Nature Materials

Cell motility drives spatial pattern formation across diverse biological systems. Here, we engineer Escherichia coli motility in semi-solid agar to control Voronoi patterns in two and three dimensions, partitioning space into regions closest to their respective inoculation seeds. Consistent with our reaction-diffusion model, we observed that collisions between expansion fronts generate either biomass depletion (''gaps'') or accumulation (''anti-gaps''), governed by the relative diffusion rates of bacteria and nutrients. By engineering strains with distinct expansion rates and tuneable motility, and by integrating these experimental data into a dynamic Voronoi model, we achieved precise control over pattern geometry. This enabled the generation of gaps with varying widths, curved boundaries, asymmetric structures, seedless regions, and complex composite patterns. Together, these findings establish bacterial Voronoi patterns as a programmable platform for engineering multicellular spatial organization, with potential applications in synthetic biology and materials science.

Cell shape changes during migration, division, or differentiation require the dynamic regulation of actin network mechanics. Actin crosslinkers are central to this regulation, controlling network connectivity and the transmission of contractile forces. A large diversity of crosslinkers exists, differing in length, domain structure, and binding kinetics, yet why cells deploy specific crosslinkers in a physiological context remains unclear. To bridge this gap, we developed a light-controlled actin crosslinker toolbox spanning three physiologically relevant lengths: ~9 nm (fascin-like), ~16 nm (fimbrin-like), and ~56 nm (alpha-actinin-like). Using magnetic pincher experiments and in silico modelling, we show that short and mid-length crosslinkers dynamically tune cortical stiffness and thickness in a density- and myosin-dependent manner, with short crosslinkers also driving pronounced stress-stiffening as the cortex is deformed. Strikingly, minute-scale activation reveals a length-dependent switch in cell behaviour: short crosslinkers cause cortical delamination, while long ones instead drive cell polarization and symmetry breaking. This switch can be overridden by perturbing actin turnover, which unlocks polarization in mid-length crosslinkers that otherwise delaminate. Crosslinker-induced polarization is not merely a local cortical event: it directs subsequent cell spreading, coupling a nanometre-scale molecular choice to a cell-scale decision about movement. Together, these findings establish a versatile optogenetic platform for manipulating actin crosslinking, and show that the cortex can encode a behavioural switch directly in its material architecture.

Tissue mechanics influence diverse biological processes, yet directly linking stiffness measurements to spatially resolved molecular states in intact tissues remains challenging. Here we developed a paired-surface spatial mechanomics approach to map Young's modulus by nanoindentation on a fresh tissue surface and co-register the stiffness grid with 10x Genomics Visium HD spatial transcriptome bins from the immediately adjacent, parallel surface. Applied to the mouse ovary, which has spatially distinct compartments and undergoes extracellular matrix remodeling with cycle and age, the workflow generated >2,900 matched measurements across 21 regions of interest. Nanoindentation at 50-m grid spacing enabled millimeter-scale stiffness maps while balancing acquisition time in fresh tissues, with ~92 4-m transcriptome bins assigned to each stiffness value. Global and compartment-specific analyses associated stiffer regions with lower elastic fiber programs and higher inflammatory signaling, with age-dependent differences. This correlative strategy integrates experimentally measured mechanics with spatial omics in fresh tissues.

Spatial-omics workflows enable molecular analysis within tissue spatial context. Despite the prognostic value of tissue stiffness, these approaches have not incorporated direct, mechanical measurements. This omission reflects several challenges, including sample requirements, low throughput, specialized equipment, and complex data registration. Here, we introduce mechanoMaST (mechanics mapped to spatial transcriptomics), the first workflow to combine absolute mechanical measurements with spatial-omics. It pairs atomic force microscopy-based nanoindentation stiffness maps with spatial transcriptomics maps from adjacent tissue cryosections. The two modalities are then computationally co-registered to enable direct spatial correlation at 100 um resolution, with mapping accuracy quantified through error propagation, providing ground-truth mechanical data directly linked to spatial gene expression. We demonstrate mechanoMaST in human colorectal cancer liver metastasis, generating a spatial resource from 10 patients and revealing a four-gene stiffness signature. mechanoMaST is readily adaptable to other tissues across development and disease, and extendable to additional spatial-omics modalities in adjacent sections.

