Biology subjects

Nandi, S. K.

Publications and source records attributed to Nandi, S. K..

6 recordsLinked to original sources

bioRxiv2026

Cell Mechanics Regulate Membrane Tubulation-Driven Trogocytosis in Adherent Cells

Trogocytosis is a widespread and physiologically important process in which one cell ingests fragments of another. It has been observed in diverse biological contexts, such as in Entamoeba histolytica, a human enteric parasite that nibbles host intestinal cells via trogocytosis, thereby invading the tissue and leading to lethal extra-intestinal disease, and in macrophages on interaction with adherent tumor monolayers. Despite its physiological relevance, knowledge of trogocytosis with adherent cells remains elusive. Here, we established a monolayer-based trogocytosis assay and uncovered a distinct membrane-tube-mediated trogocytic mechanism operative in adherent cells. We characterized it into four sequential events: contact, membrane tubulation, stretching, and scission. By targeting the proteic constituents of target cell stiffness, we show that trogocytic output exhibits a non-monotonic dependence on the viscoelastic properties of the target cell, with maximal uptake occurring in an intermediate mechanical regime. Further, we integrated live-cell trogocytosis observations with a viscoelastic model-based theoretical framework to propose a tube-breaking mechanism across distinct mechanical subtypes. Finally, using micropatterning, we demonstrated that target cell shape influences trogocytosis kinetics. This work suggests that trogocytosis is sensitive to the mechanical state of the target cell.

cell biology↗

bioRxiv2025

Glassy dynamics in active epithelia emerge from an interplay of mechanochemical feedback and crowding.

Glassy dynamics in dense epithelial cells remain a subject of debate, as theory predicts its emergence only at unrealistically low cellular activity, yet experimental studies have shown glassy dynamics at physiologically active conditions. In this study, we address this paradox by integrating experimental observations in epithelial monolayers with an active vertex model. We demonstrate that while crowding is essential, it is not sufficient for glassy dynamics to emerge. A mechanochemical feedback loop (MCFL-1), mediated by cell shape changes through the contractile actomyosin network is required to drive glass transition in dense epithelial tissues. Such mechanochemical feedback is captured experimentally via a crosstalk between actin-based cell clustering and dynamic heterogeneity, as well as via force induced actin reorganization in epithelial cells. Incorporating MCFL into the vertex model reveals contrasting results from those previously predicted by theories-we show that the MCFL can counteract cell division-induced fluidisation and enable glassy dynamics to emerge through active cell-to-cell communication. Furthermore, our analysis reveal, for the first time, the existence of novel collective mechanochemical oscillations that arise from the crosstalk of MCFL-1 with oscillatory MCFL-2, capturing ERK mediated cell shape changes. Together, we demonstrate that an interplay between crowding and active mechanochemical feedback enables the emergence of glass-like traits and collective biochemical oscillations in epithelial tissues with active cell-to-cell contacts.

biophysics↗

bioRxiv2024

How motility drives the glassy dynamics in confluent epithelial monolayers?

As wounds heal, embryos develop, cancer spreads, or asthma progresses, the cellular monolayer undergoes glass transition between solid-like jammed and fluid-like flowing states. During some of these processes, the cells undergo an epithelial-to-mesenchymal transition (EMT): they acquire in-plane polarity and become motile. Thus, how motility drives the glassy dynamics in epithelial systems is critical for the EMT process. However, no analytical framework that is indispensable for deeper insights exists. Here, we develop such a theory inspired by a well-known glass theory. One crucial result of this work is that the confluency affects the effective persistence time-scale of active force, described by its rotational diffusivity, [Formula]. [Formula] differs from the bare rotational diffusivity, Dr, of the motile force due to cell shape dynamics, which acts to rectify the force dynamics: [Formula] is equal to Dr when Dr is small and saturates when Dr is large. We test the theoretical prediction of [Formula] and how it affects the relaxation dynamics in our simulations of active Vertex model. This novel effect of [Formula] is crucial to understanding the new and previously published simulation data of active glassy dynamics in epithelial monolayers.

biophysics↗

bioRxiv2021

The origin of universal cell shape variability in a confluent epithelial monolayer

Cell shape is fundamental in biology. The average cell shape can influence crucial biological functions, such as cell fate and division orientation. But cell-to-cell shape variability is often regarded as noise. In contrast, recent works reveal that shape variability in diverse epithelial monolayers follows a nearly universal distribution. However, the origin and implications of this universality are unclear. Here, assuming contractility and adhesion are crucial for cell shape, characterized via aspect ratio (AR), we develop a mean-field analytical theory for shape variability. We find that a single parameter, , containing all the system-specific details, describes the probability distribution function (PDF) of AR; this leads to a universal relation between the standard deviation and the average of AR. The PDF for the scaled AR is not strictly but almost universal. The functional form is not related to jamming, contrary to common beliefs, but a consequence of a mathematical property. In addition, we obtain the scaled area distribution, described by the parameter {micro}. We show that and {micro} together can distinguish the effects of changing physical conditions, such as maturation, on different system properties. The theory is verified in simulations of two distinct models of epithelial monolayers and agrees well with existing experiments. We demonstrate that in a confluent monolayer, average shape determines both the shape variability and dynamics. Our results imply the cell shape variability is inevitable, where a single parameter describes both statics and dynamics and provides a framework to analyze and compare diverse epithelial systems.

biophysics↗

bioRxiv2020

Glassiness in cellular Potts model of biological tissue is controlled by disordered energy landscape

Glassy dynamics in a confluent monolayer is indispensable in morphogenesis, wound healing, bronchial asthma, and many others; a detailed theoretical understanding for such a system is, therefore, important. We combine numerical simulations of a cellular Potts model and an analytical study based on random first order transition (RFOT) theory of glass, develop a comprehensive theoretical framework for a confluent glassy system, and show that glassiness is controlled by the underlying disordered energy landscape. Our study elucidates the crucial role of geometric constraints in bringing about two distinct regimes in the dynamics, as the target perimeter P0 is varied. The extended RFOT theory provides a number of testable predictions that we verify in our simulations. The unusual sub-Arrhenius relaxation results from the distinctive interaction potential arising from the perimeter constraint in a regime controlled by geometric restriction. Fragility of the system decreases with increasing P0 in the low-P0 regime, whereas the dynamics is independent of P0 in the other regime. The mechanism, controlling glassiness in a confluent system, is different in our study in comparison with vertex model simulations, and can be tested in experiments.

biophysics↗

bioRxiv2020

Designer protein assemblies with tunable phase diagrams in living cells

The self-organization of proteins into specific assemblies is a hallmark of biological systems. Principles governing protein-protein interactions have long been known. However, principles by which such nanoscale interactions generate diverse phenotypes of mesoscale assemblies, including phase-separated compartments, remains challenging to characterize and understand. To illuminate such principles, we create a system of two proteins designed to interact and form mesh-like assemblies in living cells. We devise a novel strategy to map high-resolution phase diagrams in vivo, which provide mesoscale self-assembly signatures of our system. The structural modularity of the two protein components allows straightforward modification of their molecular properties, enabling us to characterize how point mutations that change their interaction affinity impact the phase diagram and material state of the assemblies in vivo. Both, the phase diagrams and their dependence on interaction affinity were captured by theory and simulations, including out-of-equilibrium effects seen in growing cells. Applying our system to interrogate biological mechanisms of self-assembly, we find that co-translational protein binding suffices to recruit an mRNA to the designed micron-scale structures.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