Jimmy Kuang-Hsien Hu

Epithelial tissues undergo dynamic transitions between fluid-like collective motion and mechanically jammed states during development, injury repair, and disease progression. However, the cellular programs that drive these transitions and regulate collective behavior remain unclear. Using a controlled crowding model integrated with live-cell imaging and time-resolved multiomics, we demonstrate that epithelial crowding triggers early metabolic changes characterized by increased mitochondrial pyruvate anaplerosis that precedes the jamming transition. Restricting mitochondrial pyruvate import increased collective cell motility and delayed jamming in crowded monolayers. This unjammed state is driven by enhanced cytoskeletal remodeling and requires RhoA-myosin II activity. Mechanistically, we show that elevated cytoskeletal signaling promotes macropinocytic uptake, which serves as a required feedback loop to maintain motility. These findings identify mitochondrial pyruvate utilization as an important regulatory input linking metabolic remodeling to the endocytic control of epithelial fluidity.

Background: The continuously growing mouse incisor serves as a model for stem cell‐driven tooth renewal. Although mice possess maxillary and mandibular incisors, most studies have focused on the mandible. Potential differences in structure and renewal between these serially homologous organs remain insufficiently characterized. Results: Mandibular incisors are longer and contain greater enamel volume, mineral density, and mineral content than maxillary incisors, whereas maxillary incisors are more curved and display a larger cross‐sectional area. Mineral density increases along the apical‐to‐incisal axis in both teeth, although mandibular incisors exhibit greater mineral deposition and retention. The maxillary incisor contains a larger pool of cycling progenitors with proliferation dynamics comparable to those of the mandibular incisor. Although ameloblast differentiation initiates at a similar position in both incisors, the mandibular incisor contains a ~20% longer secretory‐stage ameloblast region. Consistent with this observation, gene expression analysis reveals earlier Igfbpl1 expression onset in the mandible. Conclusions: Homologous mouse incisors differ in progenitor pool size, ameloblast maturation, and enamel formation. Increased enamel output in the mandible is associated with a prolonged secretory phase, whereas the maxilla contains an expanded progenitor pool. These findings support the maxillary incisor as a complementary model for studying mechanisms that regulate tooth renewal.

Single-cell multimodal omics offer unprecedented resolution of cellular networks, yet translating continuous computational attributions into structured, testable biological mechanisms remains a persistent bottleneck. To address this limitation, we introduce an analytical pipeline employing decision trees to discretize continuous neural network attributions into explicit regulatory thresholds. These boundaries then structurally constrain large language models, enabling them to integrate established literature with empirical data to synthesize context-specific hypotheses. Applying this continuous-to-discrete framework across sparse datasets yielded novel biological mechanisms. Specifically, the framework articulated a cytoskeletal gating hierarchy governing EGF-stimulated pathways, identified transcriptomic drivers of input resistance in cortical interneurons, and delineated translational logic predicting Ki-67 abundance within spatial transcriptomics. Retrospective benchmarking validated the capacity of the framework to autonomously reconstruct published regulatory logic. Supported by a locally deployable open-weight language model and a code-free interface, this approach establishes an auditable methodology to extract robust experimental hypotheses from high-dimensional single-cell data.

Epithelial tissues undergo dynamic transitions between fluid-like collective motion and mechanically jammed states during development, injury repair, and disease progression. However, the cellular programs that drive these transitions and regulate collective behavior remain unclear. Using a controlled crowding model integrated with live-cell imaging and time-resolved multi-omics, we demonstrate that epithelial crowding triggers early metabolic changes characterized by increased mitochondrial pyruvate anaplerosis that precedes the jamming transition. Functional inhibition of mitochondrial pyruvate import is sufficient to sustain collective cell motility, impeding jamming transition in crowded cells. This unjammed state is driven by enhanced cytoskeletal remodeling and requires RhoA-myosin II activity. Mechanistically, we show that elevated cytoskeletal signaling promotes macropinocytic uptake, which serves as a required feedback loop to maintain motility. These findings identify mitochondrial pyruvate utilization as a key regulator that links metabolic remodeling to the endocytic control of epithelial fluidity.

Objective(s): Yes‐Associated Protein (YAP) is a critical regulator of cell proliferation and differentiation, having the capacity to convert differentiated cells into somatic stem cells in several contexts. Here we investigate the plasticity of adult mouse dental epithelial cells by testing the effects of ectopic YAP activation in dental epithelial progenitors and differentiated ameloblasts during incisor renewal. Materials and Methods: Using mice with dental epithelial deletion of Lats1 and Lats2 , which encode negative regulators of YAP, we assessed how ectopic YAP activation altered tissue structure, cell proliferation, and differentiation via histological analysis, EdU/BrdU labeling, and immunostaining. We also treated primary dental epithelial cells in 3D culture with TRULI, a LATS inhibitor, to test cell plasticity outside the context of an intact tissue. Results: YAP overactivation in the incisor epithelium induced ectopic cell proliferation in the apical bud and prolonged the proliferative state of dental epithelial progenitors, leading to a thickened suprabasal layer. However, ameloblasts remained non‐proliferative. Tissue structures and differentiation of pre‐ameloblasts were disrupted. Finally, LATS inhibition was able to induce colony formation in some dissociated, 3D‐cultured ameloblasts. Conclusion: YAP activation promotes the expansion of dental epithelial progenitors but not ameloblasts in vivo, suggesting irreversible differentiation during tooth renewal. However, when dissociated, some ameloblasts acquire plasticity. This offers a strategy to manipulate proliferation in dental epithelial cells under different conditions and may have broader applications in orthodontics, where a modular control of progenitors and differentiated cells is critical for ensuring safe stem cell‐based treatments.

