Biology subjects

Merkel, M.

Publications and source records attributed to Merkel, M..

9 recordsLinked to original sources

bioRxiv2026

Quantification of cellular contributions to multi-cellular pattern formation

Multi-cellular pattern formation is a key process in organism development, regeneration, and disease. Such multi-cellular patterns include, for instance, cell density and gene expression patterns. Here, we develop a cell-track-based method that quantifies how much individual cellular processes contribute to the emergence of large-scale patterns. These cellular processes include changes in cellular expression levels, cell motion, cell divisions, and apoptosis. We validate our method using synthetic data, before demonstrating it on two sets of experimental data. Our method is purely geometric and does not require any mechanistic assumptions about the underlying pattern-forming processes, making it very generic and robust. It thus enables unbiased, data-driven study of the mechanisms driving pattern formation across a broad class of systems.

biophysics↗

bioRxiv2026

A non-invasive approach for understanding localized force generation in 3D tissues

The development, maintenance and repair of epithelial tissues critically rely on adhesion complexes that ensure structural integrity while enabling dynamic remodeling. Such tissue remodeling underpins both physiological morphogenesis and pathological transformation. Central to these processes are mechanical forces, which tightly couple cytoskeletal organization to adhesion dynamics. Despite extensive investigations in two-dimensional (2D) systems, how these interactions are orchestrated within polarized three-dimensional (3D) epithelia remains largely unresolved. Here, we introduce a new, non-invasive strategy to probe localized force generation within 3D epithelial tissues. We engineered elastic polyacrylamide (PAAm) microbeads with cell-mimetic size and mechanical properties, enabling their seamless integration. In contrast to conventional bead injection approaches, these PAAm microbeads were spontaneously engulfed by the tissue, thereby establishing an intrinsic interface through which bead deformation can be directly correlated with local cytoskeletal architecture and adhesion organization, as visualized through high-resolution imaging combined with quantitative 3D computational reconstruction. Using this approach, we demonstrated that localized mechanical perturbations trigger pronounced cytoskeletal remodelling while preserving global tissue polarity. We further identified the extracellular matrix composition as key determinant of bead-tissue interactions, with collagen-I coating promoting robust adhesion and efficient incorporation. At the bead-cell interface, cells assembled tension-bearing focal adhesions and organized actin stress fibers, revealing the emergence of active cortical stress. Strikingly, quantitative analysis of bead deformation revealed a previously unrecognized mechanical duality: spatially segregated regions of pulling and pushing forces coexisted at the microscale, directly correlated with local cytoskeleton dynamics. This finding challenges the prevailing view of homogenous force application and instead supports a model in which cells deploy highly coordinated and spatially patterned force-generating strategies. Altogether, this integrative and non-invasive strategy offers a comprehensive pipeline for dissecting the dynamic interplay between cellular processes and tissue mechanics during morphogenesis in 3D model systems.

cell biology↗

bioRxiv2024

Self organisation of invasive breast cancer driven by the interplay of active and passive nematic dynamics

In invasive breast cancer, cell clusters of varying sizes and shapes are embedded in the fibrous extracellular matrix (ECM). Although the prevailing view attributes this structure to increasing disorder resulting from loss of function and dedifferentiation, our findings reveal that it arises through a process of active self-organization driven by cancer cell motility. Simulations and histological analyses of tumours from over 2,000 breast cancer patients reveal that motile, aligned cancer cells within clusters move as active nematic aggregates through the surrounding highly aligned ECM fibres, which form a confining, passive nematic phase. Cellular motion leads to cluster splitting and coalescence. The degree of cluster activity, combined with heterogeneity in cell motility, is reflected in specific scaling behaviours for cluster shape, size distribution, and the distance between cluster boundaries and nematic defects in ECM alignment. Increased activity estimates correlate with tumour progression and are associated with a poorer prognosis for patients.

biophysics↗

bioRxiv2024

Epithelial-mesenchymal boundary guides cell shapes and axis elongation in embryonic explants

The spatial arrangement of tissues during development establishes regions of tissue-tissue interactions. While such interactions are prominent during gastrulation and organogenesis, how they guide morphogenesis remains unclear. Here, using Xenopus animal cap explants, we show that the coupling between epithelial and mesenchymal tissues is instrumental in robust axis elongation. We find that mesenchymal and epithelial tissues drive elongation hierarchically - the epithelium can elongate independently, while the mesenchyme requires the initial presence of the epithelium. The epithelial-mesenchymal boundary defines the direction of cell shape alignment and the axis of tissue elongation. Prior to explant elongation, epithelial cells align and elongate, a process that propagates into the underlying mesenchyme. These findings reveal how tissue boundaries can organize coherent axis elongation without external patterning cues, providing insights into the self-organization principles that guide embryonic morphogenesis.

developmental biology↗

bioRxiv2023

Marangoni-like tissue flows enhance symmetry breaking of embryonic organoids

During early development of multi-cellular animals, cells self-organize to set up the body axes, such as the primary head-to-tail axis, based on which the later body plan is defined. Several signaling pathways are known to control body axis formation. Here, we show, however, that also tissue mechanics plays an important role during this process. We focus on the emergence of a primary axis in initially spherical aggregates of mouse embryonic stem cells, which mirrors events in the early mouse embryo. These aggregates break rotational symmetry to establish an axial organization with domains of different expression profiles, e.g. of the transcription factor T/Bra and the adhesion molecule E-cadherin. Combining quantitative microscopy and physical modeling, we identify large-scale tissue flows with a recirculation component and demonstrate that they significantly contribute to symmetry breaking. We show that the recirculating flows are explained by a difference in tissue surface tension across domains, akin to Marangoni flows, which we further confirm by aggregate fusion experiments. Our work highlights that body axis formation is not only driven by biochemical processes, but that it can also be amplified by tissue flows. We expect that this type of amplification may operate in many other organoid and in-vivo systems.

