Biology subjects

Trepat, X.

Publications and source records attributed to Trepat, X..

At least 19 recordsLinked to original sources

bioRxiv2026

A minimal physical model of adhesion-dependent protrusion explains confined haptotaxis and oscillatory cell migration

Haptotaxis is the directed migration of cells along gradients of substrate adhesion, and is an important guidance mechanism in biology. Recent experiments on fibronectin-patterned tracks show that cells typically migrate toward higher adhesion, then oscillate around the adhesion maximum, with substantial variability in speed and cell length. To explain these cellular shape and migration dynamics we present a minimal model for confined haptotaxis, built around one key physical ingredient: local adhesion strength directly enhances the recruitment of protrusive actin polymerization activity at the cell edge. This coupling creates a front-rear difference in protrusive activity, biasing the cell towards polarization in the direction of the higher adhesion. Quantitative comparison with experiment shows strong agreement at multiple levels: cell population-level directionality statistics and position-dependent changes in cell length and velocity. At the single-cell level, the model reproduces the full diversity of experimentally observed trajectories, including haptotactic bias and its dependence on adhesion-gradient strength, initial position, length and speed variations, myosin II inhibition, and migration on inverted adhesion gradients. Variability in experimental trajectories and migration speed is explained by differences in intrinsic actin polymerization activity and stochastic fluctuations, accounting for the full spectrum of observed migration patterns. Together, our results identify adhesion-dependent amplification of protrusive activity as a minimal and sufficient physical mechanism for understanding haptotaxis.

biophysics↗

bioRxiv2025

A keratin bundling transition uncages the nucleus in stretchedepithelia

There is broad consensus that intermediate filaments play a key role in protecting cells and tissues from large deformations. However, little is known about how they fulfil this function. Here we demonstrate that epithelial cells undergo a slow adaptation to stretch that couples a star- bundling transition of keratin filaments and the escape of the nucleus from its keratin cage. The bundling transition begins with a depletion of keratin filaments at tri-cellular junctions followed by a progressive accumulation in thick bundles that bisect cell-cell junctions. Bundling is a cooperative process that initiates in a few scattered cells and propagates to their neighbours through desmosomes, leading to the growth of multicellular clusters that contain a percolated network of thick keratin bundles. Bundling dynamics are slow and strongly influenced by the interaction between actin and keratin. Informed by a computational model, we provide evidence that keratin bundling generates a compressive stress on the nucleus, which is relaxed by nuclear escape from the keratin cage. The topological transitions identified here provide epithelia with a multiscale mechanism to adapt to sustained stretch.

biophysics↗

bioRxiv2025

Mechanically Tunable DNA Hydrogel Microparticles for 3D Cellular Systems

Hydrogel microparticles (HMPs) are powerful tools to study and manipulate cellular behavior in 3D cell culture systems and animal models. Here, fully DNA-based HMPs are presented, whose material properties can be precisely tuned by sequence-programmable design of self-assembling DNA nanostructures. These DNA-HMPs offer control over size, stiffness, viscoelasticity and ligand presentation. They are formed by microfluidic encapsulation of two types of orthogonal DNA nanostars and a sequence-complementary DNA linker in water-in-oil droplets. By varying the valency of the DNA nanostar designs, tunable mechanical properties are achieved - spanning three orders of magnitude in Youngs modulus from 30 Pa to 6.5 kPa with distinct viscoelastic behavior. Click-chemistry based functionalization with the small fibronectin-derived peptide cyclic-RGD (c[RGD]) enables integration into fibroblast spheroids. DNA-HMPs are stably retained within the spheroids for several days and undergo design- and stiffness-dependent remodeling, indicating active interactions between the cells and the DNA-HMPs. Combining tunable material properties and inherent biocompatibility of DNA with straightforward functionalization and stimuli-responsiveness, these DNA-HMPs represent a versatile tool to probe and manipulate tissue behaviors in 3D cell cultures and in vivo models. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/665473v2_ufig1.gif" ALT="Figure 1000"> View larger version (51K): org.highwire.dtl.DTLVardef@c226ceorg.highwire.dtl.DTLVardef@81c3b3org.highwire.dtl.DTLVardef@1573ee1org.highwire.dtl.DTLVardef@e1518c_HPS_FORMAT_FIGEXP M_FIG DNA hydrogel microparticles are designed to exhibit controllable viscoelasticity and stiffness across three orders of magnitude from 30 Pa to 6.5 kPa. They are uptaken into fibroblast spheroids where they are actively remodeled by cellular forces depending on their mechanical properties. C_FIG

