Biology subjects

Salbreux, G.

Publications and source records attributed to Salbreux, G..

At least 19 recordsLinked to original sources

bioRxiv2026

A moving front of osteoblast maturation scales regenerating zebrafish bone

Successful regeneration recovers lost tissues to their original form. Here, we investigate how proliferation of bone-forming osteoblasts is timely regulated to control tissue size during zebrafish scale regeneration. Regeneration of the scale osteoblast tissue proceeds in two phases: an initial osteoblast proliferative expansion followed by hypertrophic growth without cell division. First, we show that regeneration recovers scale size by amplifying the number of osteoblasts by a fixed factor, starting from a properly scaled tissue primordium. This fixed expansion is achieved by regulating proliferation such that osteoblast number increases roughly linearly, with the rate of increase scaling with initial osteoblast number, and halting cell proliferation at a given time. To understand the mechanisms underlying this proliferation control, we used live imaging of transgenic reporters and biosensors together with transcriptomics. We uncover that proliferation arrest is imparted by a moving front of osteoblast maturation travelling outward across the scale, with dynamics that scales with tissue size. The osteoblast maturation front coincides with onset of hypertrophy and bone deposition, and it is accompanied by reduction in expression of the fibroblast growth factor receptor 3 (fgfr3) and activity of the kinases Erk (Extracellular signal-Regulated Kinase) and p38. Inhibition of Fgf/Erk signaling and osteoblast proliferation does not alter the progression of the maturation front. We show that the scaling maturation front can quantitatively explain the osteoblast proliferation dynamics and its scaling across different tissue sizes. Overall, we identify a moving front of cell maturation as a mechanism for controlling cell proliferation across a regenerating tissue.

developmental biology↗

bioRxiv2026

Shared neurogenesis onset is sufficient to explain bilateral matching in the vertebrate retina

Bilateral symmetry is a hallmark of many paired organs and often essential for optimal functionality. The vertebrate eyes are a prominent example of this, as the matched development of the two retinas is required for accurate visual processing. While macroscopic aspects of symmetry emergence across systems have been investigated, how bilateral matching is maintained once cells start to differentiate remains less understood. Here we address this question using the zebrafish retina as a model to follow neurogenic programs in vivo at single-cell resolution. We perform quantitative 3D live imaging of both retinas simultaneously and directly compare neurogenesis onset and propagation within and across embryos. We find that neurogenic waves initiate at the retinal poles and progress towards the mid-retina in a conserved spatiotemporal pattern. Within embryos, the two eyes exhibit highly similar neurogenesis dynamics when it comes to timing of neurogenesis onset, cell number increase, and spatial wave progression. Across embryos, however, variability is larger. While these observations hint at active inter-retinal coordination, a stochastic model predicts that a shared onset of neurogenesis can be sufficient to explain bilateral matching. Targeted genetic perturbation experiments support this prediction. We find that altering wave propagation affects patterning but not bilateral similarity. Disrupting neurogenesis onset timing, however, reduces bilateral symmetry between eyes. Thus, the combination of experiment and theory identifies synchronized neurogenesis onset as a key determinant of bilateral symmetry, revealing a minimal principle for how reproducible development of paired organs can emerge from stochastic processes.

developmental biology↗

bioRxiv2026

Analysis of 3D epithelial tissue packing reveals correlated patterns of cell height and skewing

Epithelia are tissues which envelop organs, exchange with and protect from their environment. The tight packing of cells within an epithelium guarantees its cohesiveness and impermeability, essential to its functions. Yet, how cells spatially arrange in three dimensions within an epithelium, and how the three-dimensional cell packing responds to geometrical constraints, is not fully understood. In a proliferating epithelium, cellular volumes vary from cell to cell, notably due to cell growth. At the same time, epithelia tend to display a smooth, continuous apical surface, indicating that cell shape determinants are spatially coupled. It is unclear how these and other factors modulate cell shape variability within the epithelium. Here, we segmented three-dimensional cell shapes of MDCK epithelia, grown in hollow spheres of alginate. With this assay, we could modulate the substrate adhesive properties, tissue curvature, and cell area density. We observed that as the tissue proliferates and cell density increases, average cell volume decreases. In contrast, cell height is relatively conserved over time, with an average value sensitive to the rigidity, curvature and adhesive strength of the substrate. We identified large and spatially correlated fluctuations in cell skewing, defined as the relative difference between apical and basal area that do not arise from curvature. Skewing is associated to spatial patterns of tilted cells whose apico-basal axis deviates from orthogonality to the substrate. Surprisingly, cell skewing and cell height are correlated, indicating internal rules for three-dimensional cell shapes. Altogether, our study identifies unexpected patterns of three-dimensional cell shape variation within a proliferative epithelium.

biophysics↗

bioRxiv2026

Multiscale curvature modulates epithelial architecture and nuclear organization.

