Biology subjects

Tlili, S.

Publications and source records attributed to Tlili, S..

10 recordsLinked to original sources

bioRxiv2024

A quantitative pipeline for whole-mount deep imaging and multiscale analysis of gastruloids

Whole-mount 3D imaging at the cellular scale is a powerful tool for exploring complex processes during morphogenesis. In organoids, it allows examining tissue architecture, cell types, and morphology simultaneously in 3D models. However, cell packing in multilayered organoid tissues hinders both deep imaging and quantification of cell-scale processes. To address these challenges, we developed an experimental and computational pipeline to extract properties at scales ranging from cell to tissue. The experimental module is based on two-photon imaging of immunostained organoids. The computational module corrects for optical artifacts, performs accurate 3D nuclei segmentation and reliably quantifies gene expression. We provide the computational module as a user-friendly Python package called Tapenade, along with napari plugins which enable joint data processing and exploration across scales. We demonstrate the pipeline by quantifying 3D spatial patterns of gene expression and nuclear morphology in gastruloids, revealing how local cell deformations and gene co-expression relate to tissue-scale organization. This quantitative pipeline improves our understanding of gastruloid development, and lays the groundwork for a wide range of multi-layered organoids and tumoroids systems

biophysics↗

bioRxiv2023

E-cadherin-dependent phosphorylation of EGFR governs a homeostatic feedback loop controlling intercellular junction viscosity and collective migration modes.

Actomyosin tension has been shown to be a ubiquitous driver of tissue morphogenesis1, 2. The Rho pathway, a prominent regulatory network influencing cortical tension, plays a central role in both tissue reorganisation and cell migration3-6. While viscous dissipation in the actin network is commonly regarded as a constant passive parameter in cell migration in both 2D and 3D contexts, there is limited knowledge concerning the regulation of dissipative forces arising from viscous drag between cells during collective rearrangement. Here, we found that the phosphorylation of Epithelial Growth Factor Receptor (EGFR) downstream of de novo E-cadherin adhesion7, 8 orchestrates a feedback loop, thereby governing intercellular viscosity via the Rac pathway regulating actin dynamics. Our findings highlight how the E-cadherin-dependent EGFR activity controls the migration mode of collective cell movements independently of intercellular tension. Combining molecular cell biology, micropatterning, and in silico simulation, our work suggests the existence of a regulatory loop by which cells can tune junctional actin viscosity, with implications for the phenomenology of morphogenetic movements.

cell biology↗

bioRxiv2021

Condensation of the Drosophila Nerve Cord is Oscillatory and depends on Coordinated Mechanical Interactions

During development, organs must form with precise shapes and sizes. Organ morphology is not always obtained through growth; a classic counterexample is condensation of the nervous system during Drosophila embryogenesis. The mechanics underlying such condensation remain poorly understood. Here, we combine in toto live-imaging, biophysical and genetic perturbations, and atomic force microscopy to characterize the condensation of the Drosophila ventral nerve cord (VNC) during embryonic development at both subcellular and tissue scales. This analysis reveals that condensation is not a unidirectional continuous process, but instead occurs through oscillatory contractions alternating from anterior and posterior ends. The VNC mechanical properties spatially and temporally vary during its condensation, and forces along its longitudinal axis are spatially heterogeneous, with larger ones exerted between neuromeres. We demonstrate that the process of VNC condensation is dependent on the coordinated mechanical activities of neurons and glia. Finally, we show that these outcomes are consistent with a viscoelastic model of condensation, which incorporates time delays due to the different time scales on which the mechanical processes act, and effective frictional interactions. In summary, we have defined the complex and progressive mechanics driving VNC condensation, providing insights into how a highly viscous tissue can autonomously change shape and size.

