Biology subjects

Alisafaei, F.

Publications and source records attributed to Alisafaei, F..

11 recordsLinked to original sources

bioRxiv2025

3D-printing-assisted, microfabricated devices reveal hierarchical and temporal mechanosensing in high-density fibroblast culture

Understanding how cells integrate mechanical forces across multiple directions, length scales, and timescales remains a fundamental challenge in mechanobiology. Deciphering how cells integrate this information is particularly important in the context of wound healing, where the timing and duration of the fibroblast-to-myofibroblast transition can determine healing outcomes. Here, we discovered that fibroblasts in engineered tissues respond to directional anisotropy in stress through a hierarchical temporal cascade, with individual cell elongation (24 hr) preceding collective alignment (40 hr), which then drives -smooth muscle actin expression and myofibroblast transition (96h). To enable this discovery, we developed a modified hydrogel-assisted stereolithographic elastomer (HASTE) prototyping platform to incorporate a detergent that improves wettability of template agar hydrogels by poly(dimethylsiloxane) elastomer. HASTE allowed rapid prototyping of intricate 3D micropost arrays that provides isotropic (8-post) versus anisotropic (4-post) boundary conditions. Fibroblasts sensed and responded to stress directionality before bulk tissue reorganization occurs. Computational modeling predicted steady-state activation patterns based on initial stress anisotropy rather than magnitude, and our experiments reveal that reaching this state requires sequential mechanosensitive processes operating across distinct timescales. This temporal hierarchy persists even when extensive cell-cell contacts might be expected to mask matrix-mediated mechanical signals. Our findings demonstrate that fibroblast mechanosensing involves adaptive responses encoded through progressive cell and tissue reorganization. Results provide insight into how nanoscale mechanosensing scales up to direct tissue-level organization, with implications for understanding wound healing, understanding fibrosis, and engineering functional tissue replacements.

bioengineering↗

bioRxiv2025

Risk-Aware Control for Insulin Delivery via Nonlinear MPC with Safety Barrier Functions and Probabilistic Learning of Uncertainties

Maintaining blood glucose within a physiologically safe range is critical for people with diabetes, as deviations can lead to acute or chronic complications. Hypoglycemia, in particular, represents an immediate threat and requires prioritized mitigation in autonomous insulin delivery systems. This paper introduces a risk-aware hybrid nonlinear model predictive control (NMPC) framework that combines data-driven uncertainty quantification with formal safety assurance through control barrier functions (CBFs). To account for key uncertainties, such as physiological time delays, unannounced meals, and stress-induced glucose variability, Gaussian processes (GPs) are employed as probabilistic estimators. The proposed method dynamically monitors glucose and regulates insulin injection to enforce safe glucose level control by preventing hypoglycemia. The proposed framework is evaluated using validated physiological simulators for various realistic scenarios. The results show a robust performance in maintaining safety under high uncertainty, preparing a foundation for translation into next phase of our research as safe autonomous diabetes management systems.

bioengineering↗

bioRxiv2025

Adhesive implant interfaces prevent fibrosis by disrupting mechanobiological feedback

