Biology subjects

Hannezo, E.

Publications and source records attributed to Hannezo, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Two populations with different cell dynamics maintain urethral epithelial homeostasis in female and male mice

The urethra is an understudied organ in both humans and animal models. Here we investigate the mouse urethra to gain insights into its tissue architecture, maintenance mechanisms, and epithelial cell dynamics in homeostasis. For this, we generated a single-cell RNA sequencing dataset that includes cells from the entire urethra of both female and male, with detailed regional information. Using lineage tracing and cell proliferation assays, we focused on two potential progenitor cell types, the Keratin 5+ and Keratin 14+ cells, which we found both capable of generating the full thickness of the epithelium, yet with opposite and complementary patterns of self-renewal. Our results further highlight key differences between females and males, as we observed a higher epithelium stratification, a unique pattern of keratins expression and a higher tissue turnover in females compared to males. This work provides valuable insights that can support future tissue engineering efforts aimed at developing urethral grafts for treating urethral disorders.

cell biology↗

bioRxiv2026

Differential turnover of apicobasal regulators drives emergent mechano-response and shape homeostasis

Epithelial cell shape plays a fundamental role in tissue dynamics. Numerous studies have established how cells drastically change their shape to promote epithelial tissue morphogenesis. However, the mechanisms enabling cells to maintain their shape remain far less understood. Here, leveraging live imaging in Drosophila epithelial tissue and theoretical modeling, we identify an emergent mechano-chemical feedback that ensures junction length and cell shape stability, without requiring a dedicated molecular force sensor. We find that an increase in junction length is associated with a passive dilution of E-Cadherin, followed by an increase in Myosin-II-dependent contractility that reduces junction length. Theoretically, we show that this regulation of junction length generically emerges when negative and positive regulators of contractility have distinct kinetics. Experiments confirm that E-Cadherin acts as a negative regulator with slow turnover. Mechanistically, local dilution of E-Cadherin passively lifts an inhibition on lateral apicobasal polarity components, allowing the RhoGEF Cyst -- with its fast turnover -- to accumulate and increase contractility. Perturbing this feedback results in aberrant cell junction and shape regulation, thereby compromising the ability of the tissue to buffer local mechanical fluctuations and global mechanical stresses. Altogether, we propose that differential turnover between apical and lateral polarity complexes provides an emergent mechano-response for junction length and cell shape homeostasis.

biophysics↗

bioRxiv2026

Mechanics and fate stochasticity shape stem cell distribution in tissues

Balancing cellular loss in tissues requires fine balance of cell proliferation and differentiation. In differentiated tissues consisting of a single cell type, a mechanical regulation of proliferation has been proposed to underlie growth-control and homeostatic steady-states. Yet, how tissues containing different cell types with distinct proliferation rates, mechanical interactions, and spatial self-organization retain robust homeostasis of cell proportions remains poorly understood. Here, we combine particle-based mechanical models of proliferative tissues with a classical hierarchy of stem, progenitor, and differentiated cells, undergoing stochastic fate choices, and show that mechanical feedback alone is sufficient to stabilize populations. We derive analytically and computationally a phase diagram of possible stable states, in particular those maintained either via slow and rare stem cells with short-lived progenitors or no stem cells and long-lived progenitors. Our simulations uncover that mechanical control of growth is sufficient, in the absence of any codes of adhesion or extrinsic niche signals, to cause stable spatial structures, with small stem cell clusters forming and maintaining dynamical renewal units. Our results demonstrate how complex spatial structures can emerge in minimal stochastic and mechanical simulations with impact to understand the homeostasis of multi-cellular systems.

