Biology subjects

Smith, A.-S.

Publications and source records attributed to Smith, A.-S..

9 recordsLinked to original sources

bioRxiv2026

Crowding governs resistance confinement and guides the improvement of adaptive therapy in a 2D melanoma model system

The emergence of treatment resistant mutants is one of the primary contributors to therapy failure in cancer. Evolution-based adaptive therapies aim to exploit the competition between sensitive and resistant cells to prolong therapeutic control. However, in the densely packed tissues of solid tumors, competition is not only determined by cell-intrinsic factors but also a result of local physical interactions between neighboring cells. The successful development of physics-informed adaptive therapies therefore hinges upon the bottom-up integration of tissue mechanics and experimentally grounded models of tumor evolution. Here, we show how population-level treatment response emerges from mechanical interactions between individual cells. Combining genetically tailored therapy-mimicry experiments in spatially structured 2D melanoma colonies with mechanistic, particle-based tissue simulations as digital twins in a real-to-sim-to-real framework, we reveal how treatment-induced changes in mechanical crowding shape a cascade of resistance expansion, spatial competitive escape, and consequent therapy failure. We then link these underlying physical mechanisms to population-level observables in an abstracted mathematical model for reinforcement-learning-based therapy optimization and a distilled treatment-decision-heuristic, which we test experimentally. Together, our results identify mechanical crowding and escape as governing principles of resistance-mediated therapy failure in solid tumours and provide a basis for mechanistically informed, evolution-based treatment strategies.

biophysics↗

bioRxiv2024

Deciphering the role of the nanoscale clustering of activating and costimulatory antibodies on T cell activation

In a joint experimental and a modeling effort, we explored the regulation of T cell activation and cytotoxicity by the nanoscale clustering and surface density of activating and costimulatory antibodies. Specifically, we simulated T cells on nanolithographically patterned arrays of clusters of these antibodies, systematically varying the cluster size from intermediate to large and overall antibody density. We found that T-cell activation correlated more with global antibody density than with cluster size, such that at low density arrays were inefficient in activation, while high density arrays saturated the signal. However, when T-cells were exposed to patterns of low global densities but small, very dense clusters, full activation of T cells was achieved. These results could be rationalized using the membrane-fluctuation-model that integrates the cooperative effects between bonds with mechanical feedback from the cell activation. This insight into the spatial organization of activating ligands provides an important understanding of the mechanism of T cell activation and allows for the design of more effective T cell activation platforms for immunotherapy.

immunology↗

bioRxiv2023

Laminin alpha 5 - induced mechanical homeostasis modulates retinal epithelium functionality

Epithelial cells are highly interconnected, whereby they acquire mesoscale mechanical properties to accomplish specific tissue functions. In homeostasis, this mechanical status can be summarised as mechanical homeostasis, regulated by the balance of intercellular tension and extracellular matrix adhesion forces. In the outer retina, the significance of this force balance and its consequences for vision remains poorly understood. We found that the density of basement membrane laminins modulates the level of retinal pigmented epithelium contractility, which directly controls its efficiency in phagocytosing photoreceptor outer segments. In vivo, the density gradient of laminins follows retinal functional demand, supporting the physiological role of laminins in controlling epithelial mechanical homeostasis. Our data suggest that laminin density and isoform heterogeneity can differentially engage integrins {beta}1 and {beta}4, the ratio of which determines the contribution of actin vs keratin cytoskeleton in balancing tissue mechanics. With this work, we suggest that the extracellular matrix-defined mechanical status of retinal pigmented epithelium is a novel parameter for visual function. SignificanceIn the retina, the retinal pigmented epithelium (RPE) is responsible for the daily phagocytosis of photoreceptor cell fragments, a process vital for visual function. Along the visual axis, there is a natural decrease in the ratio of photoreceptors to RPE cells, indicating a decrease in RPE functional demand. This study reveals that the density of laminins in RPE basement membrane also diminishes along this axis, critically influencing RPE function by regulating its contractility. For the first time, we demonstrate the presence of a laminin- defined mechanical gradient within the RPE, which determines its capacity to support photoreceptor cells. Our findings highlight the importance of mechanical properties as a key factor in visual function, offering new insights into retinal health and disease.