bioengineering↗

bioRxiv2025

Multiscale wrinkling dynamics in epithelial shells

Thin shells buckle and wrinkle when compressed. While this behavior is generally detrimental in engineering, it has been widely implicated in epithelial morphogenesis and patterning during development. Yet the rules governing buckling of active viscoelastic shells like epithelia remain unclear. Here we delineate those rules by combining an experimental system that allows us to sculpt epithelial shells and subject them to controlled deflation with a 3D computational model linking cytoskeletal dynamics to tissue mechanics. Experiments and simulations across several orders of magnitude in time and space reveal that buckling emerges for fast deflation relative to the cortexs relaxation time, and is suppressed by high contractility. We show, further, that the tissue develops wrinkle patterns with different degrees of symmetry breaking that depend on its size and viscous confinement. Strikingly, we find that epithelial buckling is a multiscale phenomenon involving long-lived supracellular folds but also short-lived subcellular wrinkles in the actin cortex. Finally, by forming epithelial shells with anisotropic curvature we rationally direct buckling into predictable wrinkle patterns. Our study shows that epithelial tissues can be understood as hierarchical materials with mechanical instabilities that can be harnessed to engineer epithelial morphogenesis.

biophysics↗

bioRxiv2025

Mechanical Coordination of Intestinal Cell Extrusion by Supracellular 3D Force Patterns

Every day, the mammalian intestinal epithelium extrudes millions of cells to sustain tissue self-renewal. Despite its fundamental role in intestinal homeostasis, the mechanisms that trigger, compartmentalize, and execute intestinal cell extrusion remain largely unknown. Here, using intestinal organoids, we map the three-dimensional forces and cytoskeletal dynamics that drive intestinal cell extrusion. We show that, unlike in other epithelia, extrusion is initiated by the sudden dissolution of a contractile myosin 2A meshwork triggered by a calcium influx. Following meshwork dissolution, the extruding cell and its neighbors generate an upwards traction force that requires myosin contractility but is generated by lamellipodial protrusions in neighboring cells. Importantly, these lamellipodia not only act as force generators but also determine whether extrusion occurs apically or basally, serving as symmetry breakers of the process. Finally, we show that compartmentalization of cell extrusion to the outside of the intestinal crypt does not require curvature and instead depends on myosin 2A. Our findings reveal that the intestinal epithelium exhibits a distinctive mode of extrusion, in which tension differentials--rather than compressive stresses from crowding--trigger and compartmentalize cell removal.

cell biology↗

bioRxiv2025

Guidance of cellular nematics into shape-programmable living surfaces

Engineering living materials capable of autonomously morphing into predetermined shapes holds great potential for applications ranging from synthetic tissue morphogenesis to soft robotics. In this regard, harnessing the inherent ability of cellular tissues to self-organize and generate robust force fields offers a promising strategy for creating self-shaping living surfaces. However, achieving precise control over tissue mechanics to direct specific morphogenetic outcomes remains a challenge. Here, we introduce a strategy to program tissue shape transformations through the nematic organization of cellular forces. By precisely controlling nematic order and topological defects, we generate millimeter-scale tissues programmed with specific multicellular tension fields. Using a theoretical framework that integrates contractile nematics with thin sheet mechanics, we explore the role of nematically guided tensions in shape morphogenesis. Experimentally, upon tissue detachment, nematically guided tension fields drive out-of-plane deformations, generating reproducible 3D shapes. By integrating tissue contractility and nematic patterning, our approach offers a robust framework for the rational design of shape-programmable living surfaces.

biophysics↗

bioRxiv2025

Theory of multiscale epithelial mechanics under stretch: from active gels to vertex models

Epithelial monolayers perform a variety of mechanical functions, which include maintaining a cohesive barrier or developing 3D shapes, while undergoing stretches over a wide range of magnitudes and loading rates. To perform these functions, they rely on a hierarchical organization, which spans molecules, cytoskeletal networks, adhesion complexes and junctional networks up to the tissue scale. While the molecular understanding and ability to manipulate cytoskeletal components within cells is rapidly increasing, how these components integrate to control tissue mechanics is far less understood, partly due to the disconnect between theoretical models of sub-cellular dynamics and those at a tissue scale. To fill this gap, here we propose a formalism bridging active-gel models of the actomyosin cortex and 3D vertex-like models at a tissue scale. We show that this unified framework recapitulates a number of seemingly disconnected epithelial time-dependent phenomenologies, including stress relaxation following stretch/unstretch maneuvers, active flattening after buckling, or nonreciprocal and non-affine pulsatile contractions. We further analyze tissue dynamics probed by a novel experimental setup operating in a pressure-controlled ensemble. Overall, the proposed framework systematically connects sub-cellular cortical dynamics and tissue mechanics, and ties a variety of epithelial phenomenologies to a common sub-cellular origin.