Delamination within stratified epithelia like the skin epidermis describes the detachment and upward motion of cells originating from the basal layer. Despite its fundamental importance for tissue development, homeostatic regeneration and repair, the mechanisms that drive delamination remain a longstanding open question. Upward motion follows cell shape changes, which are inherently driven by physical forces, but their role is elusive. Here, we investigate delamination in stratifying keratinocytes by combining imaging, force measurements and theoretical modeling. We identify a local change in force balance between differentiating cells and their environment as the key step initiating delamination. Within a homogeneous cell layer with apically polarized contractility, differentiation leads to actomyosin remodeling, redistributing cellular force exertion to the basal side. Such mechanical heterogeneity then results in differentiating cells experiencing and inward basal and outward apical forces that manifest in the formation of a +1 force defect and promote shape changes culminating in upward motion. Simultaneously, delaminating cells actively pull on their underlying neighbors, generating convergent tissue flows which close the basal layer below. Together, we propose a general physical description of delamination initiation, which may act across various multilayered epithelia.

Biomolecular condensates (BMCs) organize cellular biochemistry by concentrating selected molecules into dynamic membrane-free compartments. Yet the molecular parameters that determine not only whether condensates form, but also how they behave and what they do, remain poorly defined. Here we show that scaffold binding affinity (Kd) is a quantitative determinant of condensate phase behavior, internal dynamics and biochemical output. Using a modular SUMO-SIM system in which scaffold valency was held constant while binding affinity was systematically varied, we found that affinity governs the phase boundary, resistance to chemical perturbation, and molecular mobility of condensates in vitro and in human cells. In multicomponent mixtures, the highest-affinity scaffold dominated dense-phase composition and dynamics, revealing a hierarchical rule for condensate organization. Finally, affinity-dependent changes in condensate dynamics translated into tunable enzyme activity, establishing binding energetics as an engineerable parameter for programming condensate biochemistry.

Hyperglycaemia disrupts mitochondrial homeostasis, leading to oxidative stress, ATP depletion, lysosomal dysfunction, impaired stress signalling, and proteostasis collapse. Although static magnetic fields (SMFs) have shown therapeutic potential in diabetic models, the optimal field strength for restoring subcellular organelle integrity post high glucose associated dysfunction remains unknown. Here, using Caenorhabditis elegans exposed to 40 mM glucose, we systematically evaluated SMFs ranging from 20 to 100 mT. Hyperglycaemia induced mitochondrial fragmentation, elevated reactive oxygen species, lysosomal abnormalities, reduced ATP levels, caused developmental delay, suppression of cytoprotective stress reporters, and increased polyglutamine aggregation. Among all field strengths tested, 70 mT produced the most robust recovery, restoring mitochondrial network architecture, reducing oxidative stress, normalizing lysosomal morphology, recovering ATP homeostasis, improving developmental progression, enhancing stress-responsive signalling, reducing proteotoxic aggregates, and increasing mitochondrial resilience to secondary hypoxic stress. These findings identify an optimal therapeutic SMF window and provide the first whole-organism demonstration that appropriately tuned static magnetic fields restore mitochondrial homeostasis and reverse multiple downstream consequences of hyperglycaemic stress.

Tumor-promoting myofibroblastic carcinoma-associated fibroblasts (myCAFs) are induced by activation of transforming growth factor-{beta} signaling. However, the molecular basis of myCAF-specific transcriptional programs regulated by TGF-{beta} signaling remains poorly understood. Using a meta-analysis of single-cell RNA-seq data from 132 human breast tumor and non-tumor tissues, we show that myCAFs activate gene regulatory programs relevant to skeletal and cardiovascular development that are associated with poorer outcomes in breast cancer patients. Of note, distal-less homeobox 5 (DLX5), a master transcription factor for skeletal development, is activated in human breast myCAFs at both epigenetic and transcriptional levels. DLX5 expression is also initiated by TGF-{beta}1 treatment in human mammary fibroblasts. Immunoprecipitation and CUT&RUN assays using DLX5-expressing fibroblasts demonstrate that DLX5 interacts with Smad2/3/4 proteins, enabling their cooperative occupancy at shared genomic binding sites of target genes, thereby promoting canonical TGF-{beta} signaling and the myCAF state. DLX5-primed myCAFs also enhance paracrine TGF-{beta} signaling and neuropilin-2 expression to promote collective tumor invasion. Our findings indicate that DLX5 induces myCAF formation and promotes breast tumor progression in collaboration with canonical TGF-{beta} signaling.