Curved geometries are a defining feature of epithelial tissues, yet how cells integrate curvature cues across spatial scales remains unclear. Here, we combined wavy hydrogels with inducible self-rolling substrates to readily and independently impose local and large-scale curvatures on epithelial monolayers, recapitulating key geometric features of bronchiolar epithelia. By controlling the orientation of local curvature relative to the large-scale curvature set by the tube axis, we show that multiscale curvature induces scale-dependent and anisotropic remodeling of cell shape, nuclear organization, and tissue thickness. In contrast, nuclei maintain a robust and conserved three-dimensional geometry, with curvature primarily regulating nuclear orientation rather than shape. This hierarchical induction of specific changes to the tissue architecture shows that multiscale curvature sensing is a fundamental physical principle governing epithelial architecture.

biophysics↗

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

Cross-Species Biomechanical Determinants of Shape Diversity

How complex molecular mechanisms translate into diverse multicellular shapes remains unclear. By leveraging the bi-layered architecture of six cnidarian species that diverged 500 million years ago, we show that modularity in supracellular mechanics governs larval shape diversity. Using active surface theory, quantitative imaging, and an inducible genetic system, we identify species-specific variations in three biomechanical modules. Basally aligned stress fibers drive axial elongation, while oral geometry and aboral rigidity define shape polarity. Remarkably, manipulating these modules transforms one species shape into another, demonstrating the causal relationship between module variation and shape diversity. Our analysis also uncovers instances of mechanical redundancies, where distinct module combinations generate similar shapes. These findings provide a general framework for how molecular complexity funnels into mesoscale mechanical determinants shaping morphological diversity.

developmental biology↗

bioRxiv2025

Insect wings arose with a genetic circuit that extends the useful range of a BMP morphogen

Morphogens are produced by a subset of cells to trigger a signalling gradient that provides positional information to surrounding tissues. At increasing distances from the source, the dwindling number of morphogen molecules is expected to constrain the useful range of morphogen gradients. We have identified a genetic circuit that counteracts this limitation in developing wings of Drosophila by boosting BMP signalling at the distal end of the gradient without amplifying the signal near the source. This circuit involves Brinker, a transcription factor that represses BMP target genes while itself being repressed by BMP signalling. We suggest that temporal averaging inherent to the production of the inverse Brk gradient contributes to the enhancement of the positional information far from the Dpp source. Despite being a core component of BMP signalling in flies, Brinker is exclusively found in insects, likely in all insect species. Genomic analysis across a wide range of insects and gene expression analysis in limb primordia of the apterygote Thermobia domestica suggests that Brinker is an insect-specific innovation that was subsequently wired into the BMP signalling network in pterygotes, perhaps to enable wing development.

developmental biology↗

bioRxiv2024

Cell shape noise strength regulates shape dynamics during EMT-associated cell spreading

Cellular shape is intimately linked to cell function and state, and transitions between cell states are tightly coupled to shape changes. Yet, shape has been largely overlooked in state transitions studies. Here, we combine morphometric analysis with theoretical modeling and molecular perturbations to interrogate cell shape dynamics during epithelial-to-mesenchymal transition (EMT). Using stochastic inference, we extract the morphogenetic landscape underlying EMT. We show that within this landscape, EMT-associated cell spreading reflects a transition between shape attractors. Strikingly, we observe a peak in cell shape noise strength concomitant with spreading, and show that higher shape noise accelerates transitions between shape attractors. Our morphometric analysis framework will be widely applicable to quantitative cell shape investigations in physiology and disease. Together, our results identify a key role for cellular stochasticity as a regulator of shape change rate, and highlight that shape dynamics yield rich phenotypic information that enhances our understanding of cellular states.

biophysics↗

bioRxiv2024

Growth compensation upon changes in tissue size in the Drosophila abdomen

Attaining the appropriate size during development is essential for the function of animal tissues and organs. Robust tissue size control implies the existence of compensatory mechanisms that allow developing systems to recover from growth perturbations. However, the difficulty of directly observing normal or compensatory developmental growth means we have little understanding of the cellular behaviours that confer robustness to tissue size control. Here, we study how growth perturbations affect proliferation kinetics and the timing of growth termination of Drosophila histoblasts, the progenitors that give rise to the adult abdominal epidermis. Histoblasts undergo extensive growth and proliferation during the pupal stage, which is accessible for long-term live-imaging and precise quantitative analysis. By manipulating cell number or volume prior to the pupal growth phase, we changed the starting size of the abdomen primordium, then observed how the histoblasts adapted to these changes by altering their growth dynamics. We show that, upon a decrease in starting tissue size, the histoblasts compensate by extending their temporal proliferative window, undergoing additional cell cycles, as well as increasing their apical area to maximise coverage of the abdominal surface. When initial tissue size is increased, the histoblasts undergo fewer division cycles and arrest proliferation earlier than normal. Thus, the proliferative window of this tissue is flexible enough to buffer for changes in tissue size. Our data also suggest that the histoblasts sense both spatial and temporal cues to arrest their growth at the appropriate time and ensure accurate tissue size control.

