Biology subjects

Cohen, D. J.

Publications and source records attributed to Cohen, D. J..

At least 19 recordsLinked to original sources

bioRxiv2025

Optimal bioelectric control accelerates collective wound healing

Collective cell migration is critical in a range of biophysical processes spanning wound healing to tumor metastasis. It is therefore important to develop techniques for regulating cell motion, but while we have developed powerful migration tools from optogenetics and bioelectricity, the complex mechanics of collective systems make it difficult to determine where and when to apply these stimuli. For example, here we begin with a circular sheet of skin cells with a central hole, or "wound", and show that globally stimulating all cells to migrate radially inwards to close the gap through electrotaxis causes catastrophic mechanical damage, emerging from strong cell-cell adhesion, which we explain with an active elasticity model. We propose a solution inspired by sheepherding based on using local stimulation to learn the collective perturbation-response of the group and then drive tissue motion. First, we induce local electrotaxis to characterize the impulse-response function of quasi-1D strips of skin tissue, discovering that hyper-local stimulation triggers long-range tissue response over a length scale set by cell-cell adhesion also predicted by our model. Based on this, we apply local, concentric ring fields to in vitro circular wounds. Continuously driving cells towards the wound core kinetically traps the tissue in a jammed state and freezes healing. Pulsing the stimuli allows the tissue to relax and fluidize again, accelerating migration. Finally, we integrate the key length and timescales of tissue mechanics into a biophysically-informed continuum control model. The models predictive framework helps determine where and when to apply stimulation for optimal tissue growth which, when tested, accelerates healing 5-fold.

biophysics↗

bioRxiv2025

SCHEPHERD: A universal platform for high-throughput, high-resolution, and programmable control of cell behavior through bioelectric stimulation

Spanning frogs, fish, and humans, direct-current (DC) bioelectric cues play critical roles beyond neuro-muscular function, such as modulating morphogenesis, immune response, and healing through electrotaxis--electrically directed cell migration. Harnessing this potential requires new tools. However, standardized, accessible, and reproducible infrastructure capable of DC stimulation remains a challenge. We present SCHEPHERD: a universal, electrobioreactor integrating 8 stimulation channels and modular inserts to enable most electrotaxis assays in one device (cells, monolayers, and 3D spheroids), while enabling powerful, new capabilities. SCHEPHERD revealed through parameter sweeps that DC fields act like a steering wheel and gas pedal for cell migration. We then used live confocal imaging to observe electrically reprogrammed F-actin dynamics. Finally, our multi-polar inserts generated complex spatial electrical patterns that reorganize engineered tissue dynamics. By significantly improving accessibility through modularity and an open-source, graphically programmed stimulator, we hope SCHEPHERD can help broaden the community studying these important DC bioelectric phenomena.

bioengineering↗

bioRxiv2024

SCRATCH: A programmable, open-hardware, benchtop robot that automatically scratches cultured tissues to investigate cell migration, healing, and tissue sculpting.

Despite the widespread popularity of the scratch assay, where a pipette is dragged through cultured tissue to create an injury gap to study cell migration and healing, the manual nature of the assay carries significant drawbacks. So much of the process depends on individual manual technique, which can complicate quantification, reduce throughput, and limit the versatility and reproducibility of the approach. Here, we present a truly open-source, low-cost, accessible, and robotic scratching platform that addresses all of the core issues. Compatible with nearly all standard cell culture dishes and usable directly in a sterile culture hood, our robot makes highly reproducible scratches in a variety of complex cultured tissues with high throughput. Moreover, we demonstrate how scratching can be programmed to precisely remove areas of tissue to sculpt arbitrary tissue and wound shapes, as well as enable truly complex co-culture experiments. This system significantly improves the usefulness of the conventional scratch assay, and opens up new possibilities in complex tissue engineering and cell biological assays for realistic wound healing and migration research.

bioengineering↗

bioRxiv2024

Large-scale control over collective cell migration using light-controlled epidermal growth factor receptors

Receptor tyrosine kinases (RTKs) are thought to play key roles in coordinating cell movement at single-cell and tissue scales. The recent development of optogenetic tools for controlling RTKs and their downstream signaling pathways suggested these responses may be amenable to engineering-based control for sculpting tissue shape and function. Here, we report that a light-controlled EGF receptor (OptoEGFR) can be deployed in epithelial cell lines for precise, programmable control of long-range tissue movements. We show that in OptoEGFR-expressing tissues, light can drive millimeter-scale cell rearrangements to densify interior regions or produce rapid outgrowth at tissue edges. Light-controlled tissue movements are driven primarily by PI 3-kinase signaling, rather than diffusible signals, tissue contractility, or ERK kinase signaling as seen in other RTK-driven migration contexts. Our study suggests that synthetic, light-controlled RTKs could serve as a powerful platform for controlling cell positions and densities for diverse applications including wound healing and tissue morphogenesis.

