bims-ecemfi Biomed News
on ECM and fibroblasts
Issue of 2025–07–20
seventeen papers selected by
Badri Narayanan Narasimhan, University of California, San Diego



  1. bioRxiv. 2025 May 15. pii: 2025.05.15.654321. [Epub ahead of print]
      Cells sense and respond to their environment in a myriad of ways. In many instances they must integrate simultaneous cues ranging from the physical properties and composition of the extracellular matrix to guidance cues that stimulate chemotaxis or haptotaxis. How cells make sense of multiple simultaneous cues is an ongoing physiologically relevant question. The present study seeks to contribute to the understanding of multi-cue sensing by understanding how the transition to a confined setting with or without an added haptotactic gradient alters macrophage migration. We found that the transition to confinement is itself a directional cue capable of driving persistent migration hours after macrophages enter the confined environment. Next, we found that a haptotactic fibronectin gradient made cells even more directionally persistent under confinement. Finally, Arp2/3 complex deletion rendered macrophages unresponsive to the haptotactic gradient, but they retained directionally persistent migration due to their transition to confinement. These findings may be particularly relevant for cells that move from an adherent 2D environment into a confining 3D environment, like leukocytes and circulating tumor cells that extravasate into peripheral tissue.
    Summary Statement: Macrophages migrate persistently after they transition from 2D adhesion to an adhesive confined environment. Migration is enhanced further if cells sense a fibronectin gradient. This may have relevance to immune and cancer cell behavior.
    DOI:  https://doi.org/10.1101/2025.05.15.654321
  2. bioRxiv. 2025 Jun 09. pii: 2025.06.06.658326. [Epub ahead of print]
      Polymeric hydrogels are valuable platforms for determining how specific mechanical properties of native tissue extracellular matrix (ECM) regulate cell function. Recent research has focused on incorporating viscous and elastic properties into hydrogels to investigate cellular responses to time-dependent mechanical properties of the ECM. However, a critical aspect often overlooked is that cells continuously remodel their microenvironment in hydrogels, such as by the deposition of newly secreted (nascent) ECM. While this nascent ECM has been demonstrated to play a vital role in transmitting mechanical signals across various biological contexts, the mechanisms by which it regulates cellular function in response to time-dependent mechanical properties remain poorly understood. In this study, we developed an interpenetrating polymer network that enables independent control of viscous and elastic hydrogel properties. We show that cells cultured on high-viscosity hydrogels deposit increased nascent ECM which also correlates with enhanced hydrogel remodeling. Interestingly, higher nascent ECM deposition on high-viscosity hydrogels was decoupled from intracellular contractility. These results establish a relationship between hydrogel viscosity and nascent ECM deposition that may extend to diverse cell types and offer new insights into cell-hydrogel interactions.
    DOI:  https://doi.org/10.1101/2025.06.06.658326
  3. bioRxiv. 2025 May 11. pii: 2025.05.09.653153. [Epub ahead of print]
      Cells sense the mechanical properties of their environment through physical engagement and spreading, with high stiffness driving nuclear translocation of the mechanosensitive transcription factor YAP. Restriction of cell spread area or environmental stiffness both inhibit YAP activation and nuclear translocation. The Arp2/3 complex plays a critical role in polymerization of branched actin networks that drive cell spreading, protrusion, and migration. While YAP activation has been closely linked to cellular spreading, the specific role of actin branching in force buildup and YAP activation is unclear. To assess the role of actin branching in this process, we measured cell spreading, YAP nuclear translocation, force on the adhesion adaptor protein Talin (FRET tension sensor), and extracellular forces (traction force microscopy, TFM) in 3T3 cells with and without inhibition of actin branching. The results indicate that YAP activation still occurs when actin branching and cell spreading is reduced. Interestingly, while actin de-branching resulted in decreased force on talin, relatively little change in average traction stress was observed, highlighting the distinct difference between molecular level and cellular level force regulation of YAP. While cell spreading is a driver of YAP nuclear translocation, this is likely through indirect effects. Changes in cell spreading induced by actin branching inhibition do not significantly perturb YAP activation. Additionally, this work provides evidence that focal adhesion molecular forces are not a direct regulator of YAP activation.