developmental biology↗

bioRxiv2024

Interplay of actin nematodynamics and anisotropic tension controls endothelial mechanics

Blood vessels expand and contract actively, while continuously experiencing dynamic external stresses from the blood flow. The mechanical response of the vessel wall is that of a composite material: its mechanical properties depend on a diverse set of cellular mechanical components, which change dynamically as cells respond to external stress. Mapping the relationship between these underlying cellular processes and emergent tissue mechanics is an on-going challenge, in particular in endothelial cells. Here we use a microstretcher mimicking the native environment of blood vessels to assess both the mechanics and cellular dynamics of an endothelial tube in response to a physiological increase in luminal pressure. The characterization of the instantaneous monolayer elasticity reveals a strain-stiffening, actin-dependent and substrate-responsive behavior. In response to a maintained pressure increase, the tissue displays a fluid-like expansion, accompanied by the reorientation of cell shape and of actin fibers. This actin-driven reorientation depends on focal adhesions and adherens junctions, two key mechanosensors. We introduce a mechanical model coupling actin fiber nematodynamics with active and elastic tension generation by actin fibers in the endothelium, which recapitulates the response to pressure of endothelial tubes.

biophysics↗

bioRxiv2023

Signalling-dependent refinement of cell fate choice during tissue remodelling

How biological form emerges from cell fate decisions and tissue remodelling is a fundamental question in development biology. However, an understanding of how these processes operate side-by-side to set precise and robust patterns is largely missing. Here, we investigate this interplay during the process of vein refinement in the Drosophila pupal wing. By following reporters of signalling activity dynamically, together with tissue flows, we show that longitudinal vein refinement arises from a combination of local tissue deformation and cell fate adjustments controlled by a signalling network involving Notch, Dpp, and EGFR. Perturbing large-scale convergence and extension tissue flows does not affect vein refinement, showing that pre-patterned vein domains are able to intrinsically refine to the correct width. A minimal biophysical description taking into account key signalling interactions recapitulates the intrinsic tissue ability to establish a thin, regular vein independently of large-scale tissue flows. Supporting this prediction, artificial proveins optogenetically generated orthogonal to the axis of wing elongation refine against large-scale flows. Overall, we find that signalling-mediated updating of cell fate is a key contributor to reproducible patterning.

developmental biology↗

bioRxiv2023

Active mesh and neural network pipeline for cell aggregate segmentation

Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology, due to improvements in capacity and accuracy of microscopy techniques. Here we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary duct organoids imaged over 24 hours with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin which implement active meshes deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction. Statement of significanceIn vitro culture of organ-like structures derived from stem cells, so-called organoids, allows to image tissue morphogenetic processes with high temporal and spatial resolution. Three-dimensional segmentation of cell shape in timelapse movies of these developing organoids is however a significant challenge. In this work, we propose an image analysis pipeline for cell aggregates that combines deep learning with active contour segmentations. This combination offers a flexible and efficient way to segment three-dimensional cell images, which we illustrate with by segmenting datasets of growing mammary gland organoids and mouse embryonic stem cells.

bioinformatics↗

bioRxiv2023

The ecdysone receptor promotes or suppresses proliferation according toligand level

Steroid hormones control various cellular activities in a context-dependent manner. For example, ecdysone, which acts through a type II nuclear receptor, has seemingly opposite effects in Drosophila wing precursors, promoting proliferation during larval stages, and triggering proliferation arrest at pupariation. We find that wing precursors proliferate normally in the complete absence of the ecdysone receptor (EcR), whether ecdysone is present or not, suggesting that ecdysone overrides a default antiproliferative activity of the receptor. By contrast, termination of proliferation by high concentration of 20E at the end of larval life involves conventional gene regulation by the ligand-receptor complex. The switch from one mode of regulation to the other is determined by ligand level, as measured with a calibrated EcR transcriptional reporter and ex vivo proliferation assays. Accordingly, RNA Seq analysis uncovers distinct transcriptional responses to different doses of ecdysone. Some genes are only activated at high doses (high threshold targets) and likely to comprise genes that stop proliferation at pupariation, when ecdysone titres are high. We find that other target genes respond to all physiological concentrations of ecdysone. Some of these genes are known to promote proliferation and could therefore contribute to the pro-proliferation activity of low-level ecdysone. Finally, we show mathematically and with synthetic reporters that relatively simple combinations of regulatory elements can recapitulate the behaviour of both types of target genes.