bioengineering↗

bioRxiv2024

Cellular cruise control: energy expenditure as a regulator of collective migration in epithelia

Epithelial migration is implicit in processes ranging from gastrula development to the healing of skin, and involves the coordinated motion, force production, and resulting energy expenditure of thousands of constitutive cells. However, the spatiotemporal patterning and regulation of energy expenditure during epithelial migration remains poorly understood. Here, we propose a continuum mechan-ics framework and use it to explore how energy expenditure regulates epithelial migration. We use canonical mechanical metrics such as force, work and power to define what it means for a tissue to migrate efficiently and show that freely expanding epithelia actively regulate themselves to operate within a maximally efficient regime. We then leverage electrotaxis (directed motion in response to an externally applied electric field) as a tool to study non-homeostatic migra-tion using this new framework. We show that regulation of migration is robust to external cues and acts to to attenuate a tissues response to stimuli.

biophysics↗

bioRxiv2024

Spatial heterogeneity in collective electrotaxis: continuum modelling and applications to optimal control

Collective electrotaxis is a phenomenon that occurs when a cellular collective, for example an epithelial monolayer, is subjected to an electric field. Biologically, it is well known that the velocity of migration during the collective electrotaxis of large epithelia exhibits significant spatial heterogeneity. In this work, we demonstrate that the heterogeneity of velocities in the electrotaxing epithelium can be accounted for by a continuum model of cue competition in different tissue regions. Having established a working model of competing migratory cues in the migrating epithelium, we develop and validate a reaction-convection-diffusion model that describes the movement of an epithelial monolayer as it undergoes electrotaxis. We use the model to predict how tissue size and geometry affect the collective migration of MDCK monolayers, and to propose several ways in which electric fields can be designed such that they give rise to a desired spatial pattern of collective migration. We conclude with two examples that demonstrate practical applications of the method in designing bespoke stimulation protocols.

biophysics↗

bioRxiv2023

E-cadherin biointerfaces reprogram collective cell migration and cell cycling by forcing homeostatic conditions

Cells attach to the world around them in two ways--cell:extracellular-matrix adhesion and cell:cell adhesion--and conventional biomaterials are made to resemble the matrix to encourage integrin-based cell adhesion. However, interest is growing for cell-mimetic interfaces that mimic cell-cell interactions using cadherin proteins, as this offers a new way to program cell behavior and design synthetic implants and objects that can integrate directly into living tissues. Here, we explore how these cadherin-based materials affect collective cell behaviors, focusing specifically on collective migration and cell cycle regulation in cm-scale epithelia. We built culture substrates where half of the culture area was functionalized with matrix proteins and the contiguous half was functionalized with E-cadherin proteins, and we grew large epithelia across this Janus interface. Parts of the tissues in contact with the matrix side of the Janus interface exhibited normal collective dynamics, but an abrupt shift in behaviors happened immediately across the Janus boundary onto the E-cadherin side, where cells formed hybrid E-cadherin junctions with the substrate, migration effectively froze in place, and cell-cycling significantly decreased. E-cadherin materials suppressed long-range mechanical correlations in the tissue and mechanical information reflected off the substrate interface. These effects could not be explained by conventional density, shape index, or contact inhibition explanations. E-cadherin surfaces nearly doubled the length of the G0/G1 phase of the cell cycle, which we ultimately connected to the exclusion of matrix focal adhesions induced by the E-cadherin culture surface.

bioengineering↗

bioRxiv2022

Pump it up: bioelectric stimulation controls tissue hydrostatic pressure and water transport via electro-inflation