    DOI:  https://doi.org/10.1101/2025.05.09.653153
  4. bioRxiv. 2025 Jun 24. pii: 2025.06.18.660409. [Epub ahead of print]
      Human induced pluripotent stem cells (hiPSCs) offer patient-specific and immune-evasive sources for generating diverse cell types; yet lack of vascularization in hiPSC-derived tissues remains a major limitation for both therapeutic applications and disease modeling. Elucidating the mechanisms underlying vascular network formation in hiPSC-derived cells is therefore imperative. We and others have previously demonstrated that hiPSC-derived endothelial progenitor cells (hiPSC-EPs) self-assemble into lumenized microvascular networks when cultured in 3D norbornene-functionalized hyaluronic acid-based hydrogels. Herein we investigated the early period of culturing to characterize contractility of hiPSC-EPs. We hypothesized that multi-cell cooperativity would increase over time and would be dependent on the original hydrogel storage modulus. To quantify cellular contractility either 4 or 7 days after en-capsulation, 3D kinematic analysis was performed on single and small multi-cell clusters of hiPSC-EPs embedded in NorHA-based hydrogels. Contractile responses were significantly and non-linearly influenced by multicellularity, culture duration, and hydrogel stiffness. Novel to this study was the observation that NorHA hydrogels exhibited compressible behaviors, with greater compressibility occurring in NorHA hydrogels with lower stiffness. Hence, the kine-matic analysis was modified to incorporate separate deviatoric and volumetric strain indices. At day 7, multicellularity synergistically increased both strain components. These findings indicated that hiPSC-EP contractility and mechanical interactions with the hydrogel are governed by culture duration, multicellularity, and hydrogel stiffness; providing mechanical insight on hiPSC-EP self-assembly into microvasculature networks, a critical step towards development of functional vascular tissues for regenerative medicine and disease models.
    DOI:  https://doi.org/10.1101/2025.06.18.660409
  5. bioRxiv. 2025 Jun 08. pii: 2025.06.08.658465. [Epub ahead of print]
      Microfluidic systems incorporating or contained within hydrogels are important in creating microphysiological systems (MPSs). Often naturally derived hydrogels are used, as their inherent bioactivity supports dynamic cellular behaviors. Hydrogel biomaterials that are partly or fully synthetic are desirable in engineering systems with specific, designed properties, though they typically lack bioactive features of natural materials without additional molecular design. In particular, permissive biomaterials enable physiologically relevant dynamic cellular behaviors. Granular hydrogels offer inherent permissiveness, owning to porosity between particles and dynamic behaviors in the absence of interparticle crosslinking. However, applying these in MPS to model tissues requires stable channels to perfuse fluid in these dynamic systems. Here, we establish channels within granular hydrogels to enable perfusion through spatially controlled interparticle crosslinking. Selective crosslinking allowed for the formation of stable channels while allowing the microparticles of a granular hydrogel between two channels to remained uncrosslinked. This allowed spatiotemporal control of signals within an environment established from microparticles without interparticle crosslinking. Fluorescently tagged molecules allowed for the visualization of controlled soluble gradients between two channels within the device. Additionally, embedded 3D printing processes can be used to specify material composition within the system, demonstrating integrated technology for engineering well-defined hydrogel systems. Integrated microfluidic-based control over soluble signals in a system that is compatible with 3D printing processes will establish a basis for building MPSs for broad applications, and the ability to maintain granular systems in culture without interparticle crosslinking will enable design of synthetic hydrogels that access unique dynamic properties within these systems.