biophysics↗

bioRxiv2024

Cardiac fibroblasts cellular anisotropy is determined by YAP-dependent cellular contractility and ECM production

Cardiac fibroblasts (CFbs) determine the topological arrangement and the anisotropy of the heart tissue - essential features for maintaining tissue integrity and function - through the production and remodeling of the extracellular matrix (ECM). Under pathological conditions, CFbs can activate into myofibroblasts and promote maladaptive ECM remodeling that may lead to heart failure. Yes-Associated Protein (YAP) - a key player in cardiac fibrosis onset - has been implicated in CFb activation but its role in coordinating the supracellular organization of CFbs and in shaping the instructive properties of the ECM remains poorly understood. We addressed these questions by generating CFbs from wild-type (WT) and YAP knockout (KO) human embryonic stem cells. YAP depletion reduced the expression of cardiogenic markers and altered the transcriptomic profile of ECM- and contractility-related genes. We further demonstrated that YAP expression is required for CFbs monolayer alignment, and its absence resulted in reduced ECM deposition, decreased anisotropy, and diminished force generation. Pharmacological inhibition of cell contractility closely mirrored YAP KO phenotype, suggesting that YAP regulates both monolayer organization and ECM structure through its control over contractility. ECM cross-seeding experiments confirmed the role of ECM as a structural guide for cellular alignment. Moreover, cardiomyocytes cultured on KO CFb-derived ECM exhibited impaired sarcomere organization and altered calcium dynamics. Together, these findings demonstrate that YAP activity in CFbs governs the structural and functional properties of the ECM, influencing both fibroblast alignment and cardiomyocyte activity. Moreover, they underscore the critical role of YAP in maintaining the supracellular organization and mechanical integrity of cardiac tissue.

cell biology↗

bioRxiv2024

Single cell migration along and against confined haptotactic gradients

Directed cell migration along gradients of extracellular matrix (ECM) density -a process called haptotaxis- plays a central role in morphogenesis, the immune response, and cancer invasion. It is commonly assumed that cells respond to these gradients by migrating directionally towards the regions of highest ligand density. In contrast with this view, here we show that cells exposed to micropatterned fibronectin gradients exhibit a complex repertoire of trajectories, including directed haptotactic migration up the gradient but also linear oscillations and circles with extended periods of migration down the gradient. To explain this behavior, we developed a biophysical model of haptotactic cell migration based on a coarse-grained molecular clutch model coupled to persistent stochastic polarity dynamics. While initial haptotactic migration is explained by the differential friction at the front and back of the cell, the observed complex trajectories over longer time scales arise from the interplay between differential friction, persistence, and physical confinement. Overall, our study reveals that confinement and persistence modulate the ability of cells to sense and respond to haptotactic cues and provides a framework to understand how cells navigate complex environments.

cell biology↗

bioRxiv2024

3D micropatterned traction force microscopy: a technique to control three-dimensional cell shape while measuring cell-substrate force transmission.

Cell shape and function are intimately linked, in a way that is mediated by the forces exerted between cells and their environment. The relationship between cell shape and forces has been extensively studied for cells seeded on flat 2-dimensional (2D) substrates, but not for cells in more physiological three-dimensional (3D) settings. Here, we demonstrate a technique called 3D micropatterned traction force microscopy (3D-TFM) to confine cells in three-dimensional wells of defined shape, while simultaneously measuring the forces transmitted between cells and their microenvironment. This technique is based on the 3D micropatterning of polyacrylamide wells and on the calculation of 3D traction force from their deformation. With 3D-TFM, we show that MCF10A breast epithelial cells exert defined, reproducible patterns of forces on their microenvironment, which can be both contractile and extensile. We further show that cells switch from a global contractile to extensile behaviour as their volume is reduced. Our technique enables the quantitative study of cell mechanobiology with full access to 3D cellular forces while having accurate control over cell morphology and the mechanical conditions of the microenvironment.

bioengineering↗

bioRxiv2024

Cell-matrix force transmission regulates the loss of naïve pluripotency in mouse embryonic stem cells.