developmental biology↗

bioRxiv2020

Aster repulsion drives local ordering in an active system

Biological systems are a form of active matter, which often undergo rapid changes in their material state, e.g. liquid to solid transitions. Yet, such systems often also display remarkably ordered structures. It remains an open question as to how local ordering occurs within active systems. Here, we utilise the rapid early development of Drosophila melanogaster embryos to uncover the mechanisms driving short-ranged order. During syncytial stage, nuclei synchronously divide (within a single cell defined by the ellipsoidal eggshell) for nine cycles after which most of the nuclei reach the cell cortex. Despite the rapid nuclear division and repositioning, the spatial pattern of nuclei at the cortex is highly regular. Such precision is important for subsequent cellularisation and morphological transformations. We utilise ex vivo explants and mutant embryos to reveal that microtubule asters ensure the regular distribution and maintenance of nuclear positions in the embryo. For large networks of nuclei, such as in the embryo, we predict - and experimentally verify - the formation of force chains. The ex vivo extracts enabled us to deduce the force potential between single asters. We use this to predict how the nuclear division axis orientation in small ex vivo systems depend on aster number. Finally, we demonstrate that, upon nucleus removal from the cortex, microtubule force potentials can reorient subsequent nuclear divisions to minimise the size of pattern defects. Overall, we show that short-ranged microtubule-mediated repulsive interactions between asters can drive ordering within an active system.

biophysics↗

bioRxiv2020

Cell state transitions and collective cell movement generate an endoderm-like region in gastruloids

Shaping the animal body plan is a complex process that involves the spatial organization and patterning of the different germ layers. Recent advances in live imaging have started to unravel the cellular choreography underlying this process in mammals, however, the sequence of events transforming an unpatterned cell ensemble into structured territories is largely unknown. Here, using gastruloids -3D aggregates of mouse embryonic stem cells-we study the formation of one of the three germ layers, the endoderm. We show that the endoderm is generated from an epiblast-like homogeneous state by a three-step mechanism: (i) a loss of E-cadherin mediated contacts in parts of the aggregate leading to the appearance of islands of E-cadherin expressing cells surrounded by cells devoid of E-cadherin, (ii) a separation of these two populations with islands of E-cadherin expressing cells flowing toward the aggregate tip, and (iii) their differentiation into an endoderm population. During the flow, the islands of E-cadherin expressing cells are surrounded by cells expressing T-Brachyury, reminiscent of the process occurring at the primitive streak. Consistent with recent in vivo observations, the endoderm formation in the gastruloids does not require an epithelial-to-mesenchymal transition, but rather a maintenance of an epithelial state for a subset of cells coupled with fragmentation of E-cadherin contacts in the vicinity, and a sorting process. Our data emphasize the role of signaling and tissue flows in the establishment of the body plan.

developmental biology↗

bioRxiv2019

Interfacial energy constraints are sufficient to align cells over large distances

During development and wound healing, cells need to form long-ranged ordered structures to ensure precise formation of organs and repair damage. This requires cells to locate specific partner cells to which to adhere. How such cell matching reliably happens is an open problem, particularly in the presence of biological variability. Here, we use an equilibrium energy model to simulate how cell matching can occur with subcellular precision. A single parameter - encapsulating the competition between selective cell adhesion and cell compressibility - can reproduce experimental observations of cell alignment in the Drosophila embryonic heart. This demonstrates that adhesive differences between cells (in the case of the heart, mediated by filopodia interactions) are sufficient to drive cell matching without requiring cell rearrangements. The biophysical model can explain observed matching defects in mutant conditions and when there is significant biological variability. We also demonstrate that a dynamic vertex model gives results consistent with the equilibrium energy model. Overall, this work shows that equilibrium energy considerations are consistent with observed cell matching in cardioblasts, and has potential application to other systems, such as neuron connections and wound repair. Statement of SignificanceCells often need to identify specific neighboring cells, such as during wound repair and forming neural connections. Here, we develop a biophysical model of such cell-cell interactions within the context of the developing heart. We demonstrate that precise cell matching can occur by minimizing the energy costs of interfacial interactions. This model can explain a breadth of experimental observations despite it being a steady-state approximation of a dynamic system. This opens the possibility that such approaches may be applicable to other systems, providing a powerful yet simple framework for understanding cell matching.

systems biology↗

bioRxiv2018

Shaping the zebrafish myotome by differential friction and active stress

Organ formation is an inherently biophysical process, requiring large-scale tissue deformations. Yet, understanding how complex organ shape emerges during development remains a major challenge. During fish embryogenesis, large muscle segments, called myotomes, acquire a characteristic chevron morphology, which is believed to play a role in swimming. The final myotome shape can be altered by perturbing muscle cell differentiation or by altering the interaction between myotomes and surrounding tissues during morphogenesis. To disentangle the mechanisms contributing to shape formation of the myotome, we combine single-cell resolution live imaging with quantitative image analysis and theoretical modeling. We find that, soon after its segmentation from the presomitic mesoderm, the future myotome spreads across the underlying tissues. The mechanical coupling between the myotome and the surrounding tissues is spatially varying, resulting in spatially heterogeneous friction. Using a vertex model, we show that the interplay of differential spreading and friction is sufficient to drive the initial phase of myotome shape formation. However, we find that active stresses, generated during muscle cell differentiation, are necessary to reach the acute angle of the myotome observed in wildtype embryos. A final ingredient for formation and maintenance of the chevron shape is tissue plasticity, which is mediated by orientated cellular rearrangements. Our work sheds a new light on how a spatio-temporal sequence of local cellular events can have a non-local and irreversible mechanical impact at the tissue scale, leading to robust organ shaping.