biophysics↗

bioRxiv2026

Geometric confinement regulates ERK signaling dynamics and collective migration

Collective cell migration is a fundamental process in morphogenesis, tissue repair, cancer invasion, and frequently occurs under geometric confinement in vivo. However, how confinement interfaces with signaling pathways that coordinate collective motion remains poorly understood. Here, we confine migrating epithelial monolayers within adhesive microstripes of defined width and observe a progressive slow-down of collective migration with increasing spatial confinement. Combining biophysical modeling, live imaging of ERK activity, and pharmacological perturbations, we show that confinement increases tissue crowding while reducing cell and nuclear projected areas, thereby shifting epithelial tissues toward a mechanically compressed state associated with dampened ERK waves. Across conditions, migration speed scales with ERK signaling dynamics, which correlates with EGFR signaling as well as cell and nuclear projected areas, together serving as quantitative proxies for the confinement-imposed mechanical state. Pharmacological inhibition of ROCK restores cell spreading, ERK signaling, and migration under strong confinement, demonstrating that this state is reversible and governed by actomyosin contractility. Together, our results identify geometric confinement as a physical regulator of a contractility-dependent mechanochemical state that controls ERK signaling and collective migration in epithelial tissues.

biophysics↗

bioRxiv2026

Adult regenerative defects arise from discordant scaling of signal dependent growth and patterning

Orders of magnitude distinguish an organs size in adulthood from its size when patterning was established during embryonic development. The prospect of engineering adult organ regeneration raises the fundamental question of whether regenerative stem cell patterning should be elicited at embryonic or adult scale. Axolotls regenerate their limbs at all stages of post-embryonic life, encompassing an order of magnitude increase in animal size, but the mechanisms allowing this robust capacity remain unclear. Limb regeneration occurs by the formation of an embryonic-like progenitor zone, the blastema, whose dimensions increase with animal size, suggesting that at least some aspects of limb regeneration must scale. Here, by combining spatial transcriptomics, biophysical modelling, quantitative imaging, and functional perturbations, we found distinct scaling signatures among key signaling pathways, arguing against a body-size-dependent hormonal scaling mechanism. SHH signaling showed partial scaling that saturated in largest adult sizes, with a correspondingly early termination of blastema growth while Wnt9a-modulated digit patterning scaled at all animal sizes. As a result of this differential scaling, digit patterning wavelength was mismatched with respect to domain growth in the largest blastemas, preventing the addition of the last digit. In agreement with this model, regenerative failure can be rescued by timed supplementation of SHH. Our results show that coordinated scaling of morphogen signaling is a key requirement for adult organ regeneration.

systems biology↗

bioRxiv2026

Logic of optimal collective migration in heterogeneous tissues

Collective cell migration is a critical process in embryogenesis and cancer invasion. Recent work has shown that uniform tissues can undergo sharp rheological transitions, with collective motion emerging above a critical cell motility. In vivo, however, migration typically involves multiple populations with distinct motile and adhesive properties, and how this heterogeneity shapes collective dynamics remains unclear. Here, using two different vertex model implementations, we show that migration of heterogeneous clusters through tissues is maximized at intermediate adhesion strength: too little and the cluster fragments, too much and cluster cell cohesion suppresses the rearrangements needed for forward motion. We test our model against recent and new data on zebrafish mesendoderm invasion, where graded Nodal signalling regulates both motility and adhesion differences. By mapping measured Nodal levels to mechanical parameters, the model not only reproduces migration outcomes across homogeneous and heterogeneous clusters, but also discriminates between alternative adhesion rules. Strikingly, the inferred parameters place the system near the predicted optimum, where adhesion is strong enough to maintain cohesion yet graded enough to allow selective coupling among heterogeneous neighbors. These results identify an optimal balance between cohesion and interfacial remodeling as a general principle coordinating collective invasion in heterogeneous tissues. Significance statementCells often migrate collectively during embryonic development and cancer invasion, but tissues are rarely uniform and different cells differ both in their adhesion and activity. Using models of tissue mechanics, we show that collective invasion is maximized at an intermediate level of adhesion within the migrating cluster cells: too little and the cluster falls apart, too much and it cannot advance. We test this principle against experiments in zebrafish gastrulation, where a signaling gradient simultaneously controls both cell motility and adhesion. The model reproduces migration outcomes across a range of experiments and identifies the adhesion rule cells use to selectively stick to neighbors. These results reveal a simple mechanical logic for how heterogeneous cell collectives coordinate invasion.

biophysics↗

bioRxiv2025

Non-canonical cytokinesis driven by mechanical uncoupling via nematic flows and adhesion-based invagination

