bims-ecemfi 2025-05-04 papers

bims-ecemfi

Biomed News

on ECM and fibroblasts

Issue of 2025–05–04
eight papers selected by
Badri Narayanan Narasimhan, University of California, San Diego

Matrix Stiffness Regulates Mechanotransduction and Vascular Network Formation of hiPSC-Derived Endothelial Progenitors Encapsulated in 3D Hydrogels.
Viscoelastic extracellular matrix enhances epigenetic remodeling and cellular plasticity.
Reproducible extracellular matrices for tumor organoid culture: challenges and opportunities.
Small Accelerations of the cell generate sufficient nuclear motion to modulate transcriptional activity, driving cellular response independent of matrix strain.
4D mitochondrial network assumes distinct and predictive phenotypes through human lung and intestinal epithelial development.
FAK Differentially Mechanoregulates Cell Migration During Wound Closure.
Vimentin - Force regulator in confined environments.
Tuneable gelatin methacryloyl (GelMA) hydrogels for the directed specification of renal cell types for hiPSC-derived kidney organoid maturation.

bioRxiv. 2025 Apr 12. pii: 2025.04.11.648340. [Epub ahead of print]

Matrix Stiffness Regulates Mechanotransduction and Vascular Network Formation of hiPSC-Derived Endothelial Progenitors Encapsulated in 3D Hydrogels.

Jiwan Han, Kathleen N Halwachs, Toni West, Bryce V Larsen, Michael S Sacks, Adrianne Rosales, Janet Zoldan.

The mechanical properties of the extracellular matrix (ECM), particularly stiffness, regulate endothelial progenitor responses during vascular development, yet their behavior in physiologically compliant matrices (<1 kPa) remains underexplored. Using norbornene-modified hyaluronic acid (NorHA) hydrogels with tunable stiffness (190-884 Pa), we investigated how hydrogel stiffness influences cell morphology, endothelial maturation, mechanotransduction, and microvascular network formation in human induced pluripotent stem cell-derived endothelial progenitors (hiPSC-EPs). Our findings reveal a stiffness-dependent tradeoff between mechanotransduction and vascular network formation. At intermediate stiffness (551 Pa), cells exhibited the greatest increase in endothelial marker CD31 expression and Yes-associated protein (YAP)/ transcriptional coactivator with PDZ-binding motif (TAZ) nuclear translocation, indicating enhanced mechanotransduction and endothelial maturation. However, this did not translate to superior plexus formation. Instead, the most compliant matrix (190 Pa) supported greater vascular connectivity, characterized by longer branches (~0.03/volume vs. 0.015 at 551 Pa) and enhanced actin remodeling. 3D cell contraction measurements revealed a 15.6-fold higher basal displacement in compliant hydrogels, suggesting that cell-generated forces and matrix deformability collectively drive vascular morphogenesis. Unlike prior studies focusing on pathological stiffness ranges (>10 kPa), our results emphasize that vascularization is not solely driven by the most mechanotransductive environment but rather by a balance of compliance, contractility, and cell-induced remodeling. These findings underscore the need to design hydrogels that provide sufficient mechanotransduction for endothelial maturation while maintaining compliance to support dynamic vascular morphogenesis. This work provides a mechanically tuned framework for optimizing microenvironments to balance endothelial differentiation and vascular network formation in tissue engineering and regenerative medicine.

DOI: https://doi.org/10.1101/2025.04.11.648340
Nat Commun. 2025 Apr 30. 16(1): 4054

Viscoelastic extracellular matrix enhances epigenetic remodeling and cellular plasticity.

Yifan Wu, Yang Song, Jennifer Soto, Tyler Hoffman, Xiao Lin, Aaron Zhang, Siyu Chen, Ramzi N Massad, Xiao Han, Dongping Qi, Kun-Wei Yeh, Zhiwei Fang, Joon Eoh, Luo Gu, Amy C Rowat, Zhen Gu, Song Li.