Fibrotic encapsulation around medical implants affects millions of patients annually. Current approaches targeting inflammation or implant material properties have failed clinically, but the mechanical origins of implant-induced fibrosis remain unexplored. Here, we demonstrate that directional imbalance of mechanical forces ("tension anisotropy") is the primary driver of fibroblast activation at implant-tissue interfaces, and that it can be eliminated through adhesive bonding strategies. Computational modeling reveals a mechanistic basis for successful adhesive anti-fibrotic interfaces: conventional sutured implants generate highly anisotropic stress fields between discrete suture anchor points that activate fibroblasts, while adhesive interfaces distribute forces isotropically, maintaining a mechanical environment that does not activate fibroblasts. In vivo experiments from the literature across multiple animal models confirm these predictions: as predicted, adhesive interfaces completely prevent fibrotic capsule formation for up to 12 weeks across diverse organs, while maintaining identical implant composition and geometry compared to sutured controls. Results establish tension anisotropy as a mechanical regulator of implant fibrosis and provide a mechanistic foundation explaining why adhesive interfaces succeed where all previous anti-fibrotic strategies have failed. By addressing the root mechanical cause of fibrosis, this mechanobiology-driven approach may enable a universal approach for preventing fibrosis across all categories of implantable medical devices. Significance statementMillions of patients suffer from medical device failure due to fibrotic encapsulation, in which a surgically implanted item such as pacemaker leads or a vascular graft loses function by becoming covered with scar tissue. Implants affixed to soft tissues by sutures are especially prone to this form of failure, but implants affixed with a recently invented adhesive are not. We present the discovery that directional imbalance of forces ("tension anisotropy") drives conversion of healing tissue into scar tissue. Conventional sutured implants create highly anisotropic stress fields between anchor points that activate fibroblasts, while adhesive interfaces distribute forces isotropically, attenuating scarring. This mechanistic insight explains why adhesive implant-tissue interfaces successfully prevent fibrotic capsule formation across multiple animal models and organ systems, where all previous anti-fibrotic approaches have failed. By addressing root mechanical causes of fibrotic remodeling, this discovery provides a pathway for clinical remediation of fibrotic encapsulation.

biophysics↗

bioRxiv2025

Extracellular Matrix Physical Properties Regulate Cancer Cell Morphological Transitions in 3D Hydrogel Microtissues

Cancer cells can adopt a range of morphological states linked to distinct functional behaviors during tumor progression. Some remain in a proliferative state, forming tight clusters; others detach and elongate into an invasive state; and some retain a rounded amoeboid form with minimal matrix adhesion. However, factors that determine which morphological state a cell adopts remain poorly understood. Using a combined theoretical and experimental framework, we showed that extracellular matrix (ECM) mechanics regulate cancer cell morphology in three-dimensional (3D) environments. We developed a theoretical model based on the principle of minimum energy, which predicts that a cell will adopt the morphological state--rounded, elongated, or clustered-- that minimizes the total energy of the cell-ECM system. Using MDA-MB-231 breast cancer cells, we established a reliable protocol for encapsulating cells into 3D naturally-derived hydrogels with controlled stiffness and pore size. We validated the models predictions in vitro over an extended culture period. In soft ECMs, cells transitioned over time to an elongated morphology, while in stiff ECMs, cells favored clustered configurations. These transitions were governed by the physical-- not chemical--properties of the hydrogel-based ECM, as confirmed by using chemically distinct yet mechanically matched composite matrices. These new insights have implications for cancer invasion modeling and potential drug screening.

biophysics↗

bioRxiv2025

Tension-Induced Stiffening of Cytoskeletal Components Regulates Cardiomyocyte Contractility

Cardiomyocytes continuously experience mechanical stimuli that regulate their contractile behavior and contribute to overall heart function. Despite the importance of mechanotransduction in cardiac physiology, the mechanisms by which cardiomyocytes integrate external mechanical cues, such as stretch and environmental stiffness, remain poorly understood. In this study, we present a combined theoretical and experimental framework to investigate how strain-induced cytoskeletal stiffening modulates cardiomyocyte contractility and force generation. Our study elucidates that regulating the mechanical tension cardiomyocytes experience in tissue--whether by modulating environmental stiffness, external stretching, or cardiac fibroblast activation--can effectively tune their contractility, with cytoskeletal strain stiffening playing a central role in this mechanotransductive response.

biophysics↗

bioRxiv2024

Structure-Mechanics Principles and Mechanobiology of Fibrocartilage Pericellular Matrix: A Pivotal Role of Type V Collagen

