Biology subjects

Michaut, A.

Publications and source records attributed to Michaut, A..

9 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

Sparse mesenchymal cell networks as a fluid under tension

Sparse mesenchymal cellular networks are ubiquitous across animals, shaping both embryonic and adult structures through dynamic interactions with epithelia. Yet, the physical principles underlying their collective behaviors remain elusive, as their stellate cells and large extracellular spaces--filled with matrix or interstitial fluid--pose significant experimental and computational challenges. Here, we demonstrate that the avian presomitic mesoderm (PSM), a canonical embryonic mesenchymal tissue, behaves as a fluid under tension, exhibiting structural organization that cannot be explained by simple Brownian-like cell motion. Through quantitative modeling, we identify contact inhibition of locomotion (CIL)--where cells actively retract and move away upon contact--as a key mechanism that enables sparse mesenchymal networks to sustain macroscopic tension while flowing like a fluid. Simple continuum equations relate observable cell-scale parameters to the emergent remodeling dynamics observed in both experiments and simulations. Together, these findings put forward an unrecognized mechanical role for CIL, extending its influence beyond collective migration, and establish the fluid-under-tension state as a distinct class of tissue behavior that describes key developing embryonic tissues and may illuminate how matrix-rich adult tissues become fluidized during tumorigenesis.

biophysics↗

bioRxiv2025

Direct measurements of active forces and material properties unveil the active mechanics of early embryogenesis

Despite progress in probing tissue mechanics, direct long-term measurements in live embryonic epithelia are lacking. This limits our understanding of amniote embryonic morphogenesis, which takes place over hours or days. Here, we introduce a combined technological and analytical framework to directly measure active forces and material properties in developing quail embryos, in a minimally invasive way. We find that the embryonic epithelium behaves elastically on short timescales with a modulus [~] 2 nN {middle dot} m-1 but flows over longer timescales with a viscosity [~] 4 N {middle dot} s {middle dot} m-1, and that both properties are under active regulation. Notably, we demonstrate that cell division is an active epithelial fluidizer, with division rates correlating with tissue fluidity. This fluidization is crucial for the emergence of the primary embryonic axis, which we show is shaped by a force [~] 2 N. Altogether, our approach delivers a complete and quantitative view of early embryonic mechanics, and opens new avenues for biomechanical studies in live embryos and tissues.

developmental biology↗

bioRxiv2024

A tension-induced morphological transition shapes the avian extra-embryonic territory

The segregation of the extra-embryonic lineage is one of the earliest events and a key step in amniote development. Whereas the regulation of extra-embryonic cell fate specification has been extensively studied, little is known about the morphogenetic events underlying the formation of this lineage. Here, taking advantage of the amenability of avian embryos to live and quantitative imaging, we investigate the cell- and tissue-scale dynamics of epiboly, the process during which the epiblast expands to engulf the entire yolk. We show that tension arising from the outward migration of the epiblast border on the vitelline membrane stretches extra-embryonic cells, which reversibly transition from a columnar to squamous morphology. The propagation of this tension is strongly attenuated in the embryonic territory, which concomitantly undergoes fluid-like motion, culminating in the formation of the primitive streak. We formulate a simple viscoelastic model in which the tissue responds elastically to isotropic stress but flows in response to shear stress, and show that it recapitulates the flows and deformation of both embryonic and extra-embryonic tissues. Together, our results clarify the mechanical basis of early avian embryogenesis and provide a framework unifying the divergent mechanical behaviors observed in the contiguous embryonic and extra-embryonic territories that make up the epiblast. HighlightsO_LIThe extra-embryonic region expands radially during epiboly C_LIO_LICell area increase accounts for the rapid extra-embryonic expansion C_LIO_LIEpiboly-induced tension reversibly stretches extra-embryonic cells C_LIO_LIA simple viscoelastic model recovers the morphogenesis of the entire epiblast C_LI

developmental biology↗

bioRxiv2023

Using a micro-device with a deformable ceiling to probe stiffness heterogeneities within 3D cell aggregates

Recent advances in the field of mechanobiology have led to the development of methods to characterize single-cell or monolayer mechanical properties and link them to their functional behaviour. However, there remains a strong need to establish this link for three-dimensional multicellular aggregates, which better mimic tissue function. Here we present a platform to actuate and observe many such aggregates within one deformable micro-device. The platform consists of a single PDMS piece cast on a 3D-printed mold and bonded to a glass slide or coverslip. It consists of a chamber containing cell spheroids, which is adjacent to air cavities that are fluidically independent. Controlling the air pressure in these air cavities leads to a vertical displacement of the chambers ceiling. The device can be used in static or dynamic modes over time-scales of seconds to hours, with displacement amplitudes from a few m to several tens of microns. Further, we show how the compression protocols can be used to obtain measurements of stiffness heterogeneities within individual co-culture spheroids, by comparing image correlations of spheroids at different levels of compression with finite element simulations. The labeling of the cells and their cytoskeleton is combined with image correlation methods to relate the structure of the co-culture spheroid with its mechanical properties at different locations. The device is compatible with various microscopy techniques, including confocal microscopy, which can be used to observe the displacements and rearrangements of single cells and neighborhoods within the aggregate. The complete experimental and imaging platform can now be used to provide multi-scale measurements that link single-cell behavior with the global mechanical response of the aggregates.

