Modeling the extracellular matrix in cell migration and morphogenesis: a guide for the curious biologist

Viscoelastic cell model of sorting in the dictyostelium discoideum slug

Cell sorting and differential motion are key processes in the life cycle of Dictyostelium discoideum (Dd) and many other organisms. Here we develop a mathematical model and investigate the processes with computer simulations. The slug stage of Dd is modeled with ellipsoidal cells of two types which have viscoelastic properties. Using the force-based model we find that when the two cell types have different strengths of motive forces and or different degrees of directionality one cell type sorts to the front of the slug. These findings are consistent with previously published results using a different model formation. When one cell type is more directed than the other it will consistently sort to the front of the slug. Likewise, but less efficiently, when one cell type exerts greater motive forces than the other it will sort to the front of the slug. The most efficient and robust cell sorting due to differential motion is when both methods are employed.

Bioprinting of transparent and adhesive corneal patches: Integrating photo-crosslinkable dopamine-conjugated silk fibroin and decellularized cornea matrix for sutureless tissue integration and regeneration

Corneal injuries, a leading cause of visual impairment, are traditionally addressed through tissue transplantation. However, challenges such as donor shortages, graft rejection, and complications from suturing often limit their effectiveness. Current corneal adhesives frequently fall short in both adhesion strength and biocompatibility. We present an innovative solution: a photocurable hydrogel that integrates dopamine-conjugated methacrylated silk fibroin (d-MSF) with a decellularized corneal matrix (DCM). This hydrogel combines advanced materials to create a bioadhesive system that offers superior adhesion inspired by mussel adhesion and mimics the native tissue environment. FTIR and NMR analyses confirm that our conjugation process prevents unwanted beta-sheet aggregation, ensuring both stability and transparency. The hydrogel demonstrates excellent rheological properties, including enhanced shear-thinning and impressive shear and creep recovery, making it highly suitable for extrusion-based bioprinting. We successfully bioprinted a bilayer corneal patch, featuring a concentric ring of d-MSF as the first layer, overlaid with a second layer of DCM. The implants exhibit strong tissue adhesion, with an adhesion strength of 85 ± 5.6 KPa, and Young's modulus of 0.48 ± 0.064 MPa, ensuring excellent structural integrity. This results in a highly transparent (>80 %) and functional adhesive corneal patch. This advancement offers a promising, biocompatible alternative to traditional keratoprostheses, advancing corneal repair technology.

Modeling and Optimization of Nonlinear Viscoelastic Behavior for Tissue-Engineered Blood Vessels

Vascular tissue engineering technology uses tubular viscoelastic materials as intermediaries to transmit the mechanical stimuli required for the construction of vascular grafts. However, most existing studies rely on elastic models, which fail to capture the time-dependent nature of viscoelastic materials. Moreover, the long fabrication cycles, high costs, and complex parameter measurements in tissue engineering pose significant challenges to experimental approaches. There is thus an urgent need to develop a viscoelastic mechanical model that combines physical interpretability, computational efficiency, and predictive accuracy, enabling precise characterization of material responses and unified quantification across experimental platforms. Here, we propose an error-corrected linear solid (ECLS) model with an embedded correction term to address the predictive deviations of conventional models in nonlinear viscoelastic scenarios. Instead of expanding the traditional model structure, the ECLS incorporates an error correction method that improves predictive performance while maintaining structural simplicity. Experiments were conducted on three representative viscoelastic materials-silicone rubber, polyurethane, and polytetrafluoroethylene-to acquire time-resolved response data through stress relaxation and creep tests. The fitting performance was quantitatively evaluated using the Euclidean norm and the Akaike information criterion, enabling a systematic comparison between the ECLS model and three classical models (Kelvin-Voigt, Maxwell, and standard linear solid [SLS]). The results show that the ECLS model exhibits higher predictive accuracy over a wide time range, with an average goodness of fit (R2) of 0.99, representing an improvement of ∼6% compared to the SLS model. Furthermore, the Root Mean Square Error (RMSE) and Mean Absolute Error (MAE) of the ECLS model are at least one order of magnitude lower than those of the traditional models, significantly improving the description of nonlinear viscoelastic behavior and providing more accurate predictions of material viscoelastic mechanical behavior. Therefore, the ECLS model not only improves the modeling accuracy of viscoelastic behavior but also establishes a unified and scalable framework for predicting and optimizing the mechanical performance of tissue-engineered vessels, expanding the application potential of mechanical modeling in bioreactor design and biomaterials development.