    DOI:  https://doi.org/10.1101/2025.06.08.658465
  6. APL Bioeng. 2025 Sep;9(3): 036104
      Immunofluorescence staining of cell proteins is essential to understanding biomolecular interactions within three-dimensional (3D) hydrogel cell cultures. However, the scaffold material limits passive diffusion of antibodies through thick 3D matrices, prolonging staining and washing steps and resulting in processing times that can last for several days. Microwave irradiation has previously been shown to enhance penetration of fixatives in a variety of soft tissues by increasing the rate of diffusion through the sample, yet it is unknown if microwave irradiation can improve immunofluorescence staining of cells in 3D hydrogel cultures. Here, we demonstrate a microwave-assisted immunostaining technique that rapidly labels cells within spheroid structures embedded within thick intact hydrogels. These results show that collagen-embedded breast epithelial spheroids can be efficiently labeled with primary antibodies in less than 3.5 h. We show significantly enhanced staining and greater depth penetration with microwave-assisted staining compared to conventional benchtop staining methods. We demonstrate staining of collagen-embedded breast cancer spheroids with complete staining achieved in less than 2.5 h via the microwave, which outperforms conventional staining techniques. Moreover, we demonstrate enhanced staining of spheroids embedded in basement membrane-derived Matrigel matrices with the microwave method compared to benchtop techniques. Finally, we directly compare 2-h microwave-assisted staining to conventional 15-h longform benchtop staining and show that microwave staining increases depth penetration and intensity of stains compared to the longform staining. This work develops a microwave-assisted staining protocol that provides a rapid and reproducible method to label a variety of cell types within various 3D hydrogel cell culture systems.
    DOI:  https://doi.org/10.1063/5.0230800
  7. bioRxiv. 2025 May 05. pii: 2025.05.05.651928. [Epub ahead of print]
      For polarization and directed migration, cells use a combination of local positive feedback and long-range inhibition. We have previously used mathematical models to show the ability of this core circuit to regulate directed cell movement. However, this wave pinning model lacks important additional feedback circuits, including the recently demonstrated local negative feedback from Town and Weiner. Here we extend our models to investigate the consequences of this additional link on cell physiology. We model responses of neutrophil-like HL-60 cells to spatially-controlled optogenetic stimulation of PI3K, leading (via PIP3) to Rac activity. We sequentially build up and investigate partial differential equation (PDE) models of the key Rac, Rac-Inhibitor, and PIP3-Rac-Inhibitor circuits. We fit model parameters to temporal and spatial (cell trajectory) data. Cell shapes, motility, and responses to stimuli are modeled in 2D cell-based simulations, with PDEs for Rac and the other regulatory components solved along the cell edge. We demonstrate that the ability of modeled cells to respond to temporal as well as spatial features of guidance cues depends on the addition of the local negative feedback circuit. Furthermore, the local Rac inhibitor improves the ability of modeled cells to respond to noisy or dynamic extracellular gradients. Our work demonstrates how local negative feedback enhances dynamic polarity and gradient sensing in migratory cells.
    DOI:  https://doi.org/10.1101/2025.05.05.651928
  8. Biomaterials. 2025 Jul 12. pii: S0142-9612(25)00470-3. [Epub ahead of print]325 123551
      Stem cell therapy has been widely investigated for the treatment of chronic bladder diseases such as interstitial cystitis/bladder pain syndrome (IC/BPS). However, the delivery of stem cells into the bladder wall is limited due to the mucus layer lining the bladder wall and the frequent urination, leading to the fast clearance of stem cells from the bladder. Here, we report a soft microgelbot (μgelbot) composed of a magnetic nanochain embedded microgel in a tunable size and shape for the enhanced delivery of mesenchymal stem cells (MSCs) into the bladder wall through the mucus layer. In vitro penetration tests to optimize the shape of μgelbots show that the quadrangle shaped μgelbots effectively apply a shear force to the surrounding shear-thinning mucus layer for the enhanced penetration under a rotating magnetic field. After loading MSCs onto the μgelbot, we confirm the enhanced penetration and retention in the reconstructed mucus layer. Finally, we successfully demonstrate the paracrine effects of MSCs loaded μgelbots on chronic IC murine models, inhibiting the mast cell infiltration, collagen deposition, and bladder cell apoptosis. Taken together, we could confirm the feasibility of magnetically controlled μgelbots as a promising platform for the stem cell therapy of IC/BPS.
