Biology subjects

Copos, C.

Publications and source records attributed to Copos, C..

11 recordsLinked to original sources

bioRxiv2026

Model recapitulates regenerative limb blastema formation through local softening of the wounded epithelium

Studies of appendage regeneration in vertebrates have shown that the fundamental building block of any regenerative tissue is a blastema. The blastema is a cone-shaped accumulation that forms at the site of amputation post wound-healing and is the result of a highly coordinated process involving a cluster of cells capable of growth, migration, and differentiation. Although several key signaling pathways involved in regeneration have been identified, which cellular processes they control and how these processes are coordinated across space and time are not yet fully understood. This study introduces a computational tool to examine how the outgrowth results from the interaction of two tissue layers: the bulk (mesenchyme) and the overlying epithelium. We developed a novel hybrid agent-based modeling framework and an accompanying parameter inference pipeline to uncover the cellular properties in the epithelium and the mesenchyme driving the formation of a normal regenerative blastema with a morphology similar to that observed in experiments. Using our model, we report two conditions for blastema formation: retained local softening of the epithelial layer at the site of injury, which was confirmed experimentally with atomic force microscopy (AFM) measurements, and the involvement of the Wnt signaling pathway in the directed migration of mesenchyme cells towards the distal tip. Taken together, this combined experimental-theoretical approach provides a framework for understanding how the Wnt signaling pathway influences the formation of the early blastema at multiple levels of organization and how key cellular behaviors contribute to its formation. Author SummaryA small number of tetrapods have retained the ancestral ability to regenerate tissues and even limbs. Indifferent of species or tissue, the decisive initial stage of limb regeneration is the formation of a specialized structure called the blastema, a heterogeneous mass of mesenchymal cells, in a relatively short timescale of 2-14 days post injury or amputation. To study the mechanical and cellular conditions for limb blastema formation in the axolotl model organism, we developed a novel hybrid agent-based modeling framework and accompanying kinetic parameter inference pipeline. By recapitulating blastema morphometrics of healthy and stalled regenerative states, our model finds two conditions for blastema formation: retained local softening of the epithelial layer at the injury site post wound-healing, which we confirmed with atomic force microscopy measurements, and that the Wnt signaling pathway plays a role in the migration of mesenchyme cells to the distal tip in order to produce the blastema.

developmental biology↗

bioRxiv2025

Emergence of multiple collective motility modes in a physical model of cell chains

Collective cell migration underpins key (patho)physiological processes, ranging from embryonic development to wound healing and cancer metastasis. While notable progress has been made in elucidating mechanisms that drive collective cell motility, the classification remains incomplete. In this study, we focus on the migration patterns of small cell chains, specifically cohesive pairs of cells migrating after each other on flat surfaces. Experiments with Dictyostelium discoideum (Dd) cells, which typically display amoeboid motility, revealed two distinct motility modes in cell pairs: the individual contributor (IC) mode, where each cell generates its own traction force dipole, and the supracellular (S) mode, characterized by a single dipole. Intriguingly, the IC mode dominates in Dd pairs, but the S mode prevails in Madin-Darby canine kidney (MDCK) cell doublets, which typically undergo mesenchymal motility. This observation highlights an apparent discrepancy in emergent motility modes between cell types. To uncover the physical mechanisms driving these diverse motility modes, we developed a two-dimensional biophysical model incorporating mechanochemical details such as cell-cell adhesion, combined with membrane-cortex contractility, and cell-matrix adhesion. Our model could recapitulate many experimental observations; the IC mode emerged naturally in amoeboid doublets when both cells exerted similar traction stresses, while the S mode dominated with "stronger" leaders that essentially pull on trailers. In contrast, in our simulations, mesenchymal MDCK-like pairs largely migrated in supracellular arrangement (S mode), with traction stress patterns representative of a rear-drive system with a "pushy" trailer, rather than a front-drive system. Our findings also showed that increasing cell-matrix adhesion predisposes amoeboid cell chains to act autonomously (IC mode), but the chains motility mode was largely insensitive to changes in cell-cell adhesion parameters. Contrary to amoebas, MDCK-like cell chains showed a bias towards S mode when increasing cell-matrix adhesion and a preference on IC mode when increasing cell-cell adhesion. Extending the model to longer cell chains, we showcase the models applicability across scales, providing a foundation for exploring collective migratory behavior in other contexts.