A hybrid computational model of cancer spheroid growth with ribose-induced collagen stiffening

Metastasis, the leading cause of death in cancer patients, arises when cancer cells disseminate from a primary solid tumour to distant organs. Growth and invasion of the solid tumour often involve collective cell migration, which is profoundly influenced by cell-cell interactions and the extracellular matrix (ECM). The ECM's biochemical composition and mechanical properties, such as stiffness, regulate cancer cell behaviour and migration dynamics. Mathematical modelling serves as a pivotal tool for studying and predicting these complex dynamics, with hybrid discrete-continuous models offering a powerful approach by combining agent-based representations of cells with continuum descriptions of the surrounding microenvironment. In this study, we investigate the impact of ECM stiffness, modulated via ribose-induced collagen cross-linking, on cancer spheroid growth and invasion. We employed a hybrid discrete-continuous model implemented in PhysiCell to simulate spheroid dynamics, successfully replicating three-dimensional in vitro experiments. The model incorporates detailed representations of cell-cell and cell-ECM interactions, ECM remodelling, and cell proliferation. Our simulations align with experimental observations of two breast cancer cell lines, non-invasive MCF7 and invasive HCC 1954, under varying ECM stiffness conditions. The results demonstrate that increased ECM stiffness due to ribose-induced cross-linking inhibits spheroid invasion in invasive cells, whereas non-invasive cells remain largely unaffected. Furthermore, our simulations show that higher ECM degradation by the cells not only enables spheroid growth and invasion but also facilitates the formation of multicellular protrusions. Conversely, increasing the maximum speed that cells can reach due to cell-ECM interactions enhances spheroid growth while promoting single-cell invasion. This hybrid modelling approach enhances our understanding of the interplay between cancer cell migration, proliferation, and ECM mechanical properties, paving the way for future studies incorporating additional ECM characteristics and microenvironmental conditions.

A Simple Framework for Agent-Based Modeling with Extracellular Matrix

Extracellular matrix (ECM) is a key component of the cellular microenvironment and critical in multiple disease and developmental processes. Representing ECM and cell-ECM interactions is a challenging multiscale problem as they span molecular-level details to tissue-level dynamics. While several computational frameworks exist for ECM modeling, they often focus on very detailed modeling of individual ECM fibers or represent only a single aspect of the ECM. Using the PhysiCell agent-based modeling platform, we developed a framework of intermediate detail with the ability to capture bidirectional cell-ECM interactions. We represent a small region of ECM, an ECM element, with three variables describing its local microstructure: anisotropy, density, and overall fiber orientation. To spatially model the ECM, we use an array of ECM elements. Cells remodel local ECM microstructure and in turn, local microstructure impacts cellular motility. We demonstrate the utility of this framework and reusability of its core cell-ECM interaction model through examples in cellular invasion, wound healing, basement membrane degradation, and leader-follower collective migration. Despite the relative simplicity of the framework, it is able to capture a broad range of cell-ECM interactions of interest to the modeling community. Furthermore, variables representing the ECM microstructure are accessible through simple programming interfaces. This allows them to impact cell behaviors, such as proliferation and death, without requiring custom code for each interaction, particularly through PhysiCell's modeling grammar, enabling rapid modeling of a diverse range of cell-matrix biology. We make this framework available as a free and open source software package at https://github.com/PhysiCell-Models/collective-invasion .

