantitative analysis techniques that cover a range of time and length scales are unavailable. Here, we use a synthetic fibrous hydrogel with nonlinear mechanics to mimic and tailor the bi-directional cell-matrix interactions. Using advanced microscopy-based approaches, we acquire a comprehensive picture of how cellular traction forces, fiber remodeling, matrix stiffening, matrix properties and cellular behavior interact, highlighting for instance, the importance of a fibrous architecture and nonlinear mechanics of the matrix. Complete mapping of cell-matrix interactions at the cellular length scale provides indispensable information for the rational design of biomimetic materials to recreate realistic in vitro cell environments.

biophysics↗

bioRxiv2020

Advanced in silico validation framework forthree-dimensional Traction Force Microscopy andapplication to an in vitro model of sproutingangiogenesis

In the last decade, cellular forces in three-dimensional hydrogels that mimic the extracellular matrix have been calculated by means of Traction Force Microscopy (TFM). However, characterizing the accuracy limits of a traction recovery method is critical to avoid obscuring physiological information due to traction recovery errors. So far, 3D TFM algorithms have only been validated using simplified cell geometries, bypassing image processing steps or arbitrarily simulating focal adhesions. Moreover, it is still uncertain which of the two common traction recovery methods, i.e., forward and inverse, is more robust against the inherent challenges of 3D TFM. In this work, we established an advanced in silico validation framework that is applicable to any 3D TFM experimental setup and that can be used to correctly couple the experimental and computational aspects of 3D TFM. Advancements relate to the simultaneous incorporation of complex cell geometries, simulation of microscopy images of varying bead densities and different focal adhesion sizes and distributions. By measuring the traction recovery error with respect to ground truth solutions, we found that while highest traction recovery errors occur for cases with sparse and small focal adhesions, our implementation of the inverse method improves two-fold the accuracy with respect to the forward method (average error of 23% vs. 50%). This advantage was further supported by recovering cellular tractions around angiogenic sprouts in an in vitro model of angiogenesis. The inverse method recovered more realistic traction patterns than the forward method, showing higher traction peaks and a clearer pulling pattern at the sprout protrusion tips.

bioengineering↗