Extracellular matrices of living tissues exhibit viscoelastic properties, yet how these properties regulate chromatin and the epigenome remains unclear. Here, we show that viscoelastic substrates induce changes in nuclear architecture and epigenome, with more pronounced effects on softer surfaces. Fibroblasts on viscoelastic substrates display larger nuclei, lower chromatin compaction, and differential expression of distinct sets of genes related to the cytoskeleton and nuclear function, compared to those on elastic surfaces. Slow-relaxing viscoelastic substrates reduce lamin A/C expression and enhance nuclear remodeling. These structural changes are accompanied by a global increase in euchromatin marks and local increase in chromatin accessibility at cis-regulatory elements associated with neuronal and pluripotent genes. Consequently, viscoelastic substrates improve the reprogramming efficiency from fibroblasts into neurons and induced pluripotent stem cells. Collectively, our findings unravel the roles of matrix viscoelasticity in epigenetic regulation and cell reprogramming, with implications for designing smart materials for cell fate engineering.

DOI: https://doi.org/10.1038/s41467-025-59190-7
J Transl Med. 2025 May 01. 23(1): 497

Reproducible extracellular matrices for tumor organoid culture: challenges and opportunities.

Kan Li, Yibo He, Xue Jin, Ketao Jin, Jun Qian.

  Tumor organoid models have emerged as valuable 3D in vitro systems to study cancer behavior in a physiologically relevant environment. The composition and architecture of the extracellular matrix (ECM) play critical roles in tumor organoid culture by influencing the tumor microenvironment and tumor behavior. Traditional matrices such as Matrigel and collagen, have been widely used, but their batch-to-batch variability and limited tunability hinder their reproducibility and broader applications. To address these challenges, researchers have turned to synthetic/engineered matrices and biopolymer-based matrices, which offer precise tunability, reproducibility, and chemically defined compositions. However, these matrices also present challenges of their own. In this review, we explore the significance of ECMs in tumor organoid culture, discuss the limitations of commonly used matrices, and highlight recent advancements in engineered/synthetic matrices for improved tumor organoid modeling.

Keywords:  Extracellular matrix; Reproducibility; Tumor microenvironment; Tumor organoid; Tunability

DOI:  https://doi.org/10.1186/s12967-025-06349-x
bioRxiv. 2025 Apr 11. pii: 2025.04.07.647583. [Epub ahead of print]

Small Accelerations of the cell generate sufficient nuclear motion to modulate transcriptional activity, driving cellular response independent of matrix strain.

Nina Nikitina, Jonathan Wadsworth, Matthew Goelzer, Madison Goldfeldt, Nurbanu Bursa, Sean Howard, Chase Crandall, Amevi Semodji, Anamaria G Zavala, Stefan Judex, Janet Rubin, Trevor J Lujan, Clare K Fitzpatrick, Clinton T Rubin, Aykut Satici, Gunes Uzer.

The cell's mechanical environment is a fundamental determinant of its activity. Ostensibly, the cellular response is dependent on interactions between extracellular matrix deformations and the cell adhesome. Low-intensity vibration (LIV) induces sinusoidal mechanical accelerations that stimulate mesenchymal stem cell (MSC) anabolism despite generating minimal matrix strain. In this study, we tested the hypothesis that accelerations of less than 1g cause nuclear motions relative to the cell membrane in adherent cells, resulting in elevated stresses in the cytoskeleton that promote transcriptional activity. Coupling a piezoelectric vibration platform with real-time microscopy, we applied a 0.7g, 90Hz LIV signal that oscillates the cell with displacements of up to ±11 µm. Live-cell tracking revealed that the sinusoidal vibrations caused the nucleus to move ±1.27 µm (17% of total displacement) out of phase with the cell membrane. Disruption of the LINC complex, which mechanically couples the nucleoskeleton to the cytoskeleton, doubled the magnitude of this relative motion, indicating that the nucleo-cytoskeletal configuration plays a major role in regulating nuclear motion. Consistent with a previously reported increase in nuclear stiffness caused by LIV, machine-learning-based image segmentation of confocal micrographs showed that LIV increased both apical and basal F-actin fiber numbers, generating a denser, more branched actin network near the nucleus. Following six 20 min bouts of LIV applied to MSC, RNA sequencing identified 372 differentially expressed genes. Upregulated gene sets were linked to F-actin assembly and focal adhesion pathways. Finite element simulations showed that nuclear stresses increased by LIV up to 18% were associated with nuclei flattening and a 30-50% increase in actin-generated forces. These findings demonstrate that low-intensity accelerations, independent of matrix strain, can directly activate a response of the nucleus, leading to cytoskeletal reorganization and heightened nuclear stresses. Thus, even very small oscillatory mechanical signals can markedly influence cell outcomes, establishing a mechanosensing pathway independent of extracellular strains.

