Biology subjects

Valon, L.

Publications and source records attributed to Valon, L..

12 recordsLinked to original sources

bioRxiv2026

EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation

Investigating single-cell dynamics and morphology in tissues and embryos requires highly accurate quantitative analysis of microscopy images. Despite significant advances in the field of bioimage analysis, even the most sophisticated segmentation and tracking algorithms inevitably produce errors (e.g. : over segmentation, missing objects, miss-connected objects). Although error rate may be small, their propagation throughout a time-lapse sequence has catastrophic effects on the accuracy of tracking and extraction of single cell parameters. Extracting single cell temporal information in the context of tissue/embryo requires thus expert curation to identify and correct segmentation errors. In the movies commonly used in developmental biology and stem cell research, both the number of imaged cells and the duration of recording are large, making this manual correction task extremely time-consuming. This has now become a major bottleneck in the fields of development, stem cell biology and bioimage analysis. We present here EpiCure (Epithelial Curation), a versatile tool designed to streamline and accelerate manual curation of segmentation and tracking in 2D movies of large epithelial tissues. EpiCure uses temporal information and morphometric parameters to automatically identify segmentation and tracking errors and provides user-friendly tools to correct them. It focuses on ergonomics and offers several visualization options to help navigating in movies of tissue covering a large number of cells, speeding up the detection of errors and their curation. EpiCure is highly interoperable and supports input from a wide range of segmentation tools. It also includes multiple export filters, enabling seamless integration with downstream analysis pipelines. In this paper, using movies from several animal models, we highlight the importance of curating cell segmentation and tracking for accurate downstream analysis, and demonstrate how EpiCure helps the curation process for extracting accurate single cell dynamics and cellular events detection, making it faster and amenable on large dataset.

developmental biology↗

bioRxiv2025

Control of cellular cortical tension and shape by RhoGTPase signalling

Shape changes are ubiquitous in biology, from cytokinesis at the single cell scale to tissue-scale morphogenesis involving coordinated changes in hundreds of cells. In all cases, morphogenesis is powered by gradients in mechanical tension that arise downstream of signalling. Many pathways converge on RhoGTPases that modulate the cytoskeleton and cell contractility to control cell mechanics and, subsequently, shape. Despite their physiological importance, we lack a quantitative understanding of how changes in signalling alter cortical mechanics to drive cell shape change. Here, we use optogenetics to quantitatively characterise the relationship between the amount of RhoGEF localised to the membrane, the downstream myosin recruitment, and the subsequent mechanical changes. We then show that cortical myosin amount and cortical tension increase linearly with the amount of membranous RhoGEF signalling. Based on these data, we develop a predictive model of the temporal evolution of RhoGEF membrane localisation, cortical myosin enrichment, and cortical tension in response to a pulse of light. Using this model together with an active surface model of the cell cortex, we show that the cellular shape changes induced by localised optogenetic recruitment of RhoGEF signalling can be predicted, directly linking gradients in signalling to shape change. Significance statementShape changes are ubiquitous in biology, during division in single cells and in tissue during embryogenesis. In all cases, shape change is powered by gradients in mechanical tension that arise downstream of changes in biochemical signals. Despite their importance, we lack a quantitative understanding of how changes in signals alter cell mechanics to drive cell shape change. Here, we control the location and amount of biochemical signal using light to quantitatively characterise the relationship between signals and their resulting biological and mechanical changes. We show that mechanical change scales linearly with the amount of biochemical signal. Based on this, we develop a mathematical model that predicts cell mechanical and shape changes from the location and amount of biochemical signals.