Cleavage - the series of rapid cell divisions that follow fertilization - marks the onset of metazoan development and represents a deeply conserved evolutionary process. Across animals, two principal modes exist: complete (holoblastic) and incomplete (meroblastic) cleavage. While holoblastic cleavage resembles conventional cytokinesis both in vitro and in vivo, the mechanisms underlying meroblastic cleavage have remained poorly understood. Using zebrafish embryos as a model, we show that meroblastic cleavage proceeds through a distinct two-step mechanism. The process begins with the assembly and contraction of a large, arc-shaped actomyosin cable. However, this contractile event alone is insufficient to complete division. A second phase, driven by cadherin-mediated membrane adhesion, is required to invaginate the furrow ridge. Strikingly, this transition depends on mechanical uncoupling of the contractile cable from the surrounding cortex. We demonstrate that such uncoupling arises from an active nematic instability, which both enhances contractility along the cable and generates actin depletion zones that relieve lateral connections. Together, these findings reveal that meroblastic cleavage is governed not by a single actomyosin-based event but by a sequential interplay between cytoskeletal contraction and cadherin-dependent adhesion, highlighting a mechanism fundamentally distinct from canonical cytokinesis.

cell biology↗

bioRxiv2025

Self-organization of tumor heterogeneity and plasticity

Phenotypic heterogeneity and plasticity drive tumor growth, metastasis, therapy resistance, and relapse. This heterogeneity is mainly interpreted as a response to external signals from the microenvironment. However, here we show that cancer cells also follow intrinsic self-organized programs that are sufficient to coordinate the spatiotemporal patterning of tumor cell states. By combining quantitative measurements in tumors and organoids with theoretical modeling, we reveal emergent mechanical gradients that orchestrate cell state transitions during colorectal tumor growth. Compression at the tumor center induces a transition from a fetal-like state into a cancer stem cell (CSC) state. The CSC compartment exhibits a characteristic size determined by tumor rheological properties. Once this size is surpassed, a translationally arrested apoptotic core emerges, triggering a shift from homogeneous proliferation to a hierarchical cell turnover. These findings uncover stereotyped programs of self-organization that likely cooperate with the microenvironment to shape tumor heterogeneity and plasticity.

cancer biology↗

bioRxiv2025

A self-limiting mechanotransduction feedback loop ensures robust organ formation

Organ morphogenesis uses mechanotransduction feedback loops to convert forces into gene expression changes that regulate cell mechanics. How these loops integrate with developmental programs to ensure robust outcomes remains unclear. We show Yap mechanotransduction establishes a self-limiting positive feedback loop for semicircular canal formation in zebrafish. Canal development proceeds through bud initiation, extension, and fusion within the otic epithelium. Local swelling of hyaluronan-rich extracellular matrix (ECM) in the bud activates Yap in a spatial pattern. Yap induces its target ccn1l1, promoting further ECM expansion to sustain bud extension. This feedback loop confers developmental robustness: graded knockdown of ccn1l1 reduces extension rate, yet canal formation persists and fails only with strong disruption. Critically, the loop contains its own termination mechanism. During bud fusion, PKA-CREB signaling, activated by an adhesion GPCR, gpr126, suppresses ccn1l1, ending the loop. These findings reveal how mechanotransduction loops with built-in termination provide developmental control by integrating mechanical forces, transcriptional responses, and morphogenetic outcomes.

developmental biology↗

bioRxiv2025

Substrate heterogeneity promotes cancer cell dissemination

While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion - comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar-Parisi-Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.

biophysics↗

bioRxiv2025

Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties

For tissues to spread, they must be deformable while maintaining their structural integrity. How these opposing requirements are balanced within spreading tissues is not yet well understood. Here, we show that keratin intermediate filaments function in epithelial spreading by adapting tissue mechanical resilience to the stresses arising in the tissue during the spreading process. By analysing the expansion of the enveloping cell layer (EVL) over the large yolk cell in early zebrafish embryos in vivo, we found that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, which is essential for preventing tissue rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the force-generating processes pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production in the yolk cell and the mechanical resilience of the EVL against stresses generated by these pulling forces, thereby ensuring uniform and robust tissue spreading.