biophysics↗

bioRxiv2022

Genetic and geometric heredity interact to drive polarized flow in the Drosophila embryo

Tissue flow during morphogenesis is commonly driven by local constriction of cell cortices, which is caused by activation of actomyosin contractility. This can lead to long-range flows due to tissue viscosity. However, in the absence of cell-intrinsic polarized forces or polarity in forces external to the tissue, these flows must be symmetric and centered around the region of contraction. Polarized tissue flows have been previously demonstrated to arise from the coupling of such contractile flows to points of increased friction or adhesion to external structures. However, we show with experiments and modeling that the onset of polarized tissue flow in early Drosophila morphogenesis occurs independent of adhesion and is instead driven by a geometric coupling of apical actomyosin contractility to tissue curvature. Particularly, the onset of polarized flow is driven by a mismatch between the position of apical myosin activation and the position of peak curvature at the posterior pole of the embryo. Our work demonstrates how genetic and geometric information inherited from the mother interact to create polarized flow during embryo morphogenesis.

developmental biology↗

bioRxiv2019

Anisotropy links cell shapes to a solid-to-fluid transition during convergent extension

Within developing embryos, tissues flow and reorganize dramatically on timescales as short as minutes. This includes epithelial tissues, which often narrow and elongate in convergent extension movements due to anisotropies in external forces or in internal cell-generated forces. However, the mechanisms that allow or prevent tissue reorganization, especially in the presence of strongly anisotropic forces, remain unclear. We study this question in the converging and extending Drosophila germband epithelium, which displays planar polarized myosin II and experiences anisotropic forces from neighboring tissues, and we show that in contrast to isotropic tissues, cell shape alone is not sufficient to predict the onset of rapid cell rearrangement. From theoretical considerations and vertex model simulations, we predict that in anisotropic tissues two experimentally accessible metrics of cell patterns--the cell shape index and a cell alignment index--are required to determine whether an anisotropic tissue is in a solid-like or fluid-like state. We show that changes in cell shape and alignment over time in the Drosophila germband indicate a solid-to-fluid transition that corresponds to the onset of cell rearrangement and convergent extension in wild-type embryos and are also consistent with more solid-like behavior in bnt mutant embryos. Thus, the onset of cell rearrangement in the germband can be predicted by a combination of cell shape and alignment. These findings suggest that convergent extension is associated with a transition to more fluid-like tissue behavior, which may help accommodate tissue shape changes during rapid developmental events.

developmental biology↗

bioRxiv2019

Transthyretin-stabilizing mutation T119M is not associated with protection against vascular disease or death in the UK Biobank

BackgroundDestabilized transthyretin (TTR) can result in the progressive, fatal disease transthyretin-mediated (ATTR) amyloidosis. A stabilizing TTR mutation, T119M, is the basis for a therapeutic strategy to reduce destabilized TTR. Recently, T119M was associated with extended lifespan and lower risk of cerebrovascular disease in a Danish cohort. We aimed to determine whether this finding could be replicated in the UK Biobank.\n\nMethodsTTR T119M carriers were identified in the UK Biobank, a large prospective cohort of [~]500,000 individuals. Association between T119M genotype and inpatient diagnosis of vascular disease, cardiovascular disease, cerebrovascular disease, and mortality was analyzed.\n\nResultsFrequency of T119M within the white UK Biobank population (n=337,148) was 0.4%. Logistic regression comparing T119M carriers to non-carriers found no association between T119M and vascular disease (odds ratio [OR]=1.08; p=.27), cardiovascular disease (OR=1.08; p=.31), cerebrovascular disease (OR=1.1; p=.42), or death (OR=1.2; p=.06). Cox proportional hazards regression showed similar results (hazard ratio>1, p>.05). Age at death and vascular disease diagnosis were similar between T119M carriers and non-carriers (p=.12 and p=.38, respectively).\n\nConclusionsThere was no association between the TTR T119M genotype and risk of vascular disease or death in a large prospective cohort study, indicating that TTR tetramer stabilization through T119M is not protective in this setting.

genetics↗

bioRxiv2017

Asymmetric cell volume changes regulate epithelial morphogenesis in zebrafish Kupffers vesicle

How epithelial cell behaviors are coordinately regulated to sculpt tissue architecture is a fundamental question in biology. Kupffer's vesicle (KV), a transient organ with a fluid - filled lumen, provides a simple system to investigate the interplay between intrinsic cellular mechanisms and external forces during epithelial morphogenesis. Using 3 - dimensional (3D) analyses of single cells we identify asymmetric cell volume changes along the anteroposterior axis of KV that coincide with asymmetric cell shape changes. Blocking ion flux prevents these cell volume changes and cell shape changes. Vertex simulations suggest cell shape changes do not depend on lumen expansion. Consistent with this prediction, asymmetric changes in KV cell volume and shape occur normally when KV lumen growth fails due to leaky cell adhesions. These results indicate ion flux mediates asymmetric cell volume changes that contribute to asymmetric cell shape changes in KV, and that these changes in epithelial morphology are separable from lumen - generated forces.

cell biology↗