biophysics↗

bioRxiv2025

Integration of past caspase activity biases cell elimination in vivo

The fine tuning of apoptosis in epithelia is essential for regulating tissue size, shape, homeostasis and the maintenance of sealing properties. Regulation of cell death is mostly orchestrated by the activation of Caspases, proteases which were long thought to trigger an irreversible engagement in cell death. However, recent data in vivo and in vitro outline numerous non-apoptotic functions of caspases as well as quite ubiquitous sublethal activation of effector caspases during development. Yet, it remains unclear in many instances what drives the bifurcation between cell death engagement and cell survival upon caspase activation. The existence of a caspase activity threshold was generally considered to underpin this binary decision, but this was never assessed quantitatively in vivo especially at the single cell level. Using quantitative live imaging combined with machine learning and optogenetics in the Drosophila pupal notum (a single layer epithelium), we reveal for the first time the existence of a large heterogeneity of caspase sensitivity between cells, as well as the existence of distinct spatial domains with low or high sensitivity to caspases. Using correlative and perturbative experiments, we outline the central role of past exposure to sublethal caspase activity which sensitises cells for apoptosis for several hours. Integrating information about past caspase activation is sufficient to explain most of the global pattern of caspase sensitivity and predict at the single cell level which cells will engage in apoptosis. Finally, we demonstrate that past sublethal caspase activation in a subset of cells is sufficient to bias cell elimination at the clonal and single cell level, thus revealing an alternative mechanism of physiological cell competition. Altogether, this work reveals for the first time the existence of a new layer of apoptosis regulation in vivo downstream of effector caspases which can be developmentally regulated and bias clonal selection and the spatial pattern of cell death.

developmental biology↗

bioRxiv2025

Interfacial tension and growth both contribute to mechanical cell competition

Tissue plasticity and homeostasis rely on the mutual interplay between cell behaviour and mechanical inputs1. Yet, mechanical stress can also contribute to the evolution of some pathologies, notably by accelerating pretumoural cell expansion through the process of mechanical cell competition2-5. Mechanical cell competition is a conserved process in which one cell population is preferentially eliminated when mixed with another cell population due to its higher sensitivity to mechanical stress2,3,5-8. Most of the recent theoretical and experimental explorations of mechanical cell competition focused so far on the contribution of growth and pressure to cell elimination and were limited to few genetic contexts, including the activation of Ras in vivo2,8, and the mutation of the polarity gene scribble in mammalian cell culture3,4,9. However, it remains unclear whether other oncogenes can trigger similar mechanisms and whether growth is generally the only central regulator of cell compaction and cell elimination. Using the Drosophila pupal notum (a single layer epithelium), quantitative live imaging and vertex modelling, we revisited the mechanisms contributing to cell compaction and cell elimination during mechanical cell competition. Doing so, we outlined the co-existence of two modes of wild type (WT) cell compaction near oncogenic cells, namely the compaction driven by growth versus local compaction driven by increased tension at tumoural/WT cell interfaces in zones of high curvature (similar to "Laplace pressure"). We highlighted distinctive signatures in cell deformation and cell elimination distribution that can delineate these two modes of compaction, and we recapitulated them in silico and in vivo using genetic backgrounds affecting growth and/or interfacial tension independently. Altogether, this study reveals for the first time the contribution of interfacial tension-driven compaction to mechanical cell competition and outlines the co-existence of various modes of compaction during cell elimination and pretumoural clone expansion.

cell biology↗

bioRxiv2024

Adhesion-Controlled Mechanics of the Glial Niche Regulate Neural Stem Cell Proliferative Potential

Controlled proliferation of neural stem cells (NSCs) builds a functional nervous system during development. While their cellular niche is recognized as a signalling hub, the contribution of its structure and mechanics in regulating neurogenesis remains unexplored. The Drosophila larval central nervous system contains self-renewing NSCs in close contact with cortex glial cells. Transcriptomics identified a triad of immunoglobulin superfamily cell adhesion molecules (Dpr10/Dpr6 in glia and DIP- in NSCs) which physically and mechanically connect the NSC and glial membranes, acting as mechanoregulators. Their disruption increases glial cortical tension, causing non-autonomous mitotic defects in NSCs, characterized by abnormal spindle morphologies and impaired mitotic progression. Additionally, elevated glial tensile forces increase Lamin content in NSCs, a protective response also resulting in nuclear deformation. Ultimately NSC proliferative potential and genome integrity are compromised. Our study reveals that the native mechanical properties of the niche are transmitted to NSCs and regulate their function. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/628019v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@18137f8org.highwire.dtl.DTLVardef@819740org.highwire.dtl.DTLVardef@1f0ed0forg.highwire.dtl.DTLVardef@5ba0e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