biophysics↗

bioRxiv2023

Capturing the mechanosensitivity of cell proliferation in models of epithelium

Despite the primary role of cell proliferation in tissue development and homeostatic maintenance, the interplay between cell density, cell mechanoresponse, and cell growth and division is not yet understood. In this article we address this issue by reporting on an experimental investigation of cell proliferation on all time- and length-scales of the development of a model tissue, grown on collagen-coated glass or deformable substrates. Through extensive data analysis, we demonstrate the relation between mechanoresponse and probability for cell division, as a function of the local cell density. Motivated by these results, we construct a minimal model of cell proliferation that can recover the data. By parametrizing the growth and the dividing phases of the cell cycle, and introducing such a proliferation model in dissipative particle dynamics simulations, we recover the mechanoresponsive, time-dependent density profiles in 2D tissues growing to macroscopic scales. The importance of separating the cell population into growing and dividing cells, each characterized by a particular time scale, is further emphasized by calculations of density profiles based on adapted Fisher-Kolmogorov equations. Together, these results show that the mechanoresponse on the level of a constitutive cell and its proliferation results in a matrix-sensitive active pressure. The latter evokes massive cooperative displacement of cells in the invading tissue and is a key factor for developing large-scale structures in the steady state.

biophysics↗

bioRxiv2023

Morphology as indicator of adaptive changes of model tissues in osmotically and chemically changing environments

We investigate the formation and maintenance of the homeostatic state in the case of 2D epithelial tissues following an induction of hyperosmotic conditions, using media enriched with 80 to 320 mOsm of mannitol, NaCl, and urea. We characterise the changes in the tissue immediately after the osmotic shock, and follow it until the new homeostatic state is formed. We characterise changes in cooperative motility and proliferation pressure in the tissue upon treatment with the help of a theoretical model based on the delayed Fisher-Kolmogorov formalism, where the delay in density evolution is induced by the the finite time of the cell division. Finally we explore the adaptation of the homeostatic tissue to highly elevated osmotic conditions by evaluating the morphology and topology of cells after 20 days in incubation. We find that hyperosmotic environments together with changes in the extracellular matrix induce different mechanical states in viable tissues, where only some remain functional. The perspective is a relation between tissue topology and function, which could be explored beyond the scope of this manuscript. O_LIExperimental investigation of morphological effect of change of osmotic conditions on long-term tissue morphology and topology C_LIO_LIEffect of osmotic changes on transient tissue growth behaviour C_LIO_LIAnalysis of recovery process of tissues post-osmotic-shock C_LIO_LIToxicity limits of osmolytes in mid- to long-term tissue evolution C_LIO_LITissue adaptation to physiological changes in environment C_LIO_LILong-term tissue stabilisation under altered osmotic conditions. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/524301v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@826d28org.highwire.dtl.DTLVardef@cc7f35org.highwire.dtl.DTLVardef@1b370fborg.highwire.dtl.DTLVardef@1bea90e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

On the mechanical regulation of epithelial tissue homeostasis

Despite recent efforts to understand homeostasis in epithelial tissues, there are many unknowns surrounding this steady state. It is considered to be regulated by mechanoresponse, but unlike for single cells, this remains heavily debated for tissues. Here, we show that changes in matrix stiffness induce a non-equilibrium transition from tubular to squamous Madin-Darby Canine Kidney II tissues. Nonetheless, despite different cell morphologies and densities, all homeostatic tissues display equivalent topologies, which, hence, must be actively targeted and regulated. On the contrary, the mechanoresponse induces dramatic changes in the large-scale organization of the colonies. On stiff gels, this yields an unreported cooperative state of motile cells displaying higher densities than in the arrested homeostatic state. This suggests a more complex relation between cell density and motility than previously anticipated. Our results unequivocally relate the mechanosensitive properties of individual cells to the evolving macroscopic structures, an effect that could be important for understanding the emergent pathologies of living tissues.