DOI: https://doi.org/10.1101/2025.04.07.647583
bioRxiv. 2025 Apr 10. pii: 2025.04.09.648043. [Epub ahead of print]

4D mitochondrial network assumes distinct and predictive phenotypes through human lung and intestinal epithelial development.

Gillian McMahon, Dhruv Agarwal, Mehul Arora, Zichen Wang, Hiroyuki Hakozaki, Johannes Schöneberg.

Mitochondria form a dynamic three-dimensional network within the cell that exhibits a wide range of morphologies and behaviors. Depending on cell state, cell type, and cell fate, a cell's mitochondrial phenotype might range from relatively isolated mitochondrial segments to complex branching networks, and from stationary mitochondria to highly motile structures. While isolated mitochondrial phenotypes have been described for a subset of cell states, types, and fates, an integrated map of how mitochondrial phenotypes change over the full course of tissue development has so far been lacking. Here, we identify the mitochondrial phenotypes that appear throughout the course of lung and intestinal epithelial development from stem cells to differentiated tissue. Using human stem cell-derived intestinal and branching lung organoids that mimic developing human organs as model systems, we extract and analyze key mitochondrial biophysical phenotypes in human development. To achieve this, we employ lattice light-sheet microscopy (LLSM), which enables high-resolution, 4D (x, y, z, time) imaging of mitochondria in organoid tissues with minimal damage to the sample. We image at key developmental time points from stem cell differentiation into mature organoid tissue. For data processing, we utilize the MitoGraph and MitoTNT software packages along with our developed custom computational tools. These tools allow for automated 4D organoid to single cell image processing and quantitative 4D single cell mitochondrial temporal network tracking. This work represents the first 4D high spatiotemporal-resolution quantification of live human organoid tissues at the single-cell level through development. We identified distinct mitochondrial phenotypes unique to each organoid type and found correlations between mitochondrial phenotypes, cellular age, and cell type. Furthermore, we demonstrate that mitochondrial network characteristics can predict both organoid type and cell age. Our findings reveal fundamental aspects of mitochondrial biology that were previously unobservable, offering new insights into cell-type-specific mitochondrial dynamics and enabling new findings in relevant human model systems. We believe that our findings and methods will be essential for advancing 4D cell biology, providing a powerful framework for characterizing organelles in organoid tissues.

DOI: https://doi.org/10.1101/2025.04.09.648043
bioRxiv. 2025 Apr 07. pii: 2025.04.01.646098. [Epub ahead of print]

FAK Differentially Mechanoregulates Cell Migration During Wound Closure.

Jennifer Patten, Nourhan Albeltagy, Jacob D Bonadio, Armando Ortez, Karin Wang.

Cell migration is an essential step in wound healing. Mechanical input from the local microenvironment controls much of cell velocity and directionality during migration, which is translated into biochemical cues by focal adhesion kinase (FAK) inside the cell. FAK induces both regeneration and fibrosis. The mechanisms by which FAK decide wound fate (regenerative or fibrotic repair) in soft, normal wounds or stiff, fibrotic wounds remains unclear. Here we show that FAK differentially mechanoregulates wound behavior on soft substrates mimicking normal wounds and stiff substrates mimicking fibrotic wounds by converting mechanical substrate stimuli into variable cell velocity, directionality, and angle during wound healing. Cells on soft substrates migrate slower and less persistently; cells on stiff substrates migrate faster and more persistently with the same angle as the cells on normal wound substrates. Inhibition of FAK results in substantially slower, less persistent, and less correctly angled cell migration, which leads to slowed wound closure. Moreover, FAK inhibition impairs fibroblast ability to respond to substrate stiffness when migrating. Here we show FAK is an essential mechanoregulator of wound migration in fibroblast wound closure and is responsible for controlling cell migration dynamics in response to substrate stiffnesses mimicking normal or fibrotic wounds.
Abstract Figure:

DOI: https://doi.org/10.1101/2025.04.01.646098
Curr Opin Cell Biol. 2025 Apr 26. pii: S0955-0674(25)00059-6. [Epub ahead of print]94 102521

Vimentin - Force regulator in confined environments.