biophysics↗

bioRxiv2024

Galvanotactic directionality of cell groups depends on group size

Motile cells migrate directionally in the electric field in a process known as galvanotaxis, important and under-investigated phenomenon in wound healing and development. We previously reported that individual fish keratocyte cells migrate to the cathode in electric fields, that inhibition of PI3 kinase reverses single cells to the anode, and that large cohesive groups of either unperturbed or PI3K-inhibited cells migrate to the cathode. Here we find that small uninhibited cell groups move to the cathode, while small groups of PI3K-inhibited cells move to the anode. Small groups move faster than large groups, and groups of unperturbed cells move faster than PI3K-inhibited cell groups of comparable sizes. Shapes and sizes of large groups change little when they start migrating, while size and shapes of small groups change significantly, lamellipodia disappear from the rear edges of these groups, and their shapes start to resemble giant single cells. Our results are consistent with the computational model, according to which cells inside and at the edge of the groups pool their propulsive forces to move but interpret directional signals differently. Namely, cells in the group interior are directed to the cathode independently of their chemical state. Meanwhile, the edge cells behave like individual cells: they are directed to the cathode/anode in uninhibited/PI3K-inhibited groups, respectively. As a result, all cells drive uninhibited groups to the cathode, while larger PI3K-inhibited groups are directed by cell majority in the group interior to the cathode, while majority of the edge cells in small groups win the tug-of-war driving these groups to the anode. Significance statementMotile cells migrate directionally in electric fields. This behavior - galvanotaxis - is important in many physiological phenomena. Individual fish keratocytes migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Uninhibited cell groups move to the cathode. Surprisingly, groups of PI3K-inhibited cells exhibit bidirectional behavior: larger/smaller groups move to the cathode/anode, respectively. A mechanical model suggests that inner and outer cells interpret directional signals differently, and that a tug-of-war between the outer and inner cells directs the cell groups. These results shed light on general principles of collective cell migration.

cell biology↗

bioRxiv2024

Model supports asymmetric regulation across the intercellular junction for collective cell polarization

Symmetry breaking, which is ubiquitous in biological cells, functionally enables directed cell movement and organized embryogenesis. Prior to movement, cells break symmetry to form a well-defined cell front and rear in a process called polarization. In developing and regenerating tissues, collective cell movement requires the coordination of the polarity of the migration machineries of neighboring cells. Though several works shed light on the molecular basis of polarity, fewer studies have focused on the regulation across the cell-cell junction required for collective polarization, thus limiting our ability to connect subcellular interactions to tissue-level dynamics. Here, we investigate how polarity signals are communicated from one cell to its neighbor to ensure coordinated front-to-rear symmetry breaking with the same orientation across the group. In a theoretical setting, we exhaustively search a variety of intercellular interactions and identify the conditions required for the Rho GTPase signaling module and/or cytoskeletal dynamics to achieve either co-alignment arrangement or supracellular arrangement of the polarity axes in a group of 2 and 4 cells. Our work shows that only asymmetric regulations are favorable - such interactions involve either up-regulation of the kinetic rate of complementary polarity components or opposite regulation of the kinetic rates of the same polarity components across the cell-cell junction. Surprisingly, our results hold if we further assume the presence of an external stimulus, intrinsic cellular variability, or larger group size. The results underline the potential of using quantitative models to probe the molecular interactions required for macroscopic biological phenomena. Lastly, we posit that asymmetric regulation is achieved through junction proteins and predict that in the absence of cytoplasmic tails of such linker proteins, the likeliness of doublet co-polarity is greatly diminished. Author summaryCells of the developing embryo undergo a highly complex chain of events that define their correct shape and positioning. Among these events, a crucial role belongs to coordinated cell movement of cells of different lineages over short and long distances to give rise to mature organs and organ systems. During collective movement, individual cells typically engage their autonomous polarity machinery, while being connected to their neighbors through adhesive cell-cell interactions. Despite advances in revealing the cell-cell interactions required for collective cell migration, a comprehensive picture of the molecular basis of intercellular communication for collective guidance is missing. To address this question, we devise a generalized mechanochemical model for cell polarity in a doublet and investigate how polarity signals are transmitted from one cell to another across seemingly symmetrical junctions. We have chosen to screen through all possible intercellular conditions of the Rho GTPase signaling circuit and/or cytoskeletal dynamics. Our systematic approach provides information on over 300 distinct conditions and reveals the intercellular regulation provided by junction proteins. In addition to predicting that only asymmetric interactions favor co-polarization, ensuring movement of the group in the same direction, our analysis also highlights the need for additional regulatory mechanisms for larger cell groups.

biophysics↗

bioRxiv2022

Bridging global actin network patterns to local molecular dynamics: a combined modeling and machine learning framework