Adhesion of cells is the key factor determining functioning of multicellular organisms. Viscoelastic properties of cells can be studied by multiple methods. However, attractiveness of cells or extracellular matrix without the elastic component (dispersive adhesion) is not accessible. We present an extension of force spectrometry technology: the Multivalent Adhesive Probe Atomic Force Microscopy (MAPA) that delivers dispersive adhesion maps of live cells and biosurfaces, and identifies differences unresolved by viscoelastic probing.

The blood-brain barrier (BBB) constitutes a major bottleneck for the systemic delivery of most therapeutic agents to the central nervous system. Here, we report near-infrared reversible optoacoustic modulation of the BBB permeability (NIR-ROAMBBB), leveraging endothelial tight junction targeting hyperbranched gold nanoconstructs (HBGNCs) to amplify localized optoacoustic transduction under femtosecond laser excitation. We first synthesized HBGNCs with tunable particle sizes (62-150 nm) and consistent branch morphologies via a seed-mediated growth approach, and uncovered a non-monotonic relationship between particle dimension and optoacoustic output, where the 62 nm HBGNCs generated nearly twofold stronger optoacoustic signal than gold nanorods and gold nanostars under matched excitations. Conjugation with BV11 antibodies against junctional adhesion molecule A increased HBGNC endothelial association and cerebral accumulation, enabling focal and fluence-dependent transient BBB opening (3-6 h) under 800 nm femtosecond pulsed laser excitation, as validated by in vitro trans-endothelial electrical resistance measurements, ex vivo Evans blue extravasation staining, and in vivo NIR imaging. Featuring deep tissue penetration of NIR light, robust optoacoustic conversion of HBGNCs, and negligible femtosecond laser-induced photothermal damage, this non-invasive strategy enables precise focal modulation of BBB permeability and potential drug delivery.

Many biological processes rely on mechanical forces, with protein molecules acting as key mediators. Understanding how proteins respond to mechanical stress is essential for conditions including cardiomyopathy and muscular dystrophy. Natural proteins such as dystrophin and utrophin are composed of heterogeneous folding domains with distinct mechanical properties; deciphering domain-level behavior provides insights into disease mechanisms and informs therapeutic strategies. Single-molecule force spectroscopy (SMFS) enables probing the mechanical properties of entire proteins, yet current approaches struggle to identify heterogeneous folding domains, particularly without prior knowledge. Here, we present the first automated framework to identify heterogeneous folding domains in SMFS data, applying both existing clustering methods and a novel physics-aware deep clustering architecture, LatentUnfold. LatentUnfold learns complementary latent representations from force magnitude and the force-extension physical relationship through dual autoencoders, jointly optimized for clustering assignments. We apply our framework to experimental SMFS data collected from a synthetic two-domain protein (ddFLN4-Titin I27) as well as natural protein constructs of dystrophin and utrophin, with Monte Carlo simulated datasets serving as controlled validation. For the synthetic protein, we recover mechanical properties consistent with previously reported values for each domain. For the natural proteins, we uncover two mechanically distinct domain populations - corresponding to the N-terminal domain and spectrin-like repeats - with differences in both unfolding force and contour length increase, and reveal different unfolding order between them for the first time. This work enables domain-level biological inference, overcoming prior limitations that relied on averaging and overlooked heterogeneity, thus advancing the understanding of mechanical behavior in protein unfolding.

The ability to longitudinally track clonal evolution non-invasively would transform cancer interception strategies, long before late-stage disease when most cancer genomes are analysed. Here, we demonstrate that repeated hair sampling from the same individual followed by exome sequencing enables tracking of somatic evolution in vivo over several months after chemically induced skin carcinogenesis. We found that hair follicles accumulate a higher mutation burden than spatially-matched skin and harbour mutations that spread into surrounding epidermis and persist throughout tumour progression. DNA-damaged follicles enter sustained quiescence that delays replication and repair, creating a reservoir for long-lived mutations. During premalignant progression, carcinogen-associated mutations become enriched as follicular clones expand into adjacent skin. Mutation tracking identified genes that may govern tumour predisposition and initiation, many of which are mutated at high incidence in human cutaneous squamous cell carcinoma cohorts. Hair follicles therefore provide a non-invasive readout to forecast the early development of skin cancer, enabling patient risk stratification.