    Keywords:  Interstitial cystitis; Magnetic nanochain; Microgelbot; Paracrine effect; Stem cells
    DOI:  https://doi.org/10.1016/j.biomaterials.2025.123551
  9. Small Sci. 2025 Apr;5(4): 2400468
      Advanced cell culture platforms that vary the biophysical microenvironment are useful tools for mechanobiology studies and for directing the differentiation of adherent cells to therapeutically relevant phenotypes. Herein, the fabrication of magnetoactive nanofiber mats for integration with hydrogels as a platform for dynamic stimulation at the cell-biomaterial interface is demonstrated. Electrospinning is used to form iron oxide-loaded gelatin-based nanofibers that are stabilized and cross-linked to the surface of gelatin methacryloyl hydrogels. The presence of a magnetic field stimulates focal adhesion formation and maturation in adherent adipose-derived stromal cells, with concurrent changes in cell and nuclear morphology. Adding lineage guiding supplements has been shown to complement biophysical cues, providing optimal conditions for differentiation into osteogenic and adipogenic lineages. The presence of nanofibers at the interface is beneficial to both lineages, but stiffening through an applied magnetic field encourages further osteogenesis while inhibiting adipogenesis. The system is further demonstrated with skeletal myoblasts, where nanotopography and stiffening promote the formation of mature multinucleated muscle cells. This magnetoactive nanofiber platform could prove useful in a wide array of mechanically sensitive cell systems for fundamental studies and for cell production, with flexibility for use with virtually any hydrogel cell culture system.
    Keywords:  biomaterials; hydrogels; nanofibers; stimuli responsive; tissue engineering
    DOI:  https://doi.org/10.1002/smsc.202400468
  10. bioRxiv. 2025 Jun 17. pii: 2025.06.11.659098. [Epub ahead of print]
      Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense extracellular matrix (ECM) that sustains an immunosuppressive tumor microenvironment (TME). While this protective niche has been described, the molecular determinants orchestrating its formation and dictating its immune interactions are not well defined. Using Perturb-map, we determine how dozens of different gene perturbations shape the growth and cellular environments of PDAC clones through space and time. Our study reveals dynamic, gene-specific adaptations of immune neighborhoods during clonal selection. We identified Serpinb2 (PAI2) and Serpine1 (PAI1) as key cancer-derived mediators of TME remodeling and immune evasion. These factors promote the deposition of a fibrin-rich ECM that shapes immune cell composition, locally retains and polarizes immunosuppressive macrophages and excludes cytotoxic T cells. Deletion of either Serpinb2 or Serpine1 greatly enhanced tumor response to anti-PD1 immunotherapy in an aggressive PDAC model. Transcriptomic analysis further linked their expression to distinct PDAC subtypes and poor patient survival. Our findings demonstrate that Serpinb2 and Serpine1 establish a permissive niche for tumor progression and show how PDAC cells exploit components of the fibrinolysis pathway to remodel the ECM, alter macrophage composition, and protect themselves from immune editing, ultimately reinforcing the role of extracellular factors in shaping an immune-privileged tumor niche.
    DOI:  https://doi.org/10.1101/2025.06.11.659098
  11. bioRxiv. 2025 Jun 11. pii: 2025.06.07.658434. [Epub ahead of print]
      Biomechanical cues, including shear stress and mechanical strain, are key regulators of intestinal cellular behavior, yet their mechanostimulatory impact on fibroblasts responses during early fibrotic remodeling remains poorly understood. Using a bioengineered gut-on-a-chip model, we independently modulated flow and mechanical strain to assess fibroblast dynamics under intact or impaired epithelial barriers. Inflammation-associated fibroblasts resisted biomechanical stress, exhibiting myofibroblast-like phenotypes with hypertrophy and elevated α-smooth muscle actin aligned with stress fibers. In contrast, normal fibroblasts were highly susceptible to shear stress, undergoing matrix metalloproteinase-dependent apoptotic injury, while mechanical strain alone had minimal effect. Notably, an intact epithelial barrier was both necessary and sufficient to protect fibroblasts from shear-induced damage, suggesting that "good fences make good neighbors". Under barrier dysfunction, prolonged exposure to shear stress induced the formation of stiff fibroblast aggregates composed of mechanoadaptive myofibroblast-like cells. These findings identify mechanostimulatory cues, particularly shear stress, as critical drivers of early fibrotic remodeling in inflammatory bowel disease and underscore epithelial barrier integrity as an essential biomechanical safeguard against pathological fibroblast dysregulation.