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↗

bioRxiv2023

DeXtrusion: Automatic recognition of epithelial cell extrusion through machine learning in vivo

Epithelial cell death is highly prevalent during development and in adult tissues. It plays an essential role in the regulation of tissue size, shape, and turnover. Cell elimination relies on the concerted remodelling of cell junctions, so-called cell extrusion, which allows the seamless expulsion of dying cells. The dissection of the regulatory mechanism giving rise to a certain number and pattern of cell death was so far limited by our capacity to generate high-throughput quantitative data on cell death/extrusion number and distribution in various perturbed backgrounds. Indeed, quantitative studies of cell death rely so far on manual detection of cell extrusion events or through tedious systematic error-free segmentation and cell tracking. Recently, deep learning was used to automatically detect cell death and cell division in cell culture mostly using transmission light microscopy. However, so far, no method was developed for fluorescent images and confocal microscopy, which constitute most datasets in embryonic epithelia. Here, we devised DeXtrusion, a pipeline for automatic detection of cell extrusion/cell death events in larges movies of epithelia marked with cell contour and based on recurrent neural networks. The pipeline, initially trained on large movies of the Drosophila pupal notum marked with fluorescent E-cadherin, is easily trainable, provides fast and accurate extrusion/cell death predictions in a large range of imaging conditions, and can also detect other cellular events such as cell division or cell differentiation. It also performs well on other epithelial tissues with markers of cell junctions with reasonable retraining.

developmental biology↗

bioRxiv2022

Spindle reorientation in response to mechanical stress is an emergent property of the spindle positioning mechanisms

Proper orientation of the mitotic spindle plays a crucial role in embryos, during tissue development, and in adults, where it functions to dissipate mechanical stress to maintain tissue integrity and homeostasis. While mitotic spindles have been shown to reorient in response to external mechanical stresses, the subcellular cues that mediate spindle reorientation remain unclear. Here, we have used a combination of optogenetics and computational modelling to better understand how mitotic spindles respond to inhomogeneous tension within the actomyosin cortex. Strikingly, we find that the optogenetic activation of RhoA only influences spindle orientation when it is induced at both poles of the cell. Under these conditions, the sudden local increase in cortical tension induced by RhoA activation reduces pulling forces exerted by cortical regulators on astral microtubules. This leads to a perturbation of the torque balance exerted on the spindle, which causes it to rotate. Thus, spindle rotation in response to mechanical stress is an emergent phenomenon arising from the interaction between the spindle positioning machinery and the cell cortex.

cell biology↗

bioRxiv2021

DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.

BO_SCPLOWACKGROUNDC_SCPLOWQuantitative imaging of epithelial tissues prompts for bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common pre-processing step consists in projecting the acquired 3D volume on a 2D plane mapping the tissue surface. Indeed, while segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in Developmental and Cell Biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement. RO_SCPLOWESULTSC_SCPLOWHere we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes, and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a user-friendly and configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools. CO_SCPLOWONCLUSIONSC_SCPLOWWe find that LocalZProjector performs well even in situations where the volume to project also contains un-wanted signal in other layers. We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs.

bioinformatics↗

bioRxiv2020

Robustness of epithelial sealing is an emerging property of local ERK feedbacks driven by cell elimination