Decellularized extracellular matrices (ECMs) are widely used in regenerative medicine, yet current evaluation criteria prioritize cellular removal rather than preservation of the ECM characteristics that govern tissue behavior. Here, we demonstrate that efficient decellularization is achieved across a broad range of chemical conditions, whereas preservation of structurally and biologically relevant ECM components is confined to narrow, tissue-specific windows defined by coupled detergent interactions. Quantitative proteomics revealed that intrinsic ECM composition is strongly associated with tissue-specific susceptibility to decellularization-induced damage and provided molecular context for the distinct preservation responses between tissues. Optimized matrices retained major structural ECM components and supported tissue-specific cellular organization and cell-mediated mechanical reinforcement following cellular repopulation despite uniformly low residual DNA across protocols. Together, these findings support a shift in decellularization quality assessment from DNA-based evaluation toward preservation of biologically relevant ECM and establish a composition-driven strategy for the rational design of regenerative biomaterials with tissue-relevant biological and mechanical properties.

Biological aging is accompanied by systematic changes in epigenetic modifications and chromatin organization. The reversal of the effects of aging, rejuvenation, is experimentally achieved by the transient induction of factors that modify these marks in cells and organisms. Here, we show that key features of rejuvenation experiments emerge from the biophysical interplay between dynamic epigenetic marks and the three-dimensional conformation of chromatin. Using a minimal field theory and molecular dynamics simulations, we show that the system responds in three distinct temporal regimes. The intermediary regime fulfills necessary conditions for successful rejuvenation. In this regime, the system spends time near a separatrix, allowing for high epigenetic plasticity, while memory retained in the chromatin conformation enables restoration of the original epigenetic correlations. Analysis of sequencing data further supports the predicted coupling between chromatin compaction and epigenetic correlations. Our results provide a physical explanation for how rejuvenation may remodel age-associated epigenetic states without irreversibly erasing cellular identity. We identify a general mechanism by which memory stored in a slow structural variable permits reversible remodeling of a faster internal state.

High-grade serous ovarian carcinoma (HGSC) responds poorly to immune checkpoint blockade, partly due to a macrophage-dominated immunosuppressive microenvironment. We integrated single-cell spatial proteomics and spatial transcriptomics across 50 HGSC tumors and applied SPACEstat to resolve higher-order immune communities and their transcriptional programs. We identified six immune community types, with macrophage-dominated Myelonets representing the predominant spatial pattern of immune organisation. In chemotherapy-exposed tumors, Myelonets showed coordinated lipid metabolism-immunosuppression and inflammation-MHC-II macrophage transcriptional programs, with SPP1, C1Q, VEGF, MMPs, and CCL18 linked to immunosuppressive states and fibroblasts emerging as key mediators of macrophage communication. Chemotherapy contracted large Myelonets while increasing CD8+ T-cell organization into Lymphonets. Persistent macrophage dominance within Myelonets was associated with adverse outcomes among patients who achieved a complete response to treatment. Together, we identify Myelonets as clinically relevant, multicellular immunoregulatory niches sustained by spatiotemporally coordinated macrophage programs and stromal crosstalk.

KRAS is one of the most frequently mutated oncoproteins in cancer. Its ability to induce malignant transformation relies on metabolic reprogramming that causes cells to become dependent on aerobic glycolysis as a primary source of energy and for generating biological building blocks. Thus far, the signaling mechanism used by oncogenic KRAS to promote these changes in cancer cell metabolism has not been fully elucidated. However, through studies in pancreatic ductal adenocarcinoma (PDAC) cell lines and patient-derived organoids, we now demonstrate how oncogenic KRAS triggers an increase in glycolytic activity and identify Survivin as a newly discovered and critical KRAS-signaling partner essential for promoting these metabolic changes. We show that oncogenic KRAS potently upregulates the expression of Survivin in PDAC cells and patient-derived organoids undergoing increased glycolysis, whereas depleting Survivin expression inhibits their glycolytic activity and growth. Through a combination of cellular, biochemical, and imaging approaches, we further show that Survivin promotes the formation of unique microtubule-based structures that resemble invadosome rosettes, allowing for the recruitment of the glycolytic enzymes triose phosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to these super-structures which drives the increases in glycolysis. These findings demonstrate that by directing the assembly of a microtubule-based complex of metabolic enzymes, Survivin serves as a vital link in a KRAS signaling pathway responsible for promoting the metabolic changes necessary for the accelerated growth of PDAC cells, and thus potentially highlight new therapeutic strategies for treating KRAS-dependent cancers.

