Biology subjects

Barakat, A. I.

Publications and source records attributed to Barakat, A. I..

13 recordsLinked to original sources

bioRxiv2026

Collagen-based bilayered biomimetic tubular materials for vascular and airway applications

Biomimetic tubular scaffolds hold great promise for tackling unmet clinical needs thanks to their biocompatibility and recapitulation of cellular microenvironments, conferring the ability to promote regeneration. Potential applications include small-diameter vascular implants and grafts for airway repair, for which no viable off-the-shelf solutions currently exist. The tubular materials (4 and 8 mm internal and external diameters) presented here consist purely of type I collagen, contain no chemical crosslinkers, and reproduce the multi-scale architecture of the native tissue including the presence of collagen fibrils. A novel two-step protocol provides materials with distinct concentric layers. A porous external structure, obtained by means of ice templating combined with collagen topotactic fibrillogenesis, favours oriented cell colonization. A smooth and much less porous internal layer provides mechanical and water-tightness properties relevant for in vivo implantation and promotes the formation of an endothelial monolayer under both static and flow conditions. The compliance of the double-layered materials under physiological pressure is close to that of piglet carotid arteries. The materials are also determined to be sufficiently flexible to provide the ability to perform ex vivo anastomosis with bronchi, although the relatively low value of suture retention strength remains a limitation for in vivo suturing.

bioengineering↗

bioRxiv2025

A nematic framework for sprouting angiogenesis

Sprouting angiogenesis is critical for embryogenesis, wound healing, and tumor growth. Here we show that the liquid crystal framework, which has recently been leveraged to study various morphogenetic events, provides unique insight into angiogenic sprouting. In response to vascular endothelial growth factor, a potent pro-angiogenic factor, endothelial cells cultured on the surfaces of soft collagen hydrogels form elongated cell streams that coexist with more polygonal cell regions. Angiogenic sprouting initiates preferentially at cell stream tips, where nematic order gradients are most pronounced. We demonstrate that cell streams are associated with large traction forces that lead to 3D deformations of the underlying hydrogel and that stream formation results from a delicate balance between microtubule polymerization and actomyosin contractility. Finally, we show that active control of nematic order allows modulation of sprout formation, highlighting the key role of EC orientation gradients in angiogenic sprouting and paving the way for new therapeutic avenues. TeaserA nematic perspective reveals that sprouting angiogenesis correlates with elevated gradients in endothelial cell orientation.

biophysics↗

bioRxiv2025

Adaptation of endothelial cells to microenvironment topographical cues through lysyl oxidase like-2-mediated basement membrane scaffolding

Basement membrane (BM) provides structural support and signaling platform for blood vessels. While its major structural components are required for vascular morphogenesis, integrating BM regulators, like the lysyl oxidase LOXL2, and BM assembly in cell response to microenvironement cues remain poorly understood. Here we study the early deposition and supramolecular assembly of BM components using correlative atomic force and fluorescence microscopy. The fibrillar deposition of fibronectin is gradually remodeled and associates with the collagen IV meshwork as it organizes into BM. We demonstrate that LOXL2 is deposited with both proteins and participates in their remodeling. Alteration of BM scaffolding by LOXL2-depletion affects focal adhesion maturation and cytoskeleton remodeling. This altered BM organization maintains stress fibers, affects the distribution and activation of mechanosensors and alters cell barrier properties. Furthermore, using 3D micro-printed substrates, we demonstrate that BM assembly regulates endothelial cell response to topographical constraint. We therefore propose a mechanism directly linking the scaffolding of BM components and adaptation to the topographical signals from the microenvironment.

cell biology↗

bioRxiv2025

A Morphodynamic Network Model to Describe Cell Organization and Nematic Ordering in Monolayers