biophysics↗

bioRxiv2018

Pcdh18a-positive tip cells instruct notochord formation in zebrafish

The notochord defines the axial structure of all vertebrates during development. Notogenesis is a result of major cell reorganization in the mesoderm, the convergence and the extension of the axial cells. However, it is currently not known how these processes act together in a coordinated way during notochord formation. Analysing the tissue flow, we determined the displacement of the axial mesoderm and identified, relative to the ectoderm, an actively-migrating notochord tip cell population and a group of trailing notochordal plate cells. Molecularly, these tip cells express Protocadherin18a, a member of the cadherin superfamily. We show that Pcdh18a-mediated recycling of E-cadherin adhesion complexes transforms these tip cells into a cohesive and fast migrating cell group. In turn, these tip cells subsequently instruct the trailing mesoderm. We simulated cell migration during early mesoderm formation using a lattice-based mathematical framework, and predicted that the requirement for an anterior, local motile cell cluster could guide the intercalation of the posterior, axial cells. Indeed, grafting experiments validated the predictions and induced ectopic notochord-like rods. Our findings indicate that the tip cells influence the trailing mesodermal cell sheet by inducing the formation of the notochord.

developmental biology↗

bioRxiv2017

Collective cell migration without proliferation: density determines cell velocity and wave velocity

Collective cell migration contributes to morphogenesis, wound healing or tumor metastasis. Culturing epithelial monolayers on a substrate enables to quantify such tissue migration. By using narrow strips, we stabilise the front shape; by inhibiting cell division, we limit density increase and favor steady migration; by using long strips, we observe a confined cell monolayer migrating over days. A coherent collective movement propagates over millimeters; cells spread and density decreases from the monolayer bulk toward the front. Cell velocity ([~]micrometer per minute) increases linearly with cell radius, and does not depend explicitly on the distance to the front. Over ten periods of backwards propagating velocity waves, with wavelength [~]millimeter, are detected with a signal-to-noise ratio enabling for quantitative spatio-temporal analysis. Their velocity ([~]ten micrometers per minute) is ten times the cell velocity; it increases linearly with the cell radius. Their period ([~]two hours) is spatially homogeneous, and increases with the front density. When we inhibit the formation of lamellipodia, cell velocity drops while waves either disappear, or have a smaller amplitude and slower period. Our phenomenological model assumes that both cell and wave velocities are related with the activity of lamellipodia, and that the local stretching in the monolayer bulk modulates traction stresses. We find that parameter values close to the instability limit where waves appear yield qualitative and quantitative predictions compatible with experiments, including the facts that: waves propagate backwards; wave velocity increases with cell radius; lamellipodia inhibition attenuates, slows down or even suppresses the waves. Together, our experiments and modelling evidence the importance of lamellipodia in collective cell migration and waves.

biophysics↗

bioRxiv2017

Disrupting different Distal-less exons leads to ectopic and missing eyespots accurately modeled by reaction-diffusion mechanisms

Eyespots on the wings of nymphalid butterflies represent colorful examples of the process of pattern formation, yet the developmental origins and the mechanisms behind eyespot differentiation are still not fully understood. Here we re-examine the function of Distal-less (Dll) in eyespot development, which is still unclear. We show that CRISPR-Cas9 induced exon 2 mutations in Bicyclus anynana leads to exon skipping and ectopic eyespots on the wing. Exon 3 mutations, however, lead to null/missense transcripts, missing eyespots, lighter wing coloration, loss of scales, and a variety of other phenotypes implicating Dll in the process of eyespot differentiation. Reaction-diffusion modeling enabled exploration of the function of Dll in eyespot formation, and accurately replicated a wide-range of mutant phenotypes. These results confirm that Dll is a required activator of eyespot development, scale growth and melanization and point to a new mechanism of alternative splicing to achieve Dll over-expression phenotypes.

developmental biology↗