Biology subjects

Rostami, M.

Publications and source records attributed to Rostami, M..

5 recordsLinked to original sources

bioRxiv2026

Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium

The corneal endothelium is a non-regenerative monolayer whose health determines transplant success, yet donor tissue is assessed only by single-cell metrics that ignore how the monolayer is organized collectively. A physics-based spring constant K, derived from the radial distribution function of cell positions, captures this collective order but has remained limited to semi-manual studies without physical interpretation. Here we present Cornealia, an automated pipeline for collective-order and intercellular-force analysis. In cultured endothelial cells, collective order declines with passaging and is higher under growth-factor conditions that preserve N-cadherin junctions, differences invisible to cell density and hexagonality. Across 2,177 donor cornea images from two cohorts, collective order, distinct from classical metrics, responds most to mechanical perturbation: corneas with endothelial cell density above 2,400 cells/mm^2 mostly gain order, whereas less dense ones lose it, on one curve shared by both cohorts. Reconstructed intercellular forces track these changes. This switch lies within the minimum donor densities used by eye banks, suggesting a mechanical basis for these clinical thresholds and establishing collective order as an automatable measure of endothelial quality.

bioinformatics↗

bioRxiv2026

Signal Associa: hot tumors elicit field-spanning NK cell coordination linked to their recruitment

Cells coordinate through coupled dynamics, yet whether observed correlations reflect genuine coupling is rarely tested. Signal Associa is an open-source framework uniting six coupling methods with automated stationarization and surrogate testing. Benchmarking against six ground truth systems reveals a trichotomy of coupling regimes, each with a different best method: correlation for coupling carried by shared trends and cycles, Granger causality for linear stochastic coupling, and convergent cross-mapping for nonlinear coupling; agreement across methods identifies the regime from data. In 13 movies of natural killer (NK) cells across three colorectal tumor microenvironments, NK cells formed field-spanning coupling networks at a conserved rate; at matched exposure to tumor signal, NK cells around hot tumors were more globally integrated, and hot tumors with a more integrated NK network tended to attract more NK cells. In focal adhesions, stiffness strengthened vinculin-FAK coupling, most at protruding edges. Surrogates cut lagged-correlation false positives from 23-92% to about 5%.

systems biology↗

bioRxiv2026

Collagen V Presented at the Cell-Substrate Interface Mimics Substrate Stiffening to Enhance Fibroblast Traction, Adhesion Turnover, and Persistent Migration

Collagen type V (Col-V) is a minor fibrillar collagen that regulates collagen fibril assembly, and its haploinsufficiency causes classical Ehlers-Danlos syndrome, in which wound healing is delayed. Whether Col-V also changes how fibroblasts adhere to, pull on, and migrate across a collagen-presenting surface has not been tested directly. Here, we covalently coupled Col-I or Col-V to soft (2.7 kPa) silicone substrates and quantified the mechanical response of NIH/3T3 fibroblasts. On Col-V, cells generated about 1.5-fold higher traction, spread more, and formed smaller focal adhesions that each carried more force. Adhesions on Col-V assembled and disassembled faster. Single fibroblasts on Col-V migrated more slowly but more persistently, and fibroblast monolayers closed a 500 micrometer gap faster. Raising substrate stiffness to 13 kPa reproduced this phenotype on Col-I, including higher traction, larger spread area, and smaller focal adhesions, indicating that Col-V presentation produces an adhesion state that otherwise requires a stiffer substrate. In separate reconstituted collagen hydrogels, co-assembly with 10 to 20% Col-V yielded thinner, straighter fibrils, and 20% Col-V increased the indentation modulus of the gel. These results identify the collagen type presented at the cell-material interface as a design parameter that can partly substitute for bulk stiffness in controlling fibroblast traction and migration, and they suggest Col-V as a tunable component of collagen-based biomaterials.

bioengineering↗

bioRxiv2025

TRPV4 Dominates High Shear-Induced Initial Traction Response and Long-Term Relaxation Over Piezo1

Modulation of endothelial traction is critical for the responses of endothelial cells to fluid shear stress (FSS), which has profound implications for vascular health and atherosclerosis. Previously, we demonstrated that under high FSS, endothelial cells rapidly increase traction forces, followed by relaxation, with traction aligning in the flow direction. In contrast, low shear preconditioning induces a modest short-term increase in traction (<30 min), followed by a secondary long-term (>14 hr) rise, with traction/cells aligning perpendicular to the flow. The upstream mechanosensors driving these responses, however, remain unknown. Here, we sought the roles of Piezo1 and TRPV4 ion channels in shear-induced traction modulation. We report that HUVECs with Piezo1 silencing reduced the initial traction rise in half under high FSS compared to those by WT cells, while not affecting the traction modulation in response to low FSS or traction/cell alignment to the flow direction. Conversely, cells with siTRPV4 fully abrogated the initial traction rise, as well as alignment of traction and cells, in response to both high and low FSS conditions. Dual inhibition of Piezo1 and TRPV4 further impaired both initial and long-term traction under high FSS. Interestingly, dual-inhibited cells displayed larger initial traction responses to low FSS compared to control cells, suggesting the involvement of alternative calcium-independent pathways that become dominant when both ion channels are nonfunctional. Additionally, either ion channel inhibition led to secondary long-term traction increase even under high FSS condition. These findings suggest that while both Piezo1 and TRPV4 channels contribute to shear mechanotransduction, TRPV4 plays more dominant role than Piezo1 in mediating the initial traction rise and sustaining long-term relaxation under high or low shear stress, highlighting their critical and distinct contributions to endothelial mechanotransduction and remodeling.

cell biology↗

bioRxiv2020

Connecting actin polymer dynamics across multiple scales

Actin is an intracellular protein that constitutes a primary component of the cellular cytoskeleton and is accordingly crucial for various cell functions. Actin assembles into semi-flexible filaments that cross-link to form higher order structures within the cytoskeleton. In turn, the actin cytoskeketon regulates cell shape, and participates in cell migration and division. A variety of theoretical models have been proposed to investigate actin dynamics across distinct scales, from the stochastic nature of protein and molecular motor dynamics to the deterministic macroscopic behavior of the cytoskeleton. Yet, the relationship between molecular-level actin processes and cellular-level actin network behavior remains understudied, where prior models do not holistically bridge the two scales together. In this work, we focus on the dynamics of the formation of a branched actin structure as observed at the leading edge of motile eukaryotic cells. We construct a minimal agent-based model for the microscale branching actin dynamics, and a deterministic partial differential equation model for the macroscopic network growth and bulk diffusion. The microscale model is stochastic, as its dynamics are based on molecular level effects. The effective diffusion constant and reaction rates of the deterministic model are calculated from averaged simulations of the microscale model, using the mean displacement of the network front and characteristics of the actin network density. With this method, we design concrete metrics that connect phenomenological parameters in the reaction-diffusion system to the biochemical molecular rates typically measured experimentally. A parameter sensitivity analysis in the stochastic agent-based model shows that the effective diffusion and growth constants vary with branching parameters in a complementary way to ensure that the outward speed of the network remains fixed. These results suggest that perturbations to microscale rates can have significant consequences at the macroscopic level, and these should be taken into account when proposing continuum models of actin network dynamics.

biophysics↗