To robustly model nematic ordering in cell monolayers, it is crucial to accurately capture cell geometries, which in turn direct the formation of patterns in cell alignment. In this regard, existing agent-based models (ABMs), such as vertex and Voronoi models, lack generality. Current models often fail to accommodate complex cell geometries (such as elongated or non-convex cells) or implement thermodynamically well-posed rules for cell rearrangements. These features are essential for describing the biophysics of morphogenetic processes where irregular cell shapes and dynamic cell rearrangements play central roles. To address the limitations of existing models, we present a novel computational framework, termed the morphodynamic network model (MNM), for simulating confluent cell monolayers. The MNM is a cell center-based ABM in which the cell centers (nodes) are connected to form a dynamic triangulation (network). The node positions and network structure, recording connections between neighboring cells, evolve according to a split-step approach. First, node positions are updated with the network structure (or topology) fixed, then the network topology is updated with node positions fixed. We apply the MNM to study the morphodynamic behavior of cell monolayers, including fluidization, elasto-visco-plastic responses, nematic ordering, and substrate-induced cell alignment. The MNM is designed to capture complex behaviors and morphologies, offering a flexible and robust tool for studying multicellular phenomena.

biophysics↗

bioRxiv2024

A Variational Autoencoder Model for Clustering of Cell Nuclei on Microgroove Substrates: Potential for Disease Diagnosis

Various diseases including laminopathies and certain types of cancer are associated with abnormal nuclear mechanical properties that influence cellular and nuclear deformations in complex environments. Recently, microgroove substrates designed to mimic the anisotropic topography of the basement membrane have been shown to induce significant 3D nuclear deformations in various adherent cell types. Importantly, these deformations are different in myoblast cells derived from laminopathy patients from those in cells derived from normal individuals. Here we assess the ability of a variational autoencoder (VAE) and a Gaussian Mixture Model (GMM) to cluster patches of nuclei of both wildtype myoblast cells and myoblast cells with laminopathy-associated mutations cultured on microgroove substrates, and we explore the impact of image processing parameters on clustering performance. We show that a standard VAE with GMM is able to cluster nuclei based on their morphologies and degrees of deformations and that these clusters correspond to either wildtype myoblasts or myoblasts with LMNA mutations. The current results suggest that combining deep learning techniques with microgroove substrates enables automatic classification of nuclear deformations and thus provides a promising approach for easy and rapid diagnosis of pathologies that involve abnormalities in nuclear deformation.

cell biology↗

bioRxiv2024

Interplay of actin nematodynamics and anisotropic tension controls endothelial mechanics

Blood vessels expand and contract actively, while continuously experiencing dynamic external stresses from the blood flow. The mechanical response of the vessel wall is that of a composite material: its mechanical properties depend on a diverse set of cellular mechanical components, which change dynamically as cells respond to external stress. Mapping the relationship between these underlying cellular processes and emergent tissue mechanics is an on-going challenge, in particular in endothelial cells. Here we use a microstretcher mimicking the native environment of blood vessels to assess both the mechanics and cellular dynamics of an endothelial tube in response to a physiological increase in luminal pressure. The characterization of the instantaneous monolayer elasticity reveals a strain-stiffening, actin-dependent and substrate-responsive behavior. In response to a maintained pressure increase, the tissue displays a fluid-like expansion, accompanied by the reorientation of cell shape and of actin fibers. This actin-driven reorientation depends on focal adhesions and adherens junctions, two key mechanosensors. We introduce a mechanical model coupling actin fiber nematodynamics with active and elastic tension generation by actin fibers in the endothelium, which recapitulates the response to pressure of endothelial tubes.