Collective Transitions from Orbiting to Matrix Invasion in 3D Multicellular Spheroids

Coordinated cell rotation along a curved matrix interface can sculpt epithelial tissues into spherical morphologies. Subsequently, radially-oriented invasion of multicellular strands or branches can occur by local remodeling of the confining matrix. These symmetry-breaking transitions emerge from the dynamic reciprocity between cells and matrix, but remain poorly understood. Here, we show that epithelial cell spheroids collectively transition from circumferential orbiting to radial invasion via bi-directional interactions with the surrounding matrix curvature. Initially, spheroids exhibit an ellipsoidal shape but become rounded as orbiting occurs. However, cells gradually reorient from coordinated rotation towards outward strand invasion due to the accumulation of contractile tractions at discrete sites. Remarkably, the initial ellipsoid morphology predicts subsequent invasion of 2-4 strands roughly aligned with the major axis. We then perturb collective migration using osmotic pressure, showing that orbiting can be arrested and invasion can be reversed. We also investigate coordinated orbiting in "mosaic" spheroids, showing a small fraction of "leader" cells with weakened cell-cell adhesions can impede collective orbiting but still invade into the matrix. Finally, we establish a minimal self-propelled particle model to elucidate how collective orbiting is mediated by the crosstalk of cell-cell and cell-matrix adhesion along a curved boundary. Altogether, this work elucidates how tissue morphogenesis is governed by the interplay of collective behaviors and the local curvature of the cell-matrix, with relevance for embryonic development and tumor progression.

Mechanical signatures in cancer metastasis

The cancer metastatic cascade includes a series of mechanical barrier-crossing events, involving the physical movement of cancer cells from their primary location to a distant organ. This review describes the physical changes that influence tumour proliferation, progression, and metastasis. We identify potential mechanical signatures at every step of the metastatic cascade and discuss some latest mechanobiology-based therapeutic interventions to highlight the importance of interdisciplinary approaches in cancer diagnosis and treatment.

How cells align to structured collagen fibrils: a hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions

Many mammalian cells, including endothelial cells and fibroblasts, align and elongate along the orientation of extracellular matrix (ECM) fibers in a gel when cultured in vitro. During cell elongation, clusters of focal adhesions (FAs) form near the poles of the elongating cells. FAs are mechanosensitive clusters of adhesions that grow under mechanical tension exerted by the cells' pulling on the ECM and shrink when the tension is released. In this study, we use mathematical modeling to study the hypothesis that mechanical reciprocity between cells and the ECM is sufficient for directing cell shape changes and orientation. We show that FAs are preferentially stabilized along the orientation of ECM fibers, where cells can generate higher tension than in directions perpendicular to the ECM fibers. We present a hybrid computational model coupling three mathematical approaches: first, the cellular Potts model (CPM) describes an individual contractile cell; second, molecular dynamics (MD) represent the ECM as a network of cross-linked, deformable fibers; third, a set of ordinary differential equations (ODEs) describes the dynamics of the cell's FAs, in terms of a balance between assembly and a mechanoresponsive disassembly. The resulting computational model shows that mechanical reciprocity suffices for stiffness-dependent cell spreading, local ECM remodeling, and ECM-alignment-dependent cell elongation. These combined effects are sufficient to explain how cell morphology is influenced by the local ECM structure and mechanics.

Dynamic duo: Cell-extracellular matrix interactions in hair follicle development and regeneration

Ectodermal organs, such as hair follicles, originate from simple epithelial and mesenchymal sheets through a complex developmental process driven by interactions between these cell types. This process involves dermal condensation, placode formation, bud morphogenesis, and organogenesis, and all of these processes require intricate interactions among various tissues. Recent research has emphasized the crucial role of reciprocal and dynamic interactions between cells and the extracellular matrix (ECM), referred to as the "dynamic duo", in the development of ectodermal organs. These interactions provide spatially and temporally changing biophysical and biochemical cues within tissues. Using the hair follicle as an example, this review highlights two types of cell-ECM adhesion units-focal adhesion-type and hemidesmosome-type adhesion units-that facilitate communication between epithelial and mesenchymal cells. This review further explores how these adhesion units, along with other cell-ECM interactions, evolve during hair follicle development and regeneration, underscoring their importance in guiding both developmental and regenerative processes.