    DOI:  https://doi.org/10.1101/2025.06.07.658434
  12. Rheol Bull. 2024 Jul;93(1): 20-27
      Rheology is the science of how materials deform and flow and is a critical aspect of understanding the biomechanical functions of cell and tissue. Historically, scientists have designed simple and cost-effective instruments for assessing the mechanical properties of biological materials to inform their functionality. Cells and tissue are heterogeneous and possess complex mechanical properties. Yet, simple instruments such as falling ball viscometers and torsion pendulums, can often accurately capture and measure different aspects of how biological materials deform that are relevant to physiological conditions. Here we review the application of simple, home-built instruments suitable for probing the viscoelastic properties of biological materials, underscoring the importance of creativity and innovation of experimental tool design in the field of biomechanics.
  13. J Colloid Interface Sci. 2025 Jul 04. pii: S0021-9797(25)01736-9. [Epub ahead of print]700(Pt 1): 138345
      Colloidal hydrogels, also known as microgels, are promising scaffold materials in the biomedical field. Microgels exhibit high biocompatibility, porosity, and mechanical stability, crucial in supporting cell development. Bio-based polymers, such as fibrin or dextran, are desirable for controlling the properties of microgels. The advantage of using these polymers includes producing degradable microgels that enable the release of active components. In this work, we fabricated fibrin-dextran-methacrylate (dextran-MA) interpenetrating polymer network microgels with tunable porosity, stiffness, and degradation profiles using droplet-based microfluidics. We incorporated fibrin to promote cell growth, while adding dextran-MA ensures improved structural stability of the microgels. By systematically varying the dextran-MA concentrations, we produced fibrin-dextran-MA microgels with a tunable range of stiffness, porosity, and degradation time, highlighting the material's versatility for biomedical applications. In particular, increasing the dextran-MA content reduced pore size, thereby offering a means to control the encapsulation and release of active components. Degradation studies using plasminogen and dextranase revealed that the degradation of the microgels strongly depended on the polymer concentration. This dependency allows controlling the degradation time and the release kinetics of active components, e.g., hepatocyte growth factor (HGF). HGF encapsulated in fibrin microgels was released rapidly through diffusion, while the release from fibrin-dextran microgels was delayed until enzymatic degradation. This delayed degradation of microgels demonstrates the potential to use the microgels for programmable release. Encapsulation of HGF in fibrin and fibrin-dextran-MA microgels promoted the spreading of human mesenchymal stem cells on the microgels, highlighting their potential for personalized Tissue Engineering applications. Our studies reveal that engineered microgels composed of fibrin and dextran-MA can be used as colloidal building blocks to design biomaterials with tailored stiffness, porosity, degradation, and programmed release behavior.
    Keywords:  Dextran; Encapsulation; Fibrin; Microgels; Porosity
    DOI:  https://doi.org/10.1016/j.jcis.2025.138345
  14. bioRxiv. 2025 Jun 24. pii: 2025.06.19.660320. [Epub ahead of print]
      The fibrous structures of collagen provide physical strength and stability to tissues and organs. Abnormalities in their orientation, growth, and remodeling cause morphogenetic defects and serious diseases including fibrosis, so it is important to clarify how collagen fibers are correctly oriented and grown within tissues. However, this mechanism remains elusive, as few methods have been available to fluorescently stain collagen fibers with a simple protocol and to observe their structure in three dimensions. Here we present a facile method that enables fluorescent staining of collagen fibers in vertebrate tissues. In our method using DAF-FM, known as a NO detection probe, premature collagen fibers can be visualized via covalent binding to the allysine residues serving as precursors of cross-linking structures of collagen. In addition, we showed that the labeling method using two fluorescent probes with different colors, DAF-FM and DAR-4M, allows for pulse-chase observation of newly synthesized collagen fibers. Our method will be a breakthrough technique in future collagen studies.