Peripheral sensory neurons innervate the skin to detect mechanical, thermal, and noxious stimuli. Within the epidermis, nerve fibers terminate beneath tight junctions, shielding them from environmental exposure. Although epidermal differentiation coordinates tight junction assembly, its role in organizing nerve terminals is poorly understood. Here, we show that activation of Notch, a master regulator of epidermal differentiation, caused near-complete loss of epidermal innervation. This was largely the result of increased contractility rather than impaired differentiation. Inducing epidermal contractility was sufficient to deplete nerve fibers with striking spatial precision, and restoring normal contractility reversed this effect. Actomyosin contractility is highest in the granular layers of the epidermis, where tight junctions form and nerve fibers terminate. Ablation of nonmuscle myosin II allowed nerve fibers to extend beyond their normal termination zone and caused touch hypersensitivity. Together, these findings demonstrate that epidermal contractility positions sensory nerve endings through spatially controlled pruning and defines a mechanical boundary established by epidermal cells that restricts neuronal outgrowth.

Methods for installing synthetic functions on living cell surfaces provide powerful approaches for imaging, sensing, and manipulating cell behavior, but many require genetic modification of the target cell or chemical modification of the plasma membrane. Here, we repurpose the glycosylphosphatidylinositol-anchored protein (GPI-AP)-binding toxin aerolysin as a modular chassis for non-genetic cell-surface functionalization. We show that a non-cytotoxic, monomeric aerolysin mutant retains high-affinity and GPI-AP-dependent cell binding when genetically fused to diverse protein cargos. Fluorescent protein-aerolysin fusions robustly label multiple cell types and remain predominantly associated with the cell surface for at least 24 h, in contrast to wheat germ agglutinin, which is extensively internalized. Aerolysin can also be equipped with SpyTag/SpyCatcher to enable modular assembly with independently expressed protein cargos. Importantly, aerolysin supports functional rather than solely optical modification of the cell surface: fusion to the proximity-labeling enzyme APEX2 enables extracellular protein biotinylation, while fusion to HUH endonuclease tags enables covalent attachment of synthetic DNA to living cells. Using this latter architecture, we developed a DNA hairpin sensor that converts cell-surface nuclease activity into a fluorescent signal and distinguishes cells with different levels of extracellular nuclease activity. Together, these results establish non-cytotoxic aerolysin as a genetically encoded, soluble adapter for installing proteins, enzymes, and programmable nucleic acids onto living cells without modification of the target-cell genome.

Proteins that distinguish quiescent cells from other non-proliferative states and actively regulate their return to proliferation remain poorly understood. Here, we combined quantitative proteomics with functional image-based screening to identify regulators of the quiescence-to-proliferation transition. Amongst the functional quiescence signature proteins we identified, we focussed on integrin 11 (ITGA11) which is induced across multiple models of reversible quiescence in distinct cell types and that has low expression in proliferating and senescent cells. Although ITGA11 is dispensable for proliferation of asynchronously cycling cells, it is required for efficient cell-cycle re-entry from quiescence. Mechanistically, ITGA11 promotes YAP accumulation and nuclear localization, thereby sustaining SKP2 expression and p27 degradation during cell cycle re-entry. Depletion of p27, or pharmacological activation of YAP signalling rescues the cell-cycle re-entry defect caused by ITGA11 depletion. Together, these findings identify ITGA11 as a functional quiescence signature protein that couples extracellular matrix sensing to YAP-dependent regulation of the Skp2-p27 axis, revealing a mechanism that controls the transition from quiescence to proliferation.

Focal adhesions maintain force-bearing attachment between cells and the extracellular matrix but can also undergo dynamic remodeling. Their assembly and actomyosin tension are coupled through mechanochemical feedback. The processes underlying this feedback are not instantaneous and therefore involve a time delay. However, how this delayed feedback gives rise to stable adhesion maintenance or dynamic remodeling remains unclear. Here, paired time-lapse measurements of vinculin fluorescence and traction stress revealed distinct local adhesion-force dynamics, including low-fluctuation and recurrent fluctuation patterns. To examine how these patterns could arise, we formulated a minimal mechanochemical model coupling focal adhesion assembly and actomyosin force through delayed reciprocal feedback. The model exhibited stable and oscillatory modes depending on feedback strength, the balance of opposing feedback effects, and the effective feedback delay. Bistability and hysteretic switching also occurred in a subset of parameter space, and the oscillation period followed a power-law relation with the delay. These results suggest that stable adhesion maintenance