Maxx Swoger, Minh Tri Ho Thanh, Alison E Patteson.

Cells must navigate crowded and confining 3D environments during normal function in vivo. Essential to their ability to navigate these environments safely and efficiently is their ability to mediate and endure both self-generated and external forces. The cytoskeleton, composed of F-actin, microtubules, and intermediate filaments, provides the mechanical support necessary for force mediation. The role of F-actin and microtubules in this process has been well studied, whereas vimentin, a cytoplasmic intermediate filament associated with mesenchymal cells, is less studied. However, there is growing evidence that vimentin has functions in both force transmission and protection of the cell from mechanical stress that actin and microtubules cannot fulfill. This review focuses on recent reports highlighting vimentin's role in regulating forces in confining environments.

DOI: https://doi.org/10.1016/j.ceb.2025.102521
Biomaterials. 2025 Apr 21. pii: S0142-9612(25)00268-6. [Epub ahead of print]322 123349

Tuneable gelatin methacryloyl (GelMA) hydrogels for the directed specification of renal cell types for hiPSC-derived kidney organoid maturation.

Shane Clerkin, Krutika Singh, Jessica L Davis, Niall J Treacy, Ivan Krupa, Emmanuel G Reynaud, Robert M Lees, Sarah R Needham, Delphi MacWhite-Begg, Jacek K Wychowaniec, Dermot F Brougham, John Crean.

  Diabetic Kidney Disease (DKD) represents a significant global health burden and is recognised as the leading cause of end-stage renal disease. Kidney organoids derived from human induced Pluripotent Stem Cells (hiPSCs) have the potential to transform how we model renal disease and may provide personalised replacement tissues for patients with renal failure. However, kidney organoids remain poorly reproducible, and are structurally and functionally immature. Three-dimensional cultures that more appropriately mimic the complexity of the in vivo microenvironment are required to improve organoid maturation and structural authenticity. Here, we describe the application of semi-synthetic Gelatin Methacryloyl (GelMA) hydrogels as extracellular support matrices for the differentiation of hiPSC-derived kidney organoids. Hydrogels of defined mechanical strengths were generated by varying the concentration of GelMA solution in the presence of low concentration photo-initiator. After confirming a high level of mechanical stability of the hydrogels over extended culture periods, their effect on kidney organoid maturation was investigated. Organoids differentiated within GelMA hydrogels generated typical renal cell types including podocytes, tubular epithelia, renal interstitial cells, and some nascent vascularisation. Interestingly, kidney organoids derived within hydrogels that closely approximate the stiffness of the adult human kidney (∼5000-10,000 Pa) demonstrated improved podocyte maturation and were shown to upregulate renal vesicle-associated genes at an earlier stage following encapsulation when compared to organoids derived within softer hydrogels (∼400 Pa). A model of TGFβ-induced injury was also developed to investigate the influence of the mechanical environment in propagating early, fibrotic-like features of DKD within organoids. Growth within the softer matrix was shown to reduce pSMAD3 expression following TGFβ1 treatment, and accordingly ameliorate the expression of the myofibroblast marker α-Smooth Muscle Actin (α-SMA). This work demonstrates the suitability of GelMA hydrogels as mechanically-stable, highly-tuneable, batch-to-batch reproducible three-dimensional supports for hiPSC-derived kidney organoid growth and differentiation, and further substantiates the role of the biophysical environment in guiding processes of cell fate determination and organoid maturation.

Keywords:  Gelatin methacryloyl; Hydrogels; Mechanoregulation; Stiffness; hiPSC-derived kidney organoids

DOI:  https://doi.org/10.1016/j.biomaterials.2025.123349