Epithelial tissues sheath many organs, separating outside from inside and exquisitely regulating ion and water transport electromechanically to maintain homeostatic balance and tissue hydrostatic pressure. While it is increasingly clear that the ionic microenvironment and external electric stimuli can affect epithelial function and behavior, the coupling between electrical perturbation and tissue form remain unclear. We investigated this by combining electrical stimulation with three-dimensional epithelial tissues with hollow lumens--both kidney cysts and complex intestinal stem cell organoids. Our core finding is that physiological strength electrical stimulation of order 1-3 V/cm (with both direct and alternating currents) can drive powerful and rapid inflation of hollow tissues through a process we call electro-inflation, inducing up to a threefold increase in tissue volume and striking asymmetries in tissue form. Electro-inflation is primarily driven by field-induced ion crowding on the outer surface of the hollow tissue that creates an ion gradient across the epithelial shell, which drives increased ionic flux mediated by ion channels/transporters and subsequent osmotic water flow into the lumen. This influx generates hydrostatic pressure, and inflation results from a competition between this pressure and cell cytoskeletal tension. We validated these interpretations with computational models connecting ion crowding around tissues to tissue mechanics. Electrically stimulated cysts and organoids also exhibited pronounced asymmetry, where the epithelial shell thickened on the cathode-facing side and thinned on the anode-facing side of the tissue. We discovered that this process is the result of 3D electrotaxis-directed migration of cells in an electric field-causing a redistribution of cells around the shell. The ability of electrical cues to dramatically regulate tissue size and shape highlight the key role of the electrical micro-environment and the potential offered by manipulating these signals.

bioengineering↗

bioRxiv2021

Short-term stimulation of collective cell migration in tissues reprograms long-term supracellular dynamics

The ability to program collective cell migration can allow us to control critical multicellular processes in development, regenerative medicine, and invasive disease. However, while various technologies exist to make individual cells migrate, translating these tools to control myriad, collectively interacting cells within a single tissue poses many challenges. For instance, do cells within the same tissue interpret a global migration command differently based on where they are in the tissue? Similarly, since no stimulus is permanent, what are the long-term effects of transient commands on collective cell dynamics? We investigate these questions by bioelectrically programming large epithelial tissues to globally migrate rightward via electrotaxis. Tissues clearly developed distinct rear, middle, side, and front responses to a single global migration stimulus. Furthermore, at no point post-stimulation did tissues return to their pre-stimulation behavior, instead equilibrating to a third, new migratory state. These unique dynamics suggested that programmed migration resets tissue mechanical state, which was confirmed by transient chemical disruption of cell-cell junctions, analysis of strain wave propagation patterns, and quantification of cellular crowd dynamics. Overall, this work demonstrates how externally driving the collective migration of a tissue can reprogram baseline cell-cell interactions and collective dynamics, even well beyond the end of the global migratory cue, and emphasizes the importance of considering the supracellular context of tissues and other collectives when attempting to program crowd behaviors.

biophysics↗

bioRxiv2021

Learning the rules of collective cell migration using deep attention networks

Collective, coordinated cellular motions underpin key processes in all multicellular organisms, yet it has been difficult to express the rules behind these motions in clear, interpretable forms. Here we apply deep attention networks to analyze several canonical living tissues systems and present the underlying collective migration rules for each tissue type using only cell migration trajectory data. We use these networks to learn the behaviors of key tissue types with distinct collective behaviors--epithelial, endothelial, and metastatic breast cancer cells--and show how the results complement traditional biophysical approaches. In particular, we present attention maps indicating the relative influence of neighboring cells to the learned turning decisions of a focal cell. These attention networks reveal distinct patterns of influence and attention unique to each model tissue. Endothelial cells exhibit tightly focused attention on their immediate forward-most neighbors, while cells in more expansile epithelial tissues are more broadly influenced by neighbors in a relatively large forward sector. Attention maps of ensembles of more mesenchymal, metastatic cells reveal completely symmetric attention patterns, indicating the lack of any particular coordination or direction of interest. Moreover, we show how attention networks are capable of detecting and learning how these rules changes based on biophysical context, such as location within the tissue and cellular crowding. That these results require only cellular trajectories and no modeling assumptions highlights the potential of attention networks for providing further biological insights into complex cellular systems. Author SummaryCollective behaviors are crucial to the function of multicellular life, with large-scale, coordinated cell migration enabling processes spanning organ formation to coordinated skin healing. However, we lack effective tools to discover and cleanly express collective rules at the level of an individual cell. Here, we employ a carefully structured neural network to extract collective information directly from cell trajectory data. The network is trained on data from various systems, including well-studied cell types (HUVEC and MDCK cells) which display visually distinct forms of collective motion, and metastatic cancer cells (MDA-MB-231) which are highly uncoordinated. Using these trained networks, we can produce attention maps for each system, which indicate how a cell within a tissue takes in information from its surrounding neighbors, as a function of weights assigned to those neighbors. Thus for a cell type in which cells tend to follow the path of the cell in front, the attention maps will display high weights for cells spatially forward of the focal cell. We present results in terms of additional metrics, such as accuracy plots and number of interacting cells, and encourage future development of improved metrics.