The next revolution in computational simulations: Harnessing AI and quantum computing in molecular dynamics

The integration of artificial intelligence, machine learning and quantum computing into molecular dynamics simulations is catalyzing a revolution in computational biology, improving the accuracy and efficiency of simulations. This review describes the advancements and applications of these technologies to process vast molecular dynamics simulation datasets, adapt parameters of simulations and gain insight into complex biological processes. These advances include the use of predictive force fields, adaptive algorithms and quantum-assisted methodologies. While the integration of artificial intelligence and quantum computing with MD simulations provides insightful and stimulating improvements to our understanding of molecular mechanisms, it could introduce new issues related to data quality, interpretability of models and computational complexity. Modern multidisciplinary approaches are needed to navigate these challenges and exploit the potential of these emerging technologies for MD simulations of biomolecular systems.

The cellular Potts model on disordered lattices

The cellular Potts model, also known as the Glazier-Graner-Hogeweg model, is a lattice-based approach by which biological tissues at the level of individual cells can be numerically studied. Traditionally, a square or hexagonal underlying lattice structure is assumed for two-dimensional systems, and this is known to introduce artifacts in the structure and dynamics of the model tissues. That is, on regular lattices, cells can assume shapes that are dictated by the symmetries of the underlying lattice. Here, we developed a variant of this method that can be applied to a broad class of (ir)regular lattices. We show that on an irregular lattice deriving from a fluid-like configuration, two types of artifacts can be removed. We further report on the transition between a fluid-like disordered and a solid-like hexagonally ordered phase present for monodisperse confluent cells as a function of their surface tension. This transition shows the hallmarks of a first-order phase transition and is different from the glass/jamming transitions commonly reported for the vertex and active Voronoi models. We emphasize this by analyzing the distribution of shape parameters found in our state space. Our analysis provides a useful reference for the future study of epithelia using the (ir)regular cellular Potts model.

PhysiMeSS - a new physiCell addon for extracellular matrix modelling

The extracellular matrix, composed of macromolecules like collagen fibres, provides structural support to cells and acts as a barrier that metastatic cells degrade to spread beyond the primary tumour. While agent-based frameworks, such as PhysiCell, can simulate the spatial dynamics of tumour evolution, they only implement cells as circles (2D) or spheres (3D). To model the extracellular matrix as a network of fibres, we require a new type of agent represented by line segments (2D) or cylinders (3D). Here, we present PhysiMeSS, an addon of PhysiCell, introducing a new agent type to describe fibres and their physical interactions with cells and other fibres. PhysiMeSS implementation is available at https://github.com/PhysiMeSS/PhysiMeSS and in the official PhysiCell repository. We provide examples describing the possibilities of this framework. This tool may help tackle important biological questions, such as diseases linked to dysregulation of the extracellular matrix or the processes leading to cancer metastasis.

Spatial interactions modulate tumor growth and immune infiltration

Direct observation of tumor-immune interactions is unlikely in tumors with currently available technology, but computational simulations based on clinical data can provide insight to test hypotheses. It is hypothesized that patterns of collagen evolve as a mechanism of immune escape, but the exact nature of immune-collagen interactions is poorly understood. Spatial data quantifying collagen fiber alignment in squamous cell carcinomas indicates that late-stage disease is associated with highly aligned fibers. Our computational modeling framework discriminates between two hypotheses: immune cell migration that moves (1) parallel or (2) perpendicular to collagen fiber orientation. The modeling recapitulates immune-extracellular matrix interactions where collagen patterns provide immune protection, leading to an emergent inverse relationship between disease stage and immune coverage. Here, computational modeling provides important mechanistic insights by defining a kernel cell-cell interaction function that considers a spectrum of local (cell-scale) to global (tumor-scale) spatial interactions. Short-range interaction kernels provide a mechanism for tumor cell survival under conditions with strong Allee effects, while asymmetric tumor-immune interaction kernels lead to poor immune response. Thus, the length scale of tumor-immune interaction kernels drives tumor growth and infiltration.

Two Decades of Advances and Limitations in Organ Recellularization

The recellularization of tissues after decellularization is a relatively new technology in the field of tissue engineering (TE). Decellularization involves removing cells from a tissue or organ, leaving only the extracellular matrix (ECM). This can then be recellularized with new cells to create functional tissues or organs. The first significant mention of recellularization in decellularized tissues can be traced to research conducted in the early 2000s. One of the landmark studies in this field was published in 2008 by Ott, where researchers demonstrated the recellularization of a decellularized rat heart with cardiac cells, resulting in a functional organ capable of contraction. Since then, other important studies have been published. These studies paved the way for the widespread application of recellularization in TE, demonstrating the potential of decellularized ECM to serve as a scaffold for regenerating functional tissues. Thus, although the concept of recellularization was initially explored in previous decades, these studies from the 2000s marked a major turning point in the development and practical application of the technology for the recellularization of decellularized tissues. The article reviews the historical advances and limitations in organ recellularization in TE over the last two decades.