developmental biology↗

bioRxiv2022

Polarity-driven three-dimensional spontaneous rotation of a cell doublet

Cell mechanical interactions play a fundamental role in the self-organisation of organisms. How these interactions drive coordinated cell movement in three-dimensions remains unclear. Here we report that cell doublets embedded in a 3D extracellular matrix undergo spontaneous rotations and we investigate the rotation mechanism using live cell imaging, quantitative measurements, mechanical perturbations, and theory. We find that rotation is driven by a polarized distribution of myosin within cell cortices. The mismatched orientation of this polarized distribution breaks the doublet mirror symmetry. In addition, cells adhere at their interface through adherens junctions and with the extracellular matrix through focal contacts near myosin clusters. Using a physical theory describing the doublet as two interacting active surfaces, we find that rotation is driven by myosin-generated gradients of active tension, whose profiles are dictated by interacting cell polarity axes. We show that interface three-dimensional shapes can be understood from the Curie principle: shapes symmetries are related to broken symmetries of myosin distribution in cortices. To test for the rotation mechanism, we suppress myosin clusters using laser ablation and we generate new myosin clusters by optogenetics. Our work clarifies how polarity-oriented active mechanical forces drive collective cell motion in three dimensions.

biophysics↗

bioRxiv2022

Interacting active surfaces: a model for three-dimensional cell aggregates

We introduce a modelling and simulation framework for cell aggregates in three dimensions based on interacting active surfaces. Cell mechanics is captured by a physical description of the acto-myosin cortex that includes cortical flows, viscous forces, active tensions, and bending moments. Cells interact with each other via short-range forces capturing the effect of adhesion molecules. We discretise the model constitutive equations using a finite element method, and provide a parallel implementation in C++. We discuss examples of application of this framework to simulations involving small and medium-sized aggregates: we consider the shape and dynamics of a cell doublet, a planar cell sheet, and a growing cell aggregate. This framework opens the door to the systematic exploration of the cell to tissue-scale mechanics of cell aggregates, which plays a key role in the morphogenesis of embryos and organoids. Author summaryUnderstanding how tissue-scale morphogenesis arises from cell mechanics and cell-cell interactions is a fundamental question in developmental biology. Here we propose a mathematical and numerical framework to address this question. In this framework, each cell is described as an active surface representing the cell acto-myosin cortex, subjected to flows and shape changes according to active tensions, and to interaction with neighbouring cells in the tissue. Our method describes cellular processes such as cortical flows, cell adhesion, and cell shape changes in a deforming three-dimensional cellular aggregate. To solve the equations numerically, we employ a finite element discretisation, which allows us to solve for flows and cell shape changes with arbitrary resolution. We discuss applications of our framework to describe cell-cell adhesion in doublets, three-dimensional cell shape in a simple epithelium, and three-dimensional growth of a cell aggregate.

biophysics↗

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↗

bioRxiv2020

ECM remodeling and spatial cell cycle coordination determine tissue growth kinetics

During development, multicellular organisms undergo stereotypical patterns of tissue growth to yield organs of highly reproducible sizes and shapes. How this process is orchestrated remains unclear. Analysis of the temporal dynamics of tissue growth in the Drosophila abdomen reveals that cell cycle times are spatially correlated and that growth termination occurs through the rapid emergence of a population of arrested cells rather than a gradual slowing down of cell cycle time. Reduction in apical tension associated with tissue crowding has been proposed as a developmental growth termination mechanism. Surprisingly, we find that growth arrest in the abdomen occurs while apical tension increases, showing that in this tissue a reduction in tension does not underlie the mechanism of growth arrest. However, remodeling of the extracellular matrix is necessary for tissue expansion. Thus, changes in the tissue microenvironment, and a rapid exit from proliferation, control the formation of the adult Drosophila abdomen.

developmental biology↗

bioRxiv2020

Dual-view oblique plane microscopy (dOPM)

We present a new folded dual-view oblique plane microscopy (OPM) technique termed dOPM that enables two orthogonal views of the sample to be obtained by translating a pair of tilted mirrors in refocussing space. Using a water immersion 40x 1.15 NA primary objective, deconvolved image volumes of 200 nm beads were measured to have full width at half maxima (FWHM) of 0.35{+/-}0.04 m and 0.39{+/-}0.02 m laterally and 0.81{+/-}0.07 m axially. The laterally integrated z-sectioning value was 1.33{+/-}0.45 m using light-sheet FWHM in the frames of the two views of 4.99{+/-}0.58 m and 4.89{+/-}0.63 m. To qualitatively demonstrate that the system can reduce shadow artefacts while providing a more isotropic resolution, a multi-cellular spheroid approximately 100 m in diameter was imaged.

bioengineering↗