biophysics↗

bioRxiv2024

Microgroove substrates unveil topography-driven, dynamic 3D nuclear deformations

Navigating complex extracellular environments requires extensive deformation of cells and their nuclei. Nuclear deformations are intricately linked to nuclear structure and mechanical properties, and abnormalities in nuclear mechanics contribute to various diseases including laminopathies and cancer. Most in vitro systems used to study nuclear deformations are typically designed to generate strong whole-cell confinement relevant for specific cell types such as immune or cancer cells. Here, we use microgroove substrates as a model of anisotropic basement membrane topography and we report that adherent cells including endothelial cells and myoblasts exhibit significant 3D (in-plane and out-of-plane) nuclear deformations, with partial to complete penetration into the microgrooves. These deformations are dynamic with nuclei cyclically entering and exiting the microgrooves. AFM measurements show that these deformation cycles are accompanied by transient changes in nuclear mechanical properties. We also show that nuclear penetration into the grooves is principally driven by cell-substrate adhesion, without the need for cytoskeleton-associated forces. Finally, we demonstrate that myoblasts from patients with LMNA mutations exhibit abnormal nuclear deformations which can be rapidly identified and quantified using automated image analysis. We therefore propose the use of microgrooves as a novel simple, tunable, and high throughput system to study nuclear deformations in adherent cells, with the potential to serve as a functional diagnostic platform for pathological alterations in nuclear mechanics.

cell biology↗

bioRxiv2023

A computational model of chemically and mechanically induced platelet plug formation

ObjectivesThrombotic deposition is a major consideration in the development of implantable cardiovascular devices. Recently, it has been experimentally demonstrated that localized changes in the blood shear rate -i.e. shear gradients-play a critical role in thrombogenesis. The goal of the present work is to develop a predictive computational model of platelet plug formation that can be used to assess the thrombotic burden of cardiovascular devices, introducing for the first time the role of shear gradients. We have developed a comprehensive model of platelet-mediated thrombogenesis which includes platelet transport in the blood flow, platelet activation and aggregation induced by both biochemical and mechanical factors, kinetics and mechanics of platelet adhesion, and changes in the local fluid dynamics due to the thrombus growth. MethodsA 2D computational model was developed using the multi-physics finite element solver COMSOL 5.6. The model can be described by a coupled set of convection-diffusion-reaction equations. Platelet adhesion at the surface was modeled via flux boundary conditions. Using a moving mesh for the surface, thrombus growth and consequent alterations in blood flow were modeled. In the case of a stenosis, the notions of shear stress induced platelet activation in the contraction zone and shear gradients induced platelet deposition in the expansion zone downstream of the stenosis were studied. ResultsThe model provides the spatial and temporal evolution of platelet plug in the flow field. The computed platelet plug size evolution was validated against literature data. The results confirm the importance of considering both mechanical and chemical aggregation of platelets. ConclusionsThe developed model represents a potentially useful tool for the optimization of the design of the cardiovascular device flow path.

bioengineering↗

bioRxiv2022

Distinct contact guidance mechanisms in single endothelial cells and in monolayers

In many tissues, cell shape and orientation are controlled by a combination of internal and external biophysical cues. Anisotropic substrate topography is a ubiquitous cue that leads to cellular elongation and alignment, a process termed contact guidance, whose underlying mechanisms remain incompletely understood. Additionally, whether contact guidance responses are similar in single cells and in cellular monolayers is unknown. Here, we address these questions in vascular endothelial cells (ECs) that in vivo form a monolayer that lines blood vessels. Culturing single ECs on microgrooved substrates that constitute an idealized mimic of anisotropic basement membrane topography elicits a strong, groove depth-dependent contact guidance response. Interestingly, this response is greatly attenuated in confluent monolayers. While contact guidance in single cells is principally driven by persistence bias of cell protrusions in the direction of the grooves and is surprisingly insensitive to actin stress fiber disruption, cell shape and alignment in dense EC monolayers are driven by the organization of the basement membrane secreted by the cells, which leads to a loss of interaction with the microgrooves. The findings of distinct contact guidance mechanisms in single ECs and in EC monolayers promise to inform strategies aimed at designing topographically patterned endovascular devices.

cell biology↗

bioRxiv2022

PPP2R1A Regulates Migration Persistence through the WAVE Shell Complex

The RAC1-WAVE-Arp2/3 signaling pathway generates branched actin networks that power lamellipodium protrusion of migrating cells. Feedback is thought to control protrusion lifetime and migration persistence, but its molecular circuitry remains elusive. Using proteomics, we identified PPP2R1A among proteins differentially associated with the WAVE complex subunit ABI1 when RAC1 was activated and downstream generation of branched actin was blocked. PPP2R1A was found to associate at the lamellipodial edge with a novel form of WAVE complex, the WAVE Shell Complex (WSC), that contains NHSL1 instead of the Arp2/3 activating subunit WAVE as in the canonical WAVE Regulatory Complex (WRC). PPP2R1A was required for persistence in random and directed migration assays and for RAC1-dependent actin polymerization in cell extracts. PPP2R1A requirement was abolished by NHSL1 depletion. PPP2R1A mutations found in tumors impaired WSC binding and migration regulation, suggesting that this novel function of PPP2R1A is critical for its tumor suppressor activity.