Fission yeast Bgs1 glucan synthase participates in the control of growth polarity and membrane traffic

Rod-shaped fission yeast grows through cell wall expansion at poles and septum, synthesized by essential glucan synthases. Bgs1 synthesizes the linear β(1,3)glucan of primary septum at cytokinesis. Linear β(1,3)glucan is also present in the wall poles, suggesting additional Bgs1 roles in growth polarity. Our study reveals an essential collaboration between Bgs1 and Tea1-Tea4, but not other polarity factors, in controlling growth polarity. Simultaneous absence of Bgs1 function and Tea1-Tea4 causes complete loss of growth polarity, spread of other glucan synthases, and spherical cell formation, indicating this defect is specifically due to linear β(1,3)glucan absence. Furthermore, linear β(1,3)glucan absence induces actin patches delocalization and sterols spread, which are ultimately responsible for the growth polarity loss without Tea1-Tea4. This suggests strong similarities in Bgs1 functions controlling actin structures during cytokinesis and polarized growth. Collectively, our findings unveil that cell wall β(1,3)glucan regulates polarized growth, like the equivalent extracellular matrix in neuronal cells.

Tendon extracellular-matrix-derived tissue engineering micro-tissue for Achilles tendon injury regeneration in rats

BACKGROUND

Achilles tendon is vital in maintaining the stability and function of ankle joint. It is quite difficult to achieve the structural and functional repair of Achilles tendon in tissue engineering.

METHODS

A tissue-engineered tendon micro-tissue was prepared using rat tail tendon extracellular matrix (TECM) combined with rat adipose stem cells (ADSCs) to repair Achilles tendon injuries. The TECM was prepared by repeated freezing and thawing. The in vitro characteristics of TECM and its effect on ADSCs proliferation were detected. This tissue-engineered tendon micro-tissue for Achilles tendon repair in vivo was evaluated based on general characteristics, gait analysis, ultrasound findings, histological analysis, and biomechanical testing.

RESULTS

The results showed that the TECM scaffold had good biocompatibility for ADSCs. At 2 weeks post-surgery, collagen types I and III and tenomodulin expression were higher, and vascular endothelial growth factor expression was lower in the micro-tissue group than other groups. At 4 and 8 weeks post-surgery, the results of histological analysis and ultrasound findings showed that the repaired tendon tissue was smooth and lustrous, and was arranged regularly and evenly in the micro-tissue group. Gait analysis confirmed that better motor function recovery was noted in micro-tissue group than other groups. In addition, the mechanical properties of the repaired tendon tissue in micro-tissue group were better than other groups.

CONCLUSION

Tissue-engineered tendon micro-tissue fabricated by TECM and ADSCs has good biocompatibility and can promote structural and functional repair of tendon in vivo. This composite biomaterial has broad application prospects in tissue engineering.

A Review of Advances in Molecular Imaging of Rheumatoid Arthritis: From In Vitro to Clinic Applications Using Radiolabeled Targeting Vectors with Technetium-99m

Rheumatoid arthritis (RA) is a systemic autoimmune disorder caused by inflammation of cartilaginous diarthrodial joints that destroys joints and cartilage, resulting in synovitis and pannus formation. Timely detection and effective management of RA are pivotal for mitigating inflammatory arthritis consequences, potentially influencing disease progression. Nuclear medicine using radiolabeled targeted vectors presents a promising avenue for RA diagnosis and response to treatment assessment. Radiopharmaceutical such as technetium-99m (99mTc), combined with single photon emission computed tomography (SPECT) combined with CT (SPECT/CT), introduces a more refined diagnostic approach, enhancing accuracy through precise anatomical localization, representing a notable advancement in hybrid molecular imaging for RA evaluation. This comprehensive review discusses existing research, encompassing in vitro, in vivo, and clinical studies to explore the application of 99mTc radiolabeled targeting vectors with SPECT imaging for RA diagnosis. The purpose of this review is to highlight the potential of this strategy to enhance patient outcomes by improving the early detection and management of RA.

Preparation and evaluation of decellularized epineurium as an anti-adhesive biofilm in peripheral nerve repair

Following peripheral nerve anastomosis, the anastomotic site is prone to adhesions with surrounding tissues, consequently impacting the effectiveness of nerve repair. This study explores the development and efficacy of a decellularized epineurium as an anti-adhesive biofilm in peripheral nerve repair. Firstly, the entire epineurium was extracted from fresh porcine sciatic nerves, followed by a decellularization process. The decellularization efficiency was then thoroughly assessed. Subsequently, the decellularized epineurium underwent proteomic analysis to determine the remaining bioactive components. To ensure biosafety, the decellularized epineurium underwent cytotoxicity assays, hemolysis tests, cell affinity assays, and assessments of the immune response following subcutaneous implantation. Finally, the functionality of the biofilm was determined using a sciatic nerve transection and anastomosis model in rats. The result indicated that the decellularization process effectively removed cellular components from the epineurium while preserving a number of bioactive molecules, and this decellularized epineurium was effective in preventing adhesion while promoting nerve repairment and functional recovery. In conclusion, the decellularized epineurium represents a novel and promising anti-adhesion biofilm for enhancing surgical outcomes of peripheral nerve repair.

Evaluation of Vasculogenic Factors in the Developing Embryo at Weeks Five and Seven With a Special Focus on CD133 and TIE2 Markers

Background Human embryo vasculogenesis (blood vessel development starting from endothelial precursors) includes the ability of mesenchymal cells and pluripotent stem cells to differentiate into endothelial cells. Quantification of endothelial progenitor cells is difficult to assess during the early steps of human embryo development due to several factors, especially due to the paucity of human embryo tissue which is usually discarded after early-stage pregnancy abortive methods. CD133 (Promimin-1) is a general marker of progenitor cells, but combined with other endothelial markers such as CD34, it may identify endothelial progenitor cells during embryonic development. CD34 immunohistochemistry was previously performed by our team to identify human embryo capillaries and comparatively assess microvessel density between different human embryonic tissues. TIE2 is an angiopoietin receptor strongly involved in the newly formed blood vessel maturation due to its expression in some mesenchymal precursors for future pericytes. CD34 assesses the presence of endothelial cells but its single use does not evaluate the endothelial progenitor state as CD133 may do nor vessel maturation as TIE2 may do. Data about the dynamics of CD133/TIE2 expression in the early stages of human embryo development are scarce. Hence, in this study, we aimed to comparatively assess the dynamic of CD133+ endothelial precursors and TIE2 expression on five and seven-week-old human embryonic tissues with a special emphasis on their expression on embryonic vascular beds. Methodology CD133 and TIE2 immunohistochemistry was performed on five and seven-week-old human embryonic tissues followed by their quantification using the Qu Path digital image analysis (DIA) automated method. Results CD133 and TIE2 showed divergent patterns of expression during the initial phases of human embryonic development, specifically in the vascular endothelium of tiny capillaries. The expression of CD133 in endothelial cells lining the perfused lumen gradually decreased from five to seven-week-old embryos. It remained expressed with greater intensity in cells located at the tip of the vascular bud that emerged into pre-existing capillaries. TIE2 was much more specific than CD133, being restricted to the level of the vascular endothelium; therefore, it was easier to quantify using digital image analysis. The endothelium of the embryonic aorta was an exception to the divergent expression, as CD133 and TIE2 were consistently co-expressed in the seven-week-old embryo. The Qu Path DIA assessment increased the accuracy of CD133 and TIE2 evaluation, being the first time they were quantified by using automated software and not manually. Conclusions High heterogeneity of CD133 and TIE2 was observed between five and seven-week-old embryonic tissues as well as between different embryonic regions from the same gestational age. The unique finding of CD133/TIE2 co-expression persistence inside aortic endothelium needs further studies to elucidate the role of this co-expression.