bims-ecemfi 2026-07-19 papers

Proc Natl Acad Sci U S A. 2026 Jul 21. 123(29): e2533029123

Spatiotemporally controlled matrix softening facilitates deterministic crypt formation in human intestinal organoids.

Michael R Blatchley, Kaustav Bera, Nolan R Petrich, Bruce E Kirkpatrick, F Max Yavitt, Patrick S McGrath, Peter J Dempsey, Kristi S Anseth.

Spatially controlling morphogenesis is a challenge for many organoid systems that manifests as a limited understanding of self-organization of differentiating cells and leads to a high degree of heterogeneity in organoid morphometrics. Current methods to grow organoids rely on temporal presentation of soluble cues that are not controllably delivered, and little is known about the role of the extracellular microenvironment in this process. Here, we present a material-based strategy to spatiotemporally control morphogenesis of human intestinal organoids (HIOs) with predictable crypt morphometrics and cell composition that match their in vivo tissue counterparts. We first optimize culture conditions to generate more reproducible HIOs with predictable growth in phototunable poly (ethylene glycol)-based hydrogels, and then systematically investigate the role of light-mediated matrix softening in guiding crypt formation. The light dose delivered to crypt-sized regions adjacent to growing organoids is a key factor in maintaining organoid cell viability, as well as crypt budding and elongation. With optimized light doses, predictable epithelial shape changes result in programmable crypt formation, confirmed by the presence of proliferative (Ki67+) and niche-defining Paneth (Lyz+) cells. This methodology could be readily adopted for other budding and branching organoids to facilitate controllable changes in morphogenesis or cell migration. Sequential patterning approaches and more complex pattern designs could further open the parameter space to facilitate modeling of a wide array of engineered tissues for applications ranging from fundamental biology to disease modeling and translational medicine.

Keywords: hydrogels; morphogenesis; organoids; photopatterning

DOI: https://doi.org/10.1073/pnas.2533029123

Biomaterials. 2026 Jul 04. pii: S0142-9612(26)00443-6. [Epub ahead of print]336 124419

Mechanically regulated proteostasis by Hsp27 governs osteogenesis of mesenchymal stromal cells on soft matrices.

Ming-Chung Wu, Cheng-Te Hsiao, Wan-Yu Chiang, Helen Wenshin Yu, Yin-Quan Chen, Wo-Jun Zhang, Guan-Yu Zhuo, Arthur Chiou, Jean-Cheng Kuo.

Matrix stiffness is a critical biophysical cue that governs mesenchymal stromal cell (MSC) fate, yet the molecular mechanisms by which soft extracellular environments impair osteogenesis remain poorly defined. In this study, we utilized a stiffness-tunable in vitro model to dissect focal adhesion (FA)-mediated mechanotransduction and identified the small heat shock protein Hsp27 as a mechanosensitive regulator that selectively localizes to the FAs of MSCs on soft matrices. Proteomic profiling revealed that soft substrates reprogram FA composition to recruit chaperones and ubiquitin-proteasome system (UPS) components, with Hsp27 acting as a central effector. Mechanistically, Hsp27 facilitates the localized, proteasome-mediated degradation of the small GTPase Rac1, thereby attenuating lamellipodia formation, cytoskeletal tension, and pro-osteogenic signaling. Genetic deletion or pharmacological inhibition of Hsp27 successfully restored FA maturation, actin stress fiber architecture, and intracellular traction forces, effectively rescuing osteogenic differentiation on compliant substrates. In a murine model of age-related osteoporosis, we observed that femoral bone tissues exhibit hallmarks of matrix softening, including collagen fiber misalignment and increased marrow adiposity, accompanied by Hsp27-mediated Rac1 depletion. These findings establish Hsp27 as a mechanically responsive regulator of FA proteostasis and identify a stiffness-sensitive degradation pathway as a potential therapeutic target to restore bone formation in mechanically compromised environments.

Keywords: Matrix stiffness; Osteogenic differentiation; Osteoporosis; Small heat shock protein Hsp27

DOI: https://doi.org/10.1016/j.biomaterials.2026.124419

Curr Protoc. 2026 Jul;6(7): e70420

High-Throughput Focal Adhesion Analysis Software for Automated Detection, Tracking, and Classification of Cell-Matrix Adhesions.

Majid Rostami, Sangyoon J Han.

Focal adhesions are dynamic multi-protein complexes that mechanically link the actin cytoskeleton to the extracellular matrix through integrin receptors. A single migrating cell can contain >1000 adhesion structures simultaneously, exhibiting highly heterogeneous fates: only ∼3.5% of nascent adhesions mature into focal contacts or focal adhesions, while the majority turn over within minutes. Resolving this heterogeneity requires automated detection, tracking, and classification of individual adhesion trajectories at scale. Here we provide a step-by-step Basic Protocol for the Focal Adhesion Package, a MATLAB-based pipeline that processes time-lapse fluorescence images through 11 sequential steps, from sub-pixel stage drift correction and cell masking through point source detection, particle tracking, focal adhesion segmentation, feature extraction, and machine learning-based classification into 9 functional groups. The pipeline optionally integrates traction force microscopy and multi-channel fluorescence data to perform event detection of significant signal rise and compute temporal cross-correlations between protein recruitment and force generation at individual adhesions. For a typical 100-frame movie, total runtime is ∼40 min using CPU-parallelized optimization (∼15 min for preprocessing and detection, ∼25 min for feature extraction) on a standard workstation, with GPU acceleration reducing this to ∼27 min. We describe parameter selection criteria for each step and provide supplementary code recipes for programmatic access to outputs. The pipeline can be executed through a graphical user interface or automated using MATLAB scripts. © 2026 Wiley Periodicals LLC. Support Protocol: Software installation and set up Basic Protocol: Running the Focal Adhesion Package Alternate Protocol: Batch processing multiple movies.

Keywords: cell migration; focal adhesions; machine learning; nascent adhesions; traction force microscopy

DOI: https://doi.org/10.1002/cpz1.70420