Cells rely on their cytoskeleton for key processes including division and directed motility. Actin filaments are a primary constituent of the cytoskeleton. Although actin filaments can create a variety of network architectures linked to distinct cell functions, the microscale molecular interactions that give rise to these macroscale structures are not well understood. In this work, we investigate the microscale mechanisms that produce different branched actin network structures using an iterative classification approach. First, we employ a simple yet comprehensive agent-based model that produces synthetic actin networks with precise control over the microscale dynamics. Then we apply machine learning techniques to classify actin networks based on measurable network density and geometry, identifying key mechanistic processes that lead to particular branched actin network architectures. Extensive computational experiments reveal that the most accurate method uses a combination of supervised learning based on network density and unsupervised learning based on network symmetry. This framework can potentially serve as a powerful tool to discover the molecular interactions that produce the wide variety of actin network configurations associated with normal development as well as pathological conditions such as cancer.

biophysics↗

bioRxiv2022

Actin turnover required for adhesion-independent bleb migration

Cell migration is critical for many vital processes, such as wound healing, as well as harmful processes, like cancer metastasis. Experiments have highlighted the diversity in migration strategies employed by cells in physiologically relevant environments. In 3D fibrous matrices and confinement between two surfaces, some cells migrate using round membrane protrusions, called blebs. In bleb-based migration, the role of substrate adhesion is thought to be minimal, and it remains unclear if a cell can migrate without any adhesion complexes. We present a 2D computational fluid-structure model of a cell using cycles of bleb expansion and retraction in a channel with several geometries. The cell model consists of a plasma membrane, an underlying actin cortex, and viscous cytoplasm. Cellular structures are immersed in viscous fluid which permeates them, and the fluid equations are solved using the method of regularized Stokeslets. Simulations show that the cell cannot effectively migrate when the actin cortex is modeled as a purely elastic material. We find that cells do migrate in rigid channels if actin turnover is included with a viscoelastic description for the cortex. Our study highlights the non-trivial relationship between cell rheology and its external environment during migration with cytoplasmic streaming.

biophysics↗

bioRxiv2021

Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells

Physiological and pathological morphogenetic events involve a wide array of collective movements, suggesting that these multicellular arrangements confer biochemical and biomechanical properties that contribute to tissue scale organization. The cardiopharyngeal progenitors of the tunicate Ciona provide the simplest possible model of collective cell migration. They form cohesive bilateral cell pairs, leader-trailer polarized along the migration path as they migrate between the ventral epidermis and trunk endoderm. Here, circumventing difficulties in quantifying cellular mechanics in live embryos, we use the Cellular Potts Model to computationally probe the distributions of forces consistent with the shapes and collective polarity of migrating cell pairs. Combining computational modeling, confocal microscopy, and molecular perturbations, we first determine that cardiopharyngeal progenitors display hallmarks of supracellular organization, with differential distributions of protrusive forces, cell-matrix adhesion, and myosin-based retraction forces along the leader-trailer axis. Combined 4D simulations and experimental observations suggest that cell-cell communication helps establish a hierarchy that contributes to aligning collective polarity with the direction of migration, as observed with three or more cells both in silico and in vivo. Our approach reveals emerging properties of the migrating collective. Specifically, cell pairs are more persistent, thus migrating over longer distances, and presumably with higher accuracy. Finally, simulations suggest that polarized cell pairs literally join forces to deform the trunk endoderm, as they migrate through the extracellular space. We thus propose that the polarized supracellular organization of cardiopharyngeal progenitors confers emergent physical properties that determine mechanical interactions with their environment during morphogenesis.

developmental biology↗

bioRxiv2020

PI3K inhibition reverses migratory direction of single cells but not cell groups in electric field

Motile cells migrate directionally in the electric field in a process known as galvanotaxis. Galvanotaxis is important in wound healing, development, cell division, and nerve growth. Different cell types migrate in opposite directions in electric fields, to either cathode, or anode, and the same cell can switch the directionality depending on chemical conditions. We previously reported that individual fish keratocyte cells sense electric fields and migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Many physiological processes rely on collective, not individual, cell migration, so here we report on directional migration of cohesive cell groups in electric fields. Uninhibited cell groups of any size move to the cathode, with speed decreasing and directionality increasing with the group size. Surprisingly, large groups of PI3K-inhibited cells move to the cathode, in the direction opposite to that of individual cells, which move to the anode, while such small groups are not persistently directional. In the large groups, cells velocities are distributed unevenly: the fastest cells are at the front of the uninhibited groups, but at the middle and rear of the PI3K-inhibited groups. Our results are most consistent with the hypothesis, supported by the computational model, that cells inside and at the edge of the groups interpret directional signals differently. Namely, cells in the group interior are directed to the cathode independently of their chemical state. Meanwhile, edge cells behave like the individual cells: they are directed to the cathode/anode in uninhibited/PI3K-inhibited groups, respectively. As a result, all cells drive uninhibited groups to the cathode, but a mechanical tug-of-war between the inner and edge cells directs large PI3K-inhibited groups with cell majority in the interior to the cathode, while rendering small groups non-directional. Significance statementMotile cells migrate directionally in electric fields. This behavior - galvanotaxis - is important in many physiological phenomena. Individual fish keratocytes migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Uninhibited cell groups move to the cathode. Surprisingly, large groups of PI3K-inhibited cells also move to the cathode, in the direction opposite to that of individual cells. The fastest cells are at the front of the uninhibited groups, but at the middle and rear of the PI3K-inhibited groups. We posit that inner and edge cells interpret directional signals differently, and that a tug-of-war between the edge and inner cells directs the cell groups. These results shed light on general principles of collective cell migration.

