Biology subjects

Swaminathan, V. S.

Publications and source records attributed to Swaminathan, V. S..

7 recordsLinked to original sources

bioRxiv2026

Mechanical memory of confinement pressure governs expansion size in epithelial monolayers

Epithelial tissues undergo rapid expansion during development, repair, and morphogenesis, yet how tissue-scale growth is coordinated to re-establish homeostasis remains unclear. Here, we show that large epithelial monolayers confined at a wide range of initial densities and mechanochemical states robustly converge to the same final size and density upon release, despite differences in initial cell size, YAP activity, and cell number dynamics. To investigate the underlying mechanism, we combined quantitative experiments with a mechanochemical agent-based model in which mechanical pressure arising from confinement acts as a tissue-scale signal that modulates intracellular cell-cycle activity over time. Using this framework, we show that transient mechanical relaxation during confinement selectively elevates cell-cycle activity in higher-density tissues at the time of release, accelerating early expansion without disrupting final homeostatic outcomes. Together, these results reveal how epithelial tissues coordinate collective growth and robustly restore homeostasis during expansion. SignificanceMechanisms that re-establish homeostasis and coordinate cell proliferation in expanding epithelial tissues such as during development and tissue regeneration remain poorly understood. Here, we used a large 2D epithelial expansion model and agent-based modelling to demonstrate history-dependent regulation of colony growth, mediated by pressure sensing. We find that, typically, equilibration of pressure during confinement just before the onset of expansion results in all expanding tissues of a given starting size reaching a target density and final size independent of starting cell numbers. By transiently reducing actomyosin contractility during confinement, we selectively accelerate the expansion of high-density tissues. Our findings provide key insights into physical mechanisms that govern organ development and tissue repair.

cell biology↗

bioRxiv2025

Packing-Driven Mechanotransduction: local crowding overrides adhesion and stiffness cues for YAP Activation in Cellular Collectives

The regulation of mechanotransduction is crucial for various cellular processes, including stem cell differentiation, wound healing, and cancer progression. While the activation of mechanotransduction has been extensively studied in single cells, it remains unclear whether similar mechanisms extend to mechanotransduction in multicellular collectives. Here, by focusing on Yes-associated protein (YAP), known as the master regulator of mechanotransduction, we reveal that the local packing fraction of cells acts as the primary determinant of YAP activation in cell collectives. We further show that local packing fraction modulates the isotropic stress landscape, with sparse regions experiencing large stress fluctuations and dense regions displaying stress equilibration. Remarkably, this packing fraction-dependent regulation persists even under conditions of disrupted force transmission through cell-cell and cell-substrate adhesion, suggesting a robust and conserved relation between YAP activation and local packing fraction in cell collectives. In particular, we show that local packing fraction-dependent activation of YAP in cell collectives is independent of substrate stiffness, E-cadherin expression, and myosin contractility, in stark contrast to YAP activation in single cells. Our results thus offer a new perspective on mechanotransduction, highlighting the critical role of local packing fraction of cells in dictating YAP dynamics within multicellular contexts. These insights have significant implications for tissue engineering and understanding tumour microenvironments, where cellular het-erogeneity often drives functional outcomes.

biophysics↗

bioRxiv2025

ECM-stiffness mediated persistent fibroblast activation requires integrin and formin dependent chromatin remodeling

Transient activation of fibroblasts into contractile myofibroblasts is essential for extracellular matrix (ECM) production and remodeling during wound healing and tissue regeneration. While ECM-dependent mechanisms mediating transient activation is well studied, how fibroblasts switch from transient to a persistently activated state and drive fibrosis and aberrant tissue repair in diseases such as cancer is less understood. Here, we show that human cancer-associated fibroblasts (CAFs) switch from transient to persistently activated states upon prolonged exposure to stiff ECMs and stiffness-dependent secreted factors. This switch is accompanied by activation of ECM-stiffness-dependent mechanotransduction pathways and changes in the nuclear architecture and its association with chromatin. Mechanistically, we identify two pathways required for this switch-ECM ligand binding and complete activation of {beta}1 integrins smoothens the nuclear lamina during prolonged exposure, increases nuclear YAP, and reduces lamin-chromatin contacts while in parallel, exposure to the stiff ECM activates the formin mDia2 and independent of alterations in the nuclear architecture alters lamin-chromatin coupling, likely through its role in assembling nuclear actin. Importantly, we find that blocking either pathway prevents persistent myofibroblast activation, which is rescued by inhibition of histone deacetylases, indicating that dynamic chromatin modifications act downstream of these ECM-dependent pathways to maintain the persistently activated state. These findings link integrin-based ECM sensing to chromatin remodeling and fibroblast memory, with implications for stromal plasticity in the tumor microenvironment.