The first step in the differentiation of mouse embryonic stem cells (mESCs) is the loss of naive pluripotency. This step involves a major reshaping of cells from a rounded to a spread, adhesive phenotype. Whereas such reshaping is typically associated with increased force transmission to the extracellular matrix (ECM), the magnitude and role of cell-matrix forces in the loss of naive pluripotency is unknown. Here, we show that cell-matrix forces increase during, and are required for, the loss of naive pluripotency in mESCs. Using traction force microscopy, we show that mESCs progressively increase cell-traction forces and mechanotransduction markers as naive pluripotency dissolves. Modulation of force transmission through myosin inhibition, substrate stiffness, or spatial differences within mESC colonies regulates the process. Increased force is triggered by GSK3-mediated signalling, and the effect of force is regulated in part by its transmission to the cell nucleus. Our work unveils a major role of cell-ECM forces in pluripotency dissolution, adding an important aspect to the interplay between biochemical and biophysical cues that drive this process.

developmental biology↗

bioRxiv2024

Optogenetic generation of leader cells reveals a force-velocity relation for collective cell migration

The front of migratory cellular clusters during development, wound healing and cancer invasion is typically populated with highly protrusive cells that are called leader cells. Leader cells are thought to physically pull and direct their cohort of followers, but how leaders and followers are mechanically organized to migrate collectively remains controversial. One possibility is that the autonomous local action of a leader cell is sufficient to drive migration of the group. Yet another possibility is that a global mechanical organization is required for the group to move cohesively. Here we show that the effectiveness of leader-follower organization is proportional to the asymmetry of traction and tension within the cellular cluster. By combining hydrogel micropatterning and optogenetic activation of Rac1, we locally generate highly protrusive leaders at the edge of minimal cell groups. We find that the induced leader can robustly drag one follower but is generally unable to direct larger groups. By measuring traction forces and tension propagation in groups of increasing size, we establish a quantitative relationship between group velocity and the asymmetry of the traction and tension profiles. We propose a model of the motile cluster as an active polar fluid that explains this force-velocity relationship in terms of asymmetries in the distribution of active tractions. Our results challenge the notion of autonomous leader cells by showing that collective cell migration requires a global mechanical organization within the cluster.

cell biology↗

bioRxiv2024

Nucleocytoplasmic transport senses mechanics independently of cell density in cell monolayers.

Cells sense and respond to mechanical forces through mechanotransduction, which regulates processes in health and disease. In single cells, mechanotransduction involves the transmission of force to the cell nucleus, where it affects nucleocytoplasmic transport (NCT) and the subsequent nuclear localization of transcriptional regulators such as YAP. However, if and how NCT is mechanosensitive in multicellular systems is unclear. Here, we characterize and use a fluorescent sensor of nucleocytoplasmic transport (Sencyt) and demonstrate that nucleocytoplasmic transport responds to mechanics but not cell density in cell monolayers. Using monolayers of both epithelial and mesenchymal phenotype, we show that NCT is altered in response both to osmotic shocks, and to the inhibition of cell contractility. Further, NCT correlates with the degree of nuclear deformation measured through nuclear solidity, a shape parameter related to nuclear envelope tension. In contrast and in opposition to YAP, NCT is not affected by cell density, showing that the response of YAP to both mechanics and cell-cell contacts operates through distinct mechanisms. Our results demonstrate the generality of the mechanical regulation of NCT.

cell biology↗

bioRxiv2023

Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells

Colorectal cancer tumors are composed of heterogeneous and plastic cell populations, including a pool of cancer stem cells that express LGR5. Whether these distinct cell populations display different mechanical properties, and how these properties might contribute to metastasis is unknown. Using CRC patient derived organoids (PDOs), we found that compared to LGR5- cells, LGR5+ cancer stem cells are stiffer, adhere better to the extracellular matrix (ECM), move slower both as single cells and clusters, display higher nuclear YAP, show a higher survival rate in response to mechanical confinement, and form larger transendothelial gaps. These differences are largely explained by the downregulation of the membrane to cortex attachment proteins Ezrin/Radixin/Moesin (ERMs) in the LGR5+ cells. By analyzing scRNA-seq expression patterns from a patient cohort, we show that this downregulation is a robust signature of colorectal tumors. Our results show that LGR5- cells display a mechanically dynamic phenotype suitable for dissemination from the primary tumor whereas LGR5+ cells display a mechanically stable and resilient phenotype suitable for extravasation and metastatic growth.

cancer biology↗

bioRxiv2023

Aging and freezing of active nematic dynamics of cancer-associated fibroblasts by fibronectin matrix remodeling