biophysics↗

bioRxiv2020

Stress fibers are embedded in a contractile cortical network.

Contractile actomyosin networks generate intracellular forces essential for the regulation of cell shape, migration, and cell-fate decisions, ultimately leading to the remodeling and patterning of tissues. Although actin filaments aligned in bundles represent the main source of traction-force production in adherent cells, there is increasing evidence that these bundles form interconnected and interconvertible structures with the rest of the intracellular actin network. In this study, we explored how these bundles are connected to the surrounding cortical network and the mechanical impact of these interconnected structures on the production and distribution of traction forces on the extracellular matrix and throughout the cell. By using a combination of hydrogel micropatterning, traction-force microscopy and laser photoablation, we measured the relaxation of the cellular traction field in response to local photoablations at various positions within the cell. Our experimental results and modeling of the mechanical response of the network revealed that bundles were fully embedded along their entire length in a continuous and contractile network of cortical filaments. Moreover, the propagation of the contraction of these bundles throughout the entire cell was dependent on this embedding. In addition, these bundles appeared to originate from the alignment and coalescence of thin and unattached cortical actin filaments from the surrounding mesh.

cell biology↗

bioRxiv2020

Connecting actin polymer dynamics across multiple scales

Actin is an intracellular protein that constitutes a primary component of the cellular cytoskeleton and is accordingly crucial for various cell functions. Actin assembles into semi-flexible filaments that cross-link to form higher order structures within the cytoskeleton. In turn, the actin cytoskeketon regulates cell shape, and participates in cell migration and division. A variety of theoretical models have been proposed to investigate actin dynamics across distinct scales, from the stochastic nature of protein and molecular motor dynamics to the deterministic macroscopic behavior of the cytoskeleton. Yet, the relationship between molecular-level actin processes and cellular-level actin network behavior remains understudied, where prior models do not holistically bridge the two scales together. In this work, we focus on the dynamics of the formation of a branched actin structure as observed at the leading edge of motile eukaryotic cells. We construct a minimal agent-based model for the microscale branching actin dynamics, and a deterministic partial differential equation model for the macroscopic network growth and bulk diffusion. The microscale model is stochastic, as its dynamics are based on molecular level effects. The effective diffusion constant and reaction rates of the deterministic model are calculated from averaged simulations of the microscale model, using the mean displacement of the network front and characteristics of the actin network density. With this method, we design concrete metrics that connect phenomenological parameters in the reaction-diffusion system to the biochemical molecular rates typically measured experimentally. A parameter sensitivity analysis in the stochastic agent-based model shows that the effective diffusion and growth constants vary with branching parameters in a complementary way to ensure that the outward speed of the network remains fixed. These results suggest that perturbations to microscale rates can have significant consequences at the macroscopic level, and these should be taken into account when proposing continuum models of actin network dynamics.

biophysics↗

bioRxiv2019

A hybrid stochastic-deterministic mechanochemical model of cell polarization

Polarization is a crucial component in cell differentiation, development, and motility and its details are not yet well understood. At the onset of cell locomotion, cells break symmetry to form a well-defined cell front and rear. This polarity establishment varies across cell types: in Dictyostelium discoideum cells, it is mediated by biochemical signaling pathways and can function in the absence of a cytoskeleton, while in keratocytes it is tightly connected to cytoskeletal dynamics and mechanics. Theoretical models that have been developed to understand the onset of polarization have explored either signaling or mechanical pathways, yet few have explored mechanochemical mechanisms. However, many motile cells rely on both signaling modules and actin cytoskeleton to break symmetry and achieve a stable polarized state. We propose a general mechanochemical polarization model based on the coupling between a stochastic model for the segregation of signaling molecules and a simplified mechanical model for actin cytoskeleton network competition. We find that local linear coupling between minimally nonlinear signaling and cytoskeletal systems, separately not supporting stable polarization, yields a robustly polarized cell state.

biophysics↗