systems biology↗

bioRxiv2021

Self-assembly of tessellated tissue sheets by growth and collision

Tissues do not exist in isolation-they interact with other tissues within and across organs. While cell-cell interactions have been intensely investigated, less is known about tissue-tissue interactions. Here, we studied collisions between monolayer tissues with different geometries, cell densities, and cell types. First, we determine rules for tissue shape changes during binary collisions and describe complex cell migration at tri-tissue boundaries. Next, we demonstrate that genetically identical tissues displace each other based solely on cell density gradients, and present a physical model of tissue interactions that allows us to estimate the bulk modulus of the tissues from collision dynamics. Finally, we introduce TissEllate, a design tool for self-assembling complex tessellations from arrays of many tissues, and we use cell sheet engineering techniques to transfer these composite tissues like cellular films. Overall, our work provides insight into the mechanics of tissue collisions, harnessing them to engineer tissue composites as designable living materials.

bioengineering↗

bioRxiv2021

Tardigrades exhibit robust inter-limb coordination across walking speeds

Tardigrades must negotiate heterogeneous, fluctuating environments, and accordingly utilize locomotive strategies capable of dealing with variable terrain. We analyze the kinematics and inter-leg coordination of freely walking tardigrades (species: Hypsibius dujardini). We find that tardigrade walking replicates several key features of walking in insects despite disparities in size, skeleton, and habitat. To test the effect of environmental changes on tardigrade locomotor control circuits, we measure kinematics and inter-leg coordination during walking on two substrates of different stiffnesses. We find that the phase offset between contralateral leg pairs is flexible, while ipsilateral coordination is preserved across environmental conditions. This mirrors similar results in insects and crustaceans. We propose that these functional similarities in walking co-ordination between tardigrades and arthropods is either due to a generalized locomotor control circuit common to panarthropods, or to independent convergence onto an optimal strategy for robust multi-legged control in small animals with simple circuitry. Our results highlight the value of tardigrades as a comparative system towards understanding the mechanisms - neural and/or mechanical - underlying coordination in panarthropod locomotion.

animal behavior and cognition↗

bioRxiv2021

Cellular crowd control: overriding endogenous cell coordination makes cell migration more susceptible to external programming

As collective cell migration is essential in biological processes spanning development, healing, and cancer progression, methods to externally program cell migration are of great value. However, problems can arise if the external commands compete with strong, pre-existing collective behaviors in the tissue or system. We investigate this problem by applying a potent external migratory cue--electrical stimulation and electrotaxis--to primary mouse skin monolayers where we can tune cell-cell adhesion strength to modulate endogenous collectivity. Monolayers with high cell-cell adhesion showed strong natural coordination and resisted electrotactic control, with this conflict actively damaging the leading edge of the tissue. However, reducing pre-existing coordination in the tissue by specifically inhibiting E-cadherin-dependent cell-cell adhesion, either by disrupting the formation of cell-cell junctions with E-cadherin specific antibodies or rapidly dismantling E-cadherin junctions with calcium chelators, significantly improved controllability. Finally, we applied this paradigm of weakening existing coordination to improve control to demonstrate accelerated wound closure in vitro. These results are in keeping with those from diverse, non-cellular systems, and confirm that endogenous collectivity should be considered as a key, quantitative design variable when optimizing external control of collective migration.

bioengineering↗

bioRxiv2020

Come together: bioelectric healing-on-a-chip

There is a growing interest in bioelectric wound treatment and electrotaxis, the process by which cells detect an electric field and orient their migration along its direction, has emerged as a potential cornerstone of the endogenous wound healing response. Despite recognition of the importance of electrotaxis in wound healing, no experimental system to date demonstrates that the actual closing of a wound can be accelerated solely by the electrotaxis response itself, and in vivo systems are too complex to resolve cell migration from other healing stages such as proliferation and inflammation. This uncertainty has led to a lack of standardization between stimulation methods, model systems, and electrode technology required for device development. In this paper, we present a healing-on-chip approach that is a standardized, low-cost, model for investigating electrically accelerated wound healing. Our device provides the first convergent field geometry used in a stimulation device. We validate this device by using electrical stimulation to close a 1.5 mm gap between two large (30 mm2) primary skin keratinocyte layers to double the rate of healing over an unstimulated tissue. This proves that convergent electrotaxis is both possible and can accelerate healing, and offers a new healing-on-a-chip platform to explore future bioelectric interfaces.