Cancer-associated fibroblasts (CAFs) are one of the most abundant cell types in tumor stroma. Exhibiting an elongated morphology, CAFs align with each other, closely resembling nematic ordering in liquid crystal physics. CAFs play a pivotal role in the genesis and remodeling of the extracellular matrix (ECM), with ECM proteins, especially fibronectin, reciprocally modulating CAF alignment and coherence. Yet, the intricate feedback loops between fibronectin deposition and CAF structuring remain largely unexplored. Here, we combined CAF live imaging, traction force microscopy, ECM microfabrication, and theoretical modeling to assess how the ECM influences the dynamics of nematically ordered CAFs. We found that CAFs dynamically orchestrate a fibronectin network that mirrors their nematic ordering. Over time, this passive nematic ordering of fibronectin, in turn, steers CAF rearrangement. Contrary to most cellular systems, where defects remain dynamic at a steady state, the ECM/CAF interplay profoundly alters the behavior of both CAF and ECM nematics, leading to aging-massive slowdown, and even freezing of defect dynamics. This results in a CAFs capsule where aligned areas and defects are spatially and temporally fixed, yet active, exerting forces at the substate and transmitting forces between cells. Functionally, while defects may be permissive, it is the fibronectin loss-induced fluidization of the CAF capsule that critically undermines its barrier function.

cell biology↗

bioRxiv2023

Fibrillar adhesion dynamics govern the timescales of nuclear mechano-response via the vimentin cytoskeleton

The cell nucleus is continuously exposed to external signals, of both chemical and mechanical nature. To ensure proper cellular response, cells need to regulate not only the transmission of these signals, but also their timing and duration. Such timescale regulation is well described for fluctuating chemical signals, but if and how it applies to mechanical signals reaching the nucleus is still unknown. Here we demonstrate that the formation of fibrillar adhesions locks the nucleus in a mechanically deformed conformation, setting the mechanical response timescale to that of fibrillar adhesion remodelling ([~]1 hour). This process encompasses both mechanical deformation and associated mechanotransduction (such as via YAP), in response to both increased and decreased mechanical stimulation. The underlying mechanism is the anchoring of the vimentin cytoskeleton to fibrillar adhesions and the extracellular matrix through plectin 1f, which maintains nuclear deformation. Our results reveal a mechanism to regulate the timescale of mechanical adaptation, effectively setting a low pass filter to mechanotransduction.

biophysics↗

bioRxiv2023

Parametric modeling of mechanical effects on circadian oscillators

Circadian rhythms are archetypical examples of nonlinear oscillations. While these oscillations are usually attributed to circuits of biochemical interactions among clock genes and proteins, recent experimental studies reveal that they are also affected by the cells mechanical environment. Here we extend a standard biochemical model of circadian rhythmicity to include mechanical effects in a parametric manner. Using experimental observations to constrain the model, we suggest specific ways in which the mechanical signal might affect the clock. Additionally, a bifurcation analysis of the system predicts that these mechanical signals need to be within an optimal range for circadian oscillations to occur. Cells are nonlinear dynamical elements, which in multicellular tissues are commonly coupled to one another. Much work has been done, both theoretically and experimentally, to understand this coupling and to identify its dynamical consequences from a biochemical viewpoint. In contrast, much less is known about how the mechanical interactions between cells affect these dynamics. Recent work has shown, for instance, that circadian oscillations degrade substantially in populations of cells in vitro when cell density decreases sufficiently. Here we use this fact to constrain a standard model of circadian oscillations, and propose a way through which external mechanical signals and internal biochemical interactions could combine in clock cells.

systems biology↗

bioRxiv2022

Stiffness-dependent active wetting enables optimal collective cell durotaxis

The directed migration of cellular clusters enables morphogenesis, wound healing, and collective cancer invasion. Gradients of substrate stiffness are known to direct the migration of cellular clusters in a process called collective durotaxis, but underlying mechanisms remain unclear. Here, we unveil a connection between collective durotaxis and the wetting properties of cellular clusters. We show that clusters of cancer cells dewet soft substrates and wet stiff ones. At intermediate stiffness, at the crossover from low to high wettability, clusters on uniform-stiffness substrates become maximally motile, and clusters on stiffness gradients exhibit optimal durotaxis. Durotactic velocity increases with cluster size, stiffness gradient, and actomyosin activity. We demonstrate this behavior on substrates coated with the cell-cell adhesion protein E-cadherin and then establish its generality on substrates coated with extracellular matrix. We develop a physical model of three-dimensional active wetting that explains this mode of collective durotaxis in terms of a balance between in-plane active traction and tissue contractility, and out-of-plane surface tension. Finally, we show that the distribution of cluster displacements has a heavy tail, with infrequent but large cellular hops that contribute to durotactic migration. Our study demonstrates a physical mechanism of collective durotaxis, through both cell-cell and cell-substrate adhesion ligands, based on the wetting properties of active droplets.

biophysics↗