bioengineering↗

bioRxiv2022

Activity-driven extracellular volume expansion drives vertebrate axis elongation

The vertebrate bauplan is primarily established via the formation of embryonic tissues in a head-to-tail progression. The biomechanics of this elongation, which requires the presomitic mesoderm (PSM), remains poorly understood. Here, we find that avian PSM explants can elongate autonomously when physically confined in vitro, producing a pushing force that can largely account for the posterior elongation of the embryo. Tissue elongation results from volumetric expansion that is driven by cellular activity and accompanied by inhomogeneous increase of the extracellular fraction along the AP axis. We show that FGF signaling promotes glycolysis-dependent production of Hyaluronic Acid (HA), which is required for expansion of the posterior PSM. Our findings link body axis elongation to tissue expansion through the metabolic control of extracellular matrix production downstream of FGF signaling. One-Sentence SummaryActive tissue expansion propels body elongation independent of cell proliferation-driven growth

developmental biology↗

bioRxiv2022

Direct Force Measurement and Loading on Developing Tissues in Intact Avian Embryos

Developmental morphogenesis is driven by tissue stresses acting on tissue rheology. Direct measurements of forces in small tissues (100m-1mm) in situ such as in early embryos require high spatial precision and minimal invasiveness. Here we report tissue force microscopy (TiFM) integrating a vertical cantilever probe and live imaging to enable close-loop control of mechanical loading in early chicken embryos. By testing previously qualitatively characterized force-producing tissues in the elongating body axis, we show that TiFM quantitatively captures stress dynamics with high sensitivity. TiFM also provides the capacity of applying a stable, minimally-invasive and physiologically relevant load to drive tissue deformation, which alters morphogenetic progression and cell movements. Together, TiFM addresses a key technological gap in tissue force measurement and manipulation in small developing embryos, and promises to contribute to the quantitative understanding of complex multi-tissue mechanics during development.

developmental biology↗

bioRxiv2019

Rere-dependent Retinoic Acid signaling controls brain asymmetry and handedness

While the vertebrate brain appears largely bilaterally symmetrical in humans, it presents local morphological Left-Right (LR) asymmetries as, for instance, in the petalia. Moreover, higher functions such as speech or handedness are asymmetrically localized in the cortex. How these brain asymmetries are generated remains unknown. Here, we reveal a striking parallel between the control of bilateral symmetry in the brain and in the precursors of vertebrae called somites, where a \"default\" asymmetry is buffered by Retinoic Acid (RA) signaling. This mechanism is evident in zebrafish and mouse and, when perturbed in both species, it translates in the brain into lateralized alterations of patterning, neuronal differentiation and behavior. We demonstrate that altering levels of the mouse RA coactivator Rere results in subtle cortex asymmetry and profoundly altered handedness, linking patterning and function in the motor cortex. Together our data uncover a novel mechanism that could underlie the establishment of brain asymmetries and handedness in vertebrates.

neuroscience↗

bioRxiv2018

In vitro characterization of the human segmentation clock

The vertebral column is characterized by the periodic arrangement of vertebrae along the anterior-posterior (AP) axis. This segmental or metameric organization is established early in embryogenesis when pairs of embryonic segments called somites are rhythmically produced by the presomitic mesoderm (PSM). The tempo of somite formation is controlled by a molecular oscillator known as the segmentation clock 1,2. While this oscillator has been well characterized in model organisms 1,2, whether a similar oscillator exists in humans remains unknown. We have previously shown that human embryonic stem (ES) cells or induced pluripotent stem (iPS) cells can differentiate in vitro into PSM upon activation of the Wnt signaling pathway combined with BMP inhibition3. Here, we show that these human PSM cells exhibit Notch and YAP-dependent oscillations4 of the cyclic gene HES7 with a 5-hour period. Single cell RNA-sequencing comparison of the differentiating iPS cells with mouse PSM reveals that human PSM cells follow a similar differentiation path and exhibit a remarkably coordinated differentiation sequence. We also demonstrate that FGF signaling controls the phase and period of the oscillator. This contrasts with classical segmentation models such as the \"Clock and Wavefront\" 1,2,5, where FGF merely implements a signaling threshold specifying where oscillations stop. Overall, our work identifying the human segmentation clock represents an important breakthrough for human developmental biology.

developmental biology↗