The pericellular matrix (PCM) is the immediate microniche surrounding resident cells in various tissue types, regulating matrix turnover, cell-matrix cross-talk and disease initiation. This study elucidated the structure-mechanical properties and mechanobiological functions of the PCM in fibrocartilage, a family of connective tissues that sustain complex tensile and compressive loads in vivo. Studying the murine meniscus as the model tissue, we showed that fibrocartilage PCM contains thinner, random collagen fibrillar networks that entrap proteoglycans, a structure distinct from the densely packed, highly aligned collagen fibers in the bulk extracellular matrix (ECM). In comparison to the ECM, the PCM has a lower modulus and greater isotropy, but similar relative viscoelastic properties. In Col5a1+/D menisci, the reduction of collagen V, a minor collagen localized in the PCM, resulted in aberrant fibril thickening with increased heterogeneity. Consequently, the PCM exhibited a reduced modulus, loss of isotropy and faster viscoelastic relaxation. This disrupted PCM contributes to perturbed mechanotransduction of resident meniscal cells, as illustrated by reduced intracellular calcium signaling, as well as upregulated biosynthesis of lysyl oxidase and tenascin C. When cultured in vitro, Col5a1+/D meniscal cells synthesized a weakened nascent PCM, which had inferior properties towards protecting resident cells against applied tensile stretch. These findings underscore the PCM as a distinctive microstructure that governs fibrocartilage mechanobiology, and highlight the pivotal role of collagen V in PCM function. Targeting the PCM or its molecular constituents holds promise for enhancing not only meniscus regeneration and osteoarthritis intervention, but also addressing diseases across various fibrocartilaginous tissues.

bioengineering↗

bioRxiv2022

Mechanobiology of Fibroblast Activation in Skin Grafting

Mechanical stretching of living tissues can activate long-lived changes in tissue cells such as fibroblasts, increasing their contractility and initiating phenotypic transformations. Increased mechanical stimulus typically leads to monotonically increasing activation of fibroblasts cultured in 2D, but activation levels are difficult to predict for cells in 3D fibrous tissues, leading to variable outcomes in procedures such as skin grafting. Here we report that the source of this variation is cell-extracellular matrix (ECM) interactions and their variation with the duration and magnitude of applied stretch, and present a model that can predict the degree to which stretch will either increase or decrease long-term activation levels of fibroblasts cultured within a stretched, three-dimensional collagen matrix. Combining experimental and mathematical approaches across multiple scales, we show that the viscoplasticity of the ECM regulates this nonmonotonic, long-term cell activation. Results demonstrate that feedback between cell and ECM determines how cells retain memory of mechanical stretch.

biophysics↗

bioRxiv2022

Lipid droplets are intracellular mechanical stressors in fatty hepatocytes

Matrix stiffening and external mechanical stress have been linked to disease and cancer development in multiple tissues, including the liver, where cirrhosis (which increases stiffness markedly) is the major risk factor for hepatocellular carcinoma. Patients with non-alcoholic fatty liver disease and lipid-droplet-filled hepatocytes, however, can develop cancer in non-cirrhotic, relatively soft tissue. Here, we show that lipid droplets are intracellular mechanical stressors with similar effects to tissue stiffening, including nuclear deformation, chromatin condensation, and hepatocyte dedifferentiation. Mathematical modelling of lipid droplets as inclusions that have only mechanical interactions with other cellular components generated results consistent with our experiments. These data show that lipid droplets are intracellular sources of mechanical stress and suggest that nuclear membrane tension integrates cell responses to combined internal and external stresses. Significance StatementDeformation of the nucleus as a result of extracellular sources of stress, including increased substrate stiffness, constricted migration, and compression, has been well documented to lead to increased nuclear rupture, changes in gene expression, and accumulation of DNA damage. Lipid droplet accumulation in hepatocytes provides a unique scenario to investigate potential intracellular mechanical stresses and sources of nuclear deformation. Our results show that lipid droplets are significant mechanical elements in the cell, deforming the nucleus in a way that promotes hepatocyte dedifferentiation and resisting cytoskeletal contraction and alignment.

cell biology↗

bioRxiv2022

Vimentin Intermediate Filaments Can Enhance or Abate Active Cellular Forces in a Microenvironmental Stiffness-Dependent Manner