developmental biology↗

bioRxiv2025

Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo

Early embryo geometry is one of the most invariant species-specific traits, yet its role in ensuring developmental reproducibility and robustness remains underexplored. Here, we show that in zebrafish, the geometry of the fertilized egg - specifically its curvature and volume - serves as a critical initial condition triggering a cascade of events that exert a lasting influence on development. Specifically, it guides asymmetric cell divisions in the blastoderm, generating radial gradients of cell volume and nucleocytoplasmic ratio. These gradients generate mitotic phase waves, with individual cell cycle periods determined largely cell-autonomously by the nucleocytoplasmic ratio. Modeling and perturbation experiments demonstrate that reducing cell autonomy reshapes these waves, emphasizing the instructive role of geometry-derived volume patterns in setting the intrinsic period of the cell cycle oscillator. Remarkably, in addition to organizing cell cycles, early embryo geometry also spatially patterns zygotic genome activation (ZGA) at the midblastula transition, a key step in establishing embryonic autonomy. Disrupting geometry alters the ZGA pattern and causes ectopic germ layer specification, underscoring its developmental significance. Together, our findings reveal a novel symmetry-breaking function of early embryo geometry in coordinating cell cycle and transcriptional patterning, establishing a blueprint for robust embryogenesis.

developmental biology↗

bioRxiv2025

Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration

Tissue regeneration relies on the ability of cells to undergo de novo patterning. While tissue patterning has been viewed as the transition from initially identical un-patterned cells to an arrangement of different cell types, recent evidence suggests that initial heterogeneities between cells modulate tissue-scale pattern formation. Yet, how such heterogeneities arise and, thereafter, regulate cell type emergence in a population of cells is poorly understood. Using in vivo and in vitro mouse regenerative systems, we identify a critical tissue density that is required to induce heterogeneous inactivation of the mechanosensor YAP1. Experimental and biophysical approaches demonstrate that YAP1 cell-to-cell heterogeneity pre-patterns the first cell fate decision, via both chromatin remodelling and a supracellular feedback between FOXA1 and Delta-Notch signalling. This feedback motif induces cell fate bistability endowing memory to the system and the maintenance of patterns during homeostasis. These findings reveal a generalisable framework in which transient cell-to-cell heterogeneity, regulated by tissue-scale properties, serves as a critical control parameter for the emergence of cell fate and stable patterning during regeneration.

cell biology↗

bioRxiv2024

Self-generated chemotaxis of mixed cell populations

Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally guided by self-generated signaling gradients rather than long-range, pre-patterned cues. However, how heterogeneous mixtures of cells interact non-reciprocally and navigate through self-generated gradients remains largely unexplored. Here we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that relative chemotactic sensitivity of cell populations controls their long-time coupling and co-migration dynamics, with boundary conditions such as external cell- and attractant reservoirs substantially influencing the migration patterns. We further predict an optimal parameter regime that leads to robust and colocalized migration. We test our theoretical predictions with in vitro experiments demonstrating the co-migration of different immune cell populations, and quantitatively reproduce observed migration patterns under wild-type and perturbed conditions. Interestingly, immune cell co-migration appears close to the predicted optimal regime. Finally, we incorporate mechanical interactions into our framework, revealing a phase diagram that illustrates non-trivial interplays between chemotactic and mechanical non-reciprocity in driving collective migration. Together, our findings suggest that self-generated chemotaxis is a robust strategy for emergent multicellular navigation.