cell biology↗

bioRxiv2021

Topography-induced large-scale anti-parallel collective migration in vascular endothelium

Collective migration of vascular endothelial cells is central for embryonic development, angiogenesis, and wound closure. Although physical confinement of cell assemblies has been shown to elicit specific patterns of collective movement in various cell types, endothelial migration in vivo often occurs without confinement. Here we show that unconfined endothelial cell monolayers on microgrooved substrates that mimic the anisotropic organization of the extracellular matrix exhibit a new type of collective movement that takes the form of a periodic pattern of anti-parallel cell streams. We further establish that the development of these streams requires intact cell-cell junctions and that stream sizes are particularly sensitive to groove depth. Finally, we show that modeling the endothelial cell sheet as an active fluid with the microgrooves acting as constraints on cell orientation predicts the occurrence of the periodic anti-parallel cell streams as well as their lengths and widths. We posit that in unconfined cell assemblies, physical factors that constrain or bias cellular orientation such as anisotropic extracellular matrix cues or directed flow-derived shear forces dictate the pattern of collective cell movement.

biophysics↗

bioRxiv2021

Luminal Flow Actuation Generates Coupled Shear and Strain in a Microvessel-on-Chip

In the microvasculature, blood flow-derived forces are key regulators of vascular structure and function. Consequently, the development of hydrogel-based microvessel-on-chip systems that strive to mimic the in vivo cellular organization and mechanical environment has received great attention in recent years. However, despite intensive efforts, current microvessel- on-chip systems suffer from several limitations, most notably failure to produce physiologically relevant wall strain levels. In this study, a novel microvessel-on-chip based on the templating technique and using luminal flow actuation to generate physiologically relevant levels of wall shear stress and circumferential stretch is presented. Normal forces induced by the luminal pressure compress the surrounding soft collagen hydrogel, dilate the channel, and create large circumferential strain. The fluid pressure gradient in the system drives flow forward and generates realistic pulsatile wall shear stresses. Rigorous characterization of the system reveals the crucial role played by the poroelastic behavior of the hydrogel in determining the magnitudes of the wall shear stress and strain. The experimental measurements are combined with an analytical model of flow in both the lumen and the porous hydrogel to provide an exceptionally versatile user manual for an application-based choice of parameters in microvessels-on-chip. This unique strategy of flow actuation adds a dimension to the capabilities of microvessel-on-chip systems and provides a more general framework for improving hydrogel-based in vitro engineered platforms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/439271v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1a4fed5org.highwire.dtl.DTLVardef@15680f4org.highwire.dtl.DTLVardef@2c2a6dorg.highwire.dtl.DTLVardef@1955f52_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2019

Single-cell immuno-mechanics: rapid viscoelastic changes are a hallmark of early leukocyte activation.

To accomplish their critical task of removing infected cells and fighting pathogens, leukocytes activate by forming specialized interfaces with other cells. Using an innovative micropipette rheometer, we show in three different cell types that when stimulated by microbeads mimicking target cells, leukocytes become up to ten times stiffer and more viscous. These mechanical changes initiate within seconds after contact and evolve rapidly over minutes. Remarkably, leukocyte elastic and viscous properties evolve in parallel, preserving a well-defined ratio that constitutes a mechanical signature specific to each cell type. The current results indicate that simultaneously tracking both elastic and viscous properties during an active cell process provides a new way to investigate cell mechanical processes. Our findings also suggest that dynamic immuno-mechanical measurements provide an identifier of leukocyte type and an indicator of the cells state of activation.

biophysics↗