While the pathways regulating apoptosis and cell extrusion are rather well described1,2, what regulates the precise spatio-temporal distribution of cell elimination in tissues remains largely unknown. This is particularly relevant for epithelia with high rates of cell elimination, a widespread situation during embryogenesis3-6 and epithelial homeostasis7, where concomitant death of neighbours could impair the maintenance of epithelial sealing. However, the extent to which epithelial tissues can cope with concomitant cell death, and whether any mechanism regulates such occurrence have never been explored so far. Here, using the Drosophila pupal notum (a single layer epithelium) and a new optogenetic tool to trigger caspase activation and cell extrusion, we first show that concomitant death of clusters of at least three cells is sufficient to transiently impair epithelial sealing. Such clustered extrusion was almost never observed in vivo, suggesting the existence of a mechanism preventing concomitant elimination of neighbours. Statistical analysis and simulations of cell death distribution in the notum highlighted a transient and local protective phase occurring near every dying cell. This protection is driven by a transient activation of ERK in the direct neighbours of extruding cells which reverts caspase activation and prevents elimination of cells in clusters. Altogether, this study demonstrates that the distribution of cell elimination in epithelia is an emerging property of transient and local feedbacks through ERK activation which is required to maintain epithelial sealing in conditions of high rate of cell elimination.

developmental biology↗

bioRxiv2018

Competition for space induces cell elimination through compaction-driven ERK downregulation

The plasticity of developing tissues relies on the adjustment of cell survival and growth rate to environmental cues. This includes the effect of mechanical cues on cell survival. Accordingly, compaction of an epithelium can lead to cell extrusion and cell death. This process was proposed to contribute to tissue homeostasis but also to facilitate the expansion of pretumoral cells through the compaction and elimination of the neighbouring healthy cells. However we know very little about the pathways than can trigger apoptosis upon tissue deformation and the contribution of compaction driven death to clone expansion was never assessed in vivo. Using the Drosophila pupal notum and a new live sensor of ERK, we show that tissue compaction induces cell elimination through the downregulation of EGFR/ERK pathway and the upregulation of the pro-apoptotic protein Hid. Those results suggest that the sensitivity of EGFR/ERK pathway to mechanics could play a more general role in the fine tuning of cell elimination during morphogenesis and tissue homeostasis. Secondly, we assessed in vivo the contribution of compaction driven death to pretumoral cell expansion. We found that the activation of the oncogene Ras in clones can also downregulate ERK and activate apoptosis in the neighbouring cells through their compaction, which contributes to Ras clone expansion. The mechanical modulation of EGFR/ERK during growth-mediated competition for space may contribute to tumour progression.

developmental biology↗

bioRxiv2018

Stick-slip dynamics of cell adhesion triggers spontaneous symmetry breaking and directional migration

Directional cell motility during organism and tissue development, homeostasis and disease requires symmetry breaking. This process relies on the ability of single cells to establish a front-rear polarity, and can occur in absence of external cues. The initiation of migration has been attributed to the spontaneous polarization of cytoskeleton components, while the spatiotemporal evolution of cytoskeletal forces arising from continuous mechanical cell-substrate interaction has yet to be resolved. Here, we establish a one-dimensional microfabricated migration assay that mimics complex in vivo fibrillar environment while being compatible with high-resolution force measurements, quantitative microscopy, and optogenetics. Quantification of morphometric and mechanical parameters reveals a generic stick-slip behavior initiated by contractility-dependent stochastic detachment of adhesive contacts at one side of the cell, which is sufficient to drive directional cell motility in absence of pre-established cytoskeleton polarity or morphogen gradients. A theoretical model validates the crucial role of adhesion dynamics during spontaneous symmetry breaking, proposing that the examined phenomenon can emerge independently of a complex self-polarizing system.\n\nOne sentence summaryCells can autonomously break their symmetry through traction force oscillations (mechanical instabilities) that lead to stochastic detachment of adhesion patches on one side of the cell and the subsequent initiation of migration.

biophysics↗