biophysics↗

bioRxiv2024

Biomechanics of stem cell fate decisions in multilayered tissues

Tissue homeostasis relies on a precise balance of fate choices between renewal and differentiation, which is dysregulated during tumor initiation. Although much progress has been done over recent years to characterize the dynamics of cellular fate choices at the single cell level, their underlying mechanistic basis often remains unclear. In particular, although physical forces are increasingly characterized as regulators of cell behaviors, a unifying description of how global tissue mechanics interplays with local cellular fate choices is missing. Concentrating on skin epidermis as a paradigm for multilayered tissues with complex fate choices, we develop a 3D vertex-based model with proliferation restrained in the basal layer, showing that mechanics and competition for space naturally gives rise to homeostasis and neutral drift dynamics that are seen experimentally. We then explore the effect of introducing mechanical inhomogeneities, whereby subpopulations have differential tensions. We uncover that relatively small mechanical disparities can be sufficient to heavily tilt cellular towards symmetric renewal and exponential growth. Importantly, the simulations predict that such mechanical inhomogeneities are reflected by distinct morphological changes in single-cell shapes. This led us to derive a master relationship between two very different experimentally measurable parameters, cell shape and long-term clonal dynamics, which we validated using a model of basal cell carcinoma (BCC) consisting in clonal Smoothened overexpression in mouse tail epidermis. Altogether, we propose a theoretical framework to link mechanical forces, quantitative cellular morphologies and cellular fate outcomes in complex tissues.

biophysics↗

bioRxiv2024

Single cell migration along and against confined haptotactic gradients

Directed cell migration along gradients of extracellular matrix (ECM) density -a process called haptotaxis- plays a central role in morphogenesis, the immune response, and cancer invasion. It is commonly assumed that cells respond to these gradients by migrating directionally towards the regions of highest ligand density. In contrast with this view, here we show that cells exposed to micropatterned fibronectin gradients exhibit a complex repertoire of trajectories, including directed haptotactic migration up the gradient but also linear oscillations and circles with extended periods of migration down the gradient. To explain this behavior, we developed a biophysical model of haptotactic cell migration based on a coarse-grained molecular clutch model coupled to persistent stochastic polarity dynamics. While initial haptotactic migration is explained by the differential friction at the front and back of the cell, the observed complex trajectories over longer time scales arise from the interplay between differential friction, persistence, and physical confinement. Overall, our study reveals that confinement and persistence modulate the ability of cells to sense and respond to haptotactic cues and provides a framework to understand how cells navigate complex environments.

cell biology↗

bioRxiv2024

Differential tissue deformability underlies shape divergence of the embryonic brain and spinal cord under fluid pressure

An expanded brain enables the complex behaviours of vertebrates that promote their adaptation in diverse ecological niches1-3. Initial morphological differences between the brain and spinal cord emerge as the antero-posteriorly patterned neural plate folds to form the neural tube4-7 during embryonic development. Following neural tube closure, a dramatic expansion of the brain diverges its shape from the spinal cord8, setting their distinct morphologies for further development9,10. How the brain and the spinal cord expand differentially remains unclear. Here, using the chicken embryo as a model, we show that the hindbrain expands through dorsal tissue thinning under a positive hydrostatic pressure from the neural tube lumen11,12 while the dorsal spinal cord shape resists the same pressure. Using magnetic droplets and atomic force microscopy, we reveal that the dorsal tissue in the hindbrain is more fluid than in the spinal cord. The dorsal hindbrain harbours more migratory neural crest cells13 and exhibits reduced apical actin and a disorganised laminin matrix compared to the dorsal spinal cord. Blocking the activity of neural crest-associated matrix metalloproteinases inhibited dorsal tissue thinning, leading to abnormal brain morphology. Transplanting early dorsal hindbrain cells to the spinal cord was sufficient to create a region with expanded brain-like morphology including a thinned-out roof. Our findings open new questions in vertebrate head evolution and neural tube defects, and suggest a general role of mechanical pre-pattern in creating shape differences in epithelial tubes.

developmental biology↗

bioRxiv2023

Self-organised pattern formation in the developing neural tube by a temporal relay of BMP signalling

Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study BMP signalling dynamics in the vertebrate neural tube, we developed a new ES cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organised patterns of dorsal neural tube cell types driven by sequential phases of BMP signalling that are observed both in vitro and in vivo. Data-driven biophysical modelling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signalling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signalling in space, we uncover a BMP signalling relay that operates in time. This mechanism allows rapid initial concentrationsensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Altogether, our study provides an experimental and theoretical framework to understand how signalling dynamics are exploited in developing tissues.

developmental biology↗