biophysics↗

bioRxiv2020

Principles of organelle membranebridging established using cytosolictether mimics

The interactions between different intra-cellular organelles, including the endoplasmic reticulum, have recently been in focus thanks to the tremendous progress in imaging them using cryogenic transmission electron microscopy. However, they are still difficult to study in cellulo, and reconstituting these systems has been a standing challenge. Here we achieve this task using a giant unilamellar vesicle (GUV) and supported lipid bilayer (SLB) system. The tethers, which may reside in the cytosol when unbound, are mimicked by single (or double) stranded DNA sequences of two different lengths with ends that are self-sticky, and with terminal cholesterol moieties which insert into GUV or SLB membranes. The DNA-tethers, bound by their sticky-end, can exist in two possible states - either with both cholesterols in the same membrane or each cholesterol in a different membrane, the latter conformation leading to adhesion. Exchange of tether-molecules between the membranes occurs through the aqueous phase. By developing theoretical arguments that are supported in our experiments, we show that this possibility of exchange and the relative difference in the projected area between the two states drives the adhesion due to collective entropic considerations, rather than the usually considered enthalpy of binding. The establishment of this fundamentally different interaction between two membranes suggests that in physiological conditions, the regulation of contact formation inside cells may be very different from the case of the much studied ligand-receptor pairing on the external cell membrane.

biophysics↗

bioRxiv2020

Coexistence of long and short DNA constructs within adhesion plaques

Adhesion domains forming at the membrane interfaces between two cells or a cell and the ex-tracellular matrix commonly involve multiple proteins bridges. However, the physical mechanisms governing the domain structures are not yet fully resolved. Here we present a joint experimental and theoretical study of a mimetic model-system, based on giant unilammelar vesicles interacting with supported lipid bilayers, with which the underlying physical effects can be clearly identified. In our case, adhesion is induced by simultaneous action of DNA linkers with two different lengths. We study the organization of bridges into domains as a function of relative fraction of long and short DNA constructs. Irrespective of the composition, we systematically find adhesion domains with coexisting DNA bridge types, despite their relative differences in length of 9 nm. However, at short length scales, below the optical resolution of the microscope, simulations suggest the formation of nanodomains by the minority fraction. The nano-aggregation is more significant for long bridges, which are also more stable, even though the enthalpy of membrane insertion is the same for both species.

biophysics↗

bioRxiv2020

Molecular Scale Spatio-Chemical Control of the Activating-Inhibitory Signal Integration in NK Cells

The role of the spatial juxtaposition between activating and inhibitory receptors in cytotoxic lymphocytes has been strongly debated in the context of the inhibition of immune signaling. The challenge in addressing this problem was so far a lack of experimental tools which can simultaneously manipulate different signaling molecules. Here, we circumvent this challenge by introducing a nanoengineered multifunctional cell niche, in which activating and inhibitory ligands are positioned with molecular-scale variability and control, and applied it to elucidate the role of the spatial juxtaposition between ligands for NKG2D and KIR2DL1 - activating and inhibitory receptors in Natural Killer (NK) cells - in KIR2DL1-mediated inhibition of NKG2D signaling. We realized the niche by a nanopatterning of nanodots of different metals with molecular scale registry in one lithographic step, followed by a novel ternary functionalization of the fabricated bi-metallic pattern and its background to with three distinct biochemical moieties. We found, that within the probed range, the 40 nm gap between the activating and inhibitory ligands provided an optimal inhibition condition. Supported by theoretical modeling and simulations we interpret these findings as a consequence of the size and conformational flexibility of the ligands in their spatial interaction. Our findings provide an important insight onto the spatial mechanism of the inhibitory immune checkpoints, whose understanding is both fundamentally important, and essential for the rational design of future immunotherapies. Furthermore, our approach is highly versatile and paves the way to numerous complex molecular platforms aimed at revealing molecular mechanisms through which receptors integrate their signals.

immunology↗