Cells sense and transduce mechanical forces to regulate diverse biological processes, yet the mechanical stimuli that initiate these processes remain poorly understood. In particular, how nuclear and cytoplasmic deformations respond to external forces is unclear. Here, we developed a microscopy-based technique to quantify the extensional uniaxial strains of the nucleus and cytoplasm during cell stretching, enabling direct measurement of their bulk mechanical responses. Using this approach, we identified a previously unrecognized inverse relationship between nuclear and cytoplasmic deformation in epithelial monolayers. We demonstrate that nucleo-cytoskeletal coupling, mediated by the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, regulates this anti-correlation (Pearson correlation coefficient approx. 0.3). Disrupting LINC abolished this relationship, revealing its fundamental role in intracellular deformation partitioning. Furthermore, we found that cytoplasmic deformation is directly correlated with stretch-induced nuclear shrinkage, suggesting a mechanotransduction pathway in which cytoplasmic mechanics influence nuclear responses. Lastly, multivariable analyses established that intracellular deformation can be inferred from cell morphology, providing a predictive framework for cellular mechanical behaviour. These findings refine our understanding of nucleo-cytoskeletal coupling in governing intracellular force transmission and mechanotransduction.

Background: To understand cellular morphology, biologists have relied on traditional optical microscopy of tissues combined with tissue clearing protocols to image structures deep within tissues. Unfortunately, these protocols often struggle to retain cell boundary markers, especially at high enough resolutions necessary for precise cell segmentation. This limitation affects the ability to study changes in cell shape during major developmental events. Results: We introduce a method that preserves cell boundary markers and matches the refractive index of tissues with water. This technique enables the use of high‐magnification, long working distance water‐dipping objectives that provide sub‐micron resolution images. We subsequently segment individual cells using a trained neural network segmentation model. These segmented images facilitate quantification of cell properties of the entire three‐dimensional tissue. As a demonstration, we examine mandibles of transgenic mice that express fluorescent proteins in their cell membranes and extend this technique to a non‐model animal, the catshark, investigating its dental lamina and dermal denticles—invaginating and evaginating ectodermal structures, respectively. This technique provides insight into the mechanical environment that cells experience during developmental transitions. Conclusions: This pipeline, named MORPHOVIEW, provides a powerful tool to quantify in high throughput the 3D structures of cells and tissues during organ morphogenesis.

Cell morphology heterogeneity is pervasive in epithelial collectives, yet the underlying mechanisms driving such heterogeneity and its consequential biological ramifications remain elusive. Here, we observed a consistent correlation between the epithelial cell morphology and nucleus morphology during crowding, revealing a persistent log-normal probability distribution characterizing both cell and nucleus areas across diverse epithelial model systems. We showed that this morphological diversity arises from asymmetric partitioning during cell division. Next, we provide insights into the impact of nucleus morphology on chromatin modifications. We demonstrated that constraining nucleus leads to downregulation of the euchromatic mark H3K9ac and upregulation of the heterochromatic mark H3K27me3. Furthermore, we showed that nucleus size regulates H3K27me3 levels through histone demethylase UTX. These findings highlight the significance of cell morphology heterogeneity as a driver of chromatin state diversity, shaping functional variability within epithelial tissues.

Multicellular systems, such as epithelial cell collectives, undergo transitions similar to those in inert physical systems like sand piles and foams. To remodel or maintain tissue organization during development or disease, these collectives transition between fluid-like and solid-like states, undergoing jamming or unjamming transitions. While these transitions share principles with physical systems, understanding their regulation and implications in cell biology is challenging. Although cell jamming and unjamming follow physics principles described by the jamming diagram, they are fundamentally biological processes. In this review, we explore how cellular processes and interactions regulate jamming and unjamming transitions. We begin with an overview of how these transitions control tissue remodeling in epithelial model systems and describe recent findings of the physical principles governing tissue solidification and fluidization. We then explore the mechanistic pathways that modulate the jamming phase diagram axes, focusing on the regulation of cell fluctuations and geometric compatibility. Drawing upon seminal works in cell biology, we discuss the roles of cytoskeleton and cell–cell adhesion in controlling cell motility and geometry. This comprehensive view illustrates the molecular control of cell jamming and unjamming, crucial for tissue remodeling in various biological contexts.

For decades, biologists have relied on confocal microscopy to understand cellular morphology and fine details of tissue structure. However, traditional confocal microscopy of tissues faces limited light penetration, typically less than 100 µm, due to tissue opacity. To address this challenge, researchers have developed tissue clearing protocols compatible with confocal microscopy. Unfortunately, these protocols often struggle to retain cell boundary markers, especially at high resolutions necessary for precise cell segmentation. In this work, we introduce a method that preserves cell boundary markers and matches the refractive index of tissues with water. This technique enables the use of high-magnification, long working distance water-dipping objectives. The sub-micron resolutions achieved with this approach allows us to automatically segment each individual cell using a trained neural network segmentation model. These segmented images facilitate the quantification of cell properties and morphology of the entire three-dimensional tissue. As a demonstration of this methodology, we first examine mandibles of transgenic mice that express fluorescent proteins in their cell membranes. We then extend this technique to a non-model animal, the catshark, investigating the cellular properties of its dental lamina and dermal denticles – invaginating and evaginating ectodermal structures, respectively. Our technique thus provides a powerful tool to quantify in high throughput the 3D structures of cells and tissues during organ morphogenesis.