bioengineering↗

bioRxiv2020

An Easy-to-Fabricate Cell Stretching System Reveals Density-Dependent Mechanical Regulation of Collective Cell Movements in Epithelial Homeostasis

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSIntroductionC_ST_ABSMechanical forces regulate many facets of cell and tissue biology. Studying the effects of forces on cells requires real-time observations of single- and multi-cell dynamics in tissue models during controlled external mechanical input. Many of the existing devices used to conduct these studies are costly and complicated to fabricate, which reduces the availability of these devices to many laboratories. MethodsWe show how to fabricate a simple, low-cost, uniaxial stretching device, with readily available materials and instruments that is compatible with high-resolution time-lapse microscopy of adherent cell monolayers. In addition, we show how to construct a pressure controller that induces a repeatable degree of stretch in monolayers, as well as a custom MATLAB code to quantify individual cell strains. ResultsAs an application note using this device, we show that uniaxial stretch slows down cellular movements in a mammalian epithelial monolayer in a cell density-dependent manner. We demonstrate that the effect on cell movement involves the relocalization of myosin downstream of Rho-associated protein kinase (ROCK). ConclusionsThis mechanical device provides a platform for broader involvement of engineers and biologists in this important area of cell and tissue biology. We used this device to demonstrate the mechanical regulation of collective cell movements in epithelia.

bioengineering↗

bioRxiv2020

Practical Fluorescence Reconstruction Microscopy for High-Content Imaging

Fluorescence reconstruction microscopy (FRM) describes a class of techniques where transmitted light images are passed into a convolutional neural network that then outputs predicted epifluorescence images. This approach enables many benefits including reduced phototoxicity, freeing up of fluorescence channels, simplified sample preparation, and the ability to re-process legacy data for new insights. However, FRM can be complex to implement, and current FRM benchmarks are abstractions that are difficult to relate to how valuable or trustworthy a reconstruction is. Here, we relate the conventional benchmarks and demonstrations to practical and familiar cell biology analyses to demonstrate that FRM should be judged in context. We further demonstrate that it performs remarkably well even with lower-magnification microscopy data, as are often collected in screening and high content imaging. Specifically, we present promising results for nuclei, cell-cell junctions, and fine feature reconstruction; provide data-driven experimental design guidelines; and provide researcher-friendly code, complete sample data, and a researcher manual to enable more widespread adoption of FRM.

cell biology↗

bioRxiv2020

Tissue size controls patterns of cell proliferationand migration in freely-expanding epithelia

The coordination of cell proliferation and migration in growing tissues is crucial in development and regeneration but remains poorly understood. Here, we find that, while expanding with an edge speed independent of initial conditions, millimeter-scale epithelial monolayers exhibit internal patterns of proliferation and migration that depend not on the current but on the initial tissue size, indicating memory effects. Specifically, the core of large tissues becomes very dense, almost quiescent, and ceases cell-cycle progression. In contrast, initially-smaller tissues develop a local minimum of cell density and a tissue-spanning vortex. To explain vortex formation, we propose an active polar fluid model with a feedback between cell polarization and tissue flow. Taken together, our findings suggest that expanding epithelia decouple their internal and edge regions, which enables robust expansion dynamics despite the presence of size- and history-dependent patterns in the tissue interior.

cell biology↗

bioRxiv2019

On-demand spatiotemporal programming of collective cell migration via bioelectric stimulation

Directed cell migration is critical across biological processes spanning healing to cancer invasion, yet no existing tools allow real-time interactive guidance over such migration. We present a new bioreactor that harnesses electrotaxis--directed cell migration along electric field gradients--by integrating four independent electrodes under computer control to dynamically program electric field patterns, and hence steer cell migration. Using this platform, we programmed and characterized multiple precise, two-dimensional collective migration maneuvers in renal epithelia and primary skin keratinocyte ensembles. First, we demonstrated on-demand, 90-degree collective turning. Next, we developed a universal electrical stimulation scheme capable of programming arbitrary 2D migration maneuvers such as precise angular turns and migration in a complete circle. Our stimulation scheme proves that cells effectively time-average electric field cues, helping to elucidate the transduction time scales in electrotaxis. Together, this work represents an enabling platform for controlling cell migration with broad utility across many cell types.

bioengineering↗