The mechanical properties of cells are largely determined by the cytoskeleton, which is a complex network of interconnected biopolymers consisting of actin filaments, microtubules, and intermediate filaments. While disruption of the actin filament and microtubule networks is known to decrease and increase cell-generated forces, respectively, the effect of intermediate filaments on cellular forces is not well understood. Using a combination of theoretical modeling and experiments, we show that disruption of vimentin intermediate filaments can either increase or decrease cell-generated forces, depending on microenvironment stiffness, reconciling seemingly opposite results in the literature. On the one hand, vimentin is involved in the transmission of actomyosin-based tensile forces to the matrix and therefore enhances traction forces. On the other hand, vimentin reinforces microtubules and their stability under compression, thus promoting the role of microtubules in suppressing cellular traction forces. We show that the competition between these two opposing effects of vimentin is regulated by the microenvironment stiffness. For low matrix stiffness, the force-transmitting role of vimentin dominates over their microtubule-reinforcing role and therefore vimentin increases traction forces. At high matrix stiffness, vimentin decreases traction forces as the microtubule-reinforcing role of vimentin becomes more important with increasing matrix stiffness. Our theory reconciles seemingly disparate experimental observations on the role of vimentin in active cellular forces and provides a unified description of stiffness-dependent chemo-mechanical regulation of cell contractility by vimentin. SignificanceVimentin is a marker of the epithelial to mesenchymal transition which takes place during important biological processes including embryogenesis, metastasis, tumorigenesis, fibrosis, and wound healing. While the roles of the actin and microtubule networks in the transmission of cellular forces to the extracellular matrix are known, it is not clear how vimentin intermediate filaments impact cellular forces. Here, we show that vimentin impacts cellular forces in a matrix stiffness-dependent manner. Disruption of vimentin in cells on soft matrices reduces cellular forces, while it increases cellular forces in cells on stiff matrices. Given that cellular forces are central to both physiological and pathological processes, our study has broad implications for understanding the effect of vimentin on cellular forces in different microenvironments.

biophysics↗

bioRxiv2022

Tension anisotropy drives phenotypic transitions of cells via two-way cell-ECM feedback

Mechanical factors such as stress in the extracellular environment are known to affect phenotypic commitment of cells. However, the stress fields experienced by cells in tissues are multiaxial, and the ways that cells integrate this multiaxial information are largely unknown. Here, we report that the anisotropy of these stress fields is a critical factor triggering phenotypic transition in fibroblast cells, outweighing the previously reported role of stress amplitude. Using a combined experimental and computational approach, we discovered a self-reinforcing mechanism in which cellular protrusions interact with collagen fibers to develop tension anisotropy, which in turn stabilizes protrusions and amplifies their contractile forces. Disruption of this self-reinforcing process, either by reducing tension anisotropy or by inhibiting contractile protrusions, prevented phenotypic conversion of fibroblasts to contractile myofibroblasts.

biophysics↗

bioRxiv2021

An ex vivo culture model of kidney podocyte injury reveals mechanosensitive, synaptopodin-templating, sarcomere-like structures.

Chronic kidney diseases are widespread and incurable. The biophysical mechanisms underlying them are unclear, in part because material systems for reconstituting the microenvironment of the relevant kidney cells are limited. A critical question is how kidney podocytes (glomerular epithelial cells) regenerate the foot processes of the filtration apparatus following injury. Recently identified sarcomere-like structures (SLSs) with periodically spaced myosin IIA (a contractile protein) and synaptopodin (an actin-associated protein) appear in injured podocytes in vivo. We hypothesized that SLSs template synaptopodin in the initial stages of recovery, and tested this hypothesis by developing an ex vivo culture system that models both kidney physiology and pathophysiology. SLSs were observed in vitro for the first time as podocytes migrated out of harvested kidney glomeruli onto micropatterns of physiologically relevant proteins. SLSs emerged over two days, and cells formed foot process-like extensions from these periodically spaced proteins. SLS distributions and morphology were sensitive to actomyosin inhibitors, substrate stiffness, and extracellular matrix proteins associated with pathology. These results indicate a role for mechanobiological factors in podocyte recovery from injury, and suggest SLSs as a target for therapeutic intervention.

cell biology↗