cell biology↗

bioRxiv2025

METTL3 regulates exocytosis independently of m6A

RNA modification pathways are often mis-regulated in various cancers, with N6-methyladenosine (m6A) having a pivotal role in cancer progression and metastasis. Methyltransferase-like 3 (METTL3), a core component of the m6A methyltransferase complex, functions not only as an m6A writer but also promotes tumorigenesis through m6A-independent mechanisms. Here, we show that METTL3 is mislocalized to the cytoplasm in breast cancer tumors from patients, contributing to the oncogenic phenotype. Cytoplasmic METTL3 interacts with EXOC7, a key regulator of exocytosis, promoting its stabilization. Additionally, METTL3 regulates m6A-dependent alternative splicing of EXOC7. Silencing METTL3 impairs vesicle trafficking and the breast cancer secretome - effects that do not rely on its enzymatic activity but instead involve METTL3-mediated stabilization of EXOC7 and potentially other exocyst components. Furthermore, METTL3 knockdown impairs invadopodia formation, collagen matrix invasion, and focal adhesion morphology in vitro, while inhibition of METTL3 catalytic activity does not. Our findings uncover non-catalytic roles of METTL3 in regulating exocytosis and the cancer secretome.

molecular biology↗

bioRxiv2025

β1 Integrin-FAK-Piezo1 signalling axis drives in-situ stiffening mediated ECM remodelling and invasion of 3D breast epithelium

Stiffening of tissue is a hallmark of cancer progression, driving invasive phenotypes through complex interactions between cells and their extracellular matrix (ECM). However, the mechanisms linking mechanical cues to ECM remodelling and invasion remain incompletely understood. Here, using an in-situ stiffening model that allows for modulation of ECM stiffness around fully formed normal mammary acini embedded in their native ECM microenvironment, we identify critical steps in basement membrane (BM) and stromal ECM remodelling during invasion and discover the molecular mechanisms driving this process. We find that stiffening of the ECM around normal mammary acini results in rapid loss and degradation of laminin (LN) and upregulation of the fibronectin (FN) secretion around the acini. This priming phase is followed by the onset of invasion which requires localized upregulation of LN production and ECM remodelling. Mechanistically, ECM production and remodelling as well as invasion is mediated by {beta}1 integrin-FAK signalling, which activates mechanosensitive ion channels (MSCs). Further, we identify Piezo1 as the MSC downstream of {beta}1 integrin-FAK that drives BM disruption and stromal ECM remodelling. Taken together, our results identify the mechanisms by which stiffness can trigger invasive phenotypes from normal tissues.

cell biology↗

bioRxiv2024

Extracellular matrix dependent regulation of Septin 7 in focal adhesions promotes mechanosensing and response in fibroblasts.

Fibroblasts are contractile adherent cells that maintain tissue homeostasis by sensing a wide array of changes in the extracellular matrix (ECM) and in response, regulate the physical and compositional properties of the ECM. These diverse cues are sensed by focal adhesions (FAs) that differentially couple changes in the ECM to the actomyosin machinery via modulation of integrin activation and the resultant recruitment of several proteins. One such protein is Septin-7 (Sept-7) that belongs to the septin family and has been found in FA proteomics and interactome studies. Sept-7 however, is not considered an FA protein and is thought to regulate and be regulated by actin outside of FAs. To reconcile these differences, here we used total internal reflection microscopy to image Sept-7 localization and dynamics at the cell-ECM interface and found that that ECM-mediated integrin activation in fibroblasts regulates the formation of spatially distinct higher order Sept-7 structures at FA subpopulations. In and around FAs located in the perinuclear regions of the cell, ECM binding resulted in the formation and stabilization of Sept-7 bundles while ECM binding and complete integrin activation promoted the growth of FA-like elongated Sept-7 structures that dynamically associated with the core of peripheral FAs. Functionally, peripheral Sept-7 structures promoted the elongation of peripheral FAs while perinuclear Sept-7 bundles were critical in regulating the maturation and stabilization of perinuclear FAs. Due to this coupling between the ECM, integrin activation and regulation of Sept-7 structures, we found that Sept-7 is required for a wide range of ECM sensing functions in fibroblasts including modulating sensitivity to changes in ECM stiffness and density and in contributing to the cells ability to remodel the ECM. Collectively, our results show that Sept-7 is an FA protein that gets recruited and assembled in diverse higher order structures in an ECM dependent manner to differentially regulate FA subpopulations and promote mechanosensing and ECM remodelling functions in fibroblasts.

cell biology↗

bioRxiv2022

Extracellular matrix sensing via modulation of orientational order of integrins and F-actin in focal adhesions

Specificity of cellular responses to distinct cues from the extracellular matrix (ECM) requires precise and sensitive decoding of information from the cell surface. However, how known mechanisms of mechanosensing such as force dependent catch bonds and conformational changes in focal adhesion (FA) proteins can confer this sensitivity is not known. Using a combination of polarization microscopy and computational modeling, here we identify regulation of orientational order or molecular co-alignment of FA proteins as a mechanism able to precisely tune cell sensitivity to the ECM. We find that V integrins and F-actin in FAs show changes in orientational order in an ECM-mediated integrin activation dependent manner. This magnitude of orientational order is sensitive to changes in ECM density but independent of myosin-II activity though actomyosin contractility can further fine-tune it. A molecular clutch model for integrin binding ECM ligands demonstrates that orientational order of integrin-ECM binding and catch bonds tune cellular sensitivity to ECM density. This mechanism is also able to decouple ECM density changes from changes in ECM stiffness thus also contributing to specificity. Taken together, our results suggest relative geometric organization of FA components as an important regulator of mechanotransduction.

cell biology↗