    DOI:  https://doi.org/10.1101/2025.06.19.660320
  15. Nat Immunol. 2025 Jul 15.
      Efficient immune responses rely on the capacity of leukocytes to traverse diverse and complex tissues. To meet such changing environmental conditions, leukocytes usually adopt an ameboid configuration, using their forward-positioned nucleus as a probe to identify and follow the path of least resistance among pre-existing pores. We show that, in dense environments where even the largest pores preclude free passage, leukocytes position their nucleus behind the centrosome and organelles. The local compression imposed on the cell body by its surroundings triggers assembly of a central F-actin pool, located between cell front and nucleus. Central actin pushes outward to transiently dilate a path for organelles and nucleus. Pools of central and front actin are tightly coupled and experimental depletion of the central pool enhances actin accumulation and protrusion formation at the cell front. Although this shifted balance speeds up cells in permissive environments, migration in restrictive environments is impaired, as the unleashed leading edge dissociates from the trapped cell body. Our findings establish an actin regulatory loop that balances path dilation with advancement of the leading edge to maintain cellular coherence.
    DOI:  https://doi.org/10.1038/s41590-025-02211-w
  16. Int J Mol Sci. 2025 Jun 30. pii: 6301. [Epub ahead of print]26(13):
      Cell technologies have provided promising tools for modulating the properties of multipotent mesenchymal stem/stromal cells (MSCs) to meet the needs of cell therapy as well as tissue engineering and regenerative medicine (TERM). Ex vivo preconditioning is directed at enhancing the engraftment of MSCs and activating their secretory activity, primarily the production of soluble mediators. The present review aims to highlight the underestimated effect of the most accepted preconditioning approaches on the modification of the important set of insoluble molecules secreted by MSCs into extracellular space-the extracellular matrix (ECM). A thorough review of the published literature was performed, with particular emphasis on ECM-related data. The analysis of data on ECM changes showed that most of the applied preconditioning methods-hypoxia, inflammatory priming, pharmacological agents, 3D culture, and scaffolds-generally stimulate ECM production, increase the deposition of growth factors, promote alignment, and increase ECM stiffness. There are already preliminary results demonstrating the successful application of preconditioned ECM for promoting angiogenesis, targeted stromal lineage differentiation, and other therapeutic goals. The prospects for further research in this area are discussed.
    Keywords:  3D culture; extracellular matrix; hypoxia; in vitro preconditioning; inflammatory mediators; multipotent mesenchymal stem/stromal cells (MSCs); pharmacological agents; regenerative medicine and tissue engineering; scaffolds
    DOI:  https://doi.org/10.3390/ijms26136301
  17. Small Sci. 2025 Apr;5(4): 2400400
      Hydrogels with micro/nano-structures precisely prepared by femtosecond-laser processing technology are biomaterials that mimic the natural extracellular matrix and can achieve the precise regulation of biological properties, such as cell behavior and structural-mechanical properties. They also play a crucial role in biomedical fields such as regenerative medicine, bionanostructural construction, drug transport, and particle manipulation. This study summarizes the central role of the nonlinear absorption property of femtosecond lasers in the preparation of hydrogel micro/nano-structures. Based on the electron-dynamics model and electron-density flood theory, the two main processing types of the femtosecond laser-processed hydrogel, additive and subtractive manufacturing, are discussed in depth. The modification mechanisms such as the photon-electron energy-field conversion, multiphoton absorption effect, and bubble-driven bio-link molding are analyzed. Additionally, the stimulus-response diversification and functional biomimicry properties of the structural hydrogels under the influences of different laser action modes and hydrogel composition ratios are investigated for their biomedical applications, such as microactuators, drug delivery, microscaffolds, and the in vitro simulation of vascular networks. On this basis, the advantages and limitations of the current technology are summarized and a reasonable prediction for future research on the law of action of the femtosecond-laser preparation of hydrogel micro/nano-structures is made.
    Keywords:  biomedical; femtosecond lasers; hydrogels; micro/nano‐structure
    DOI:  https://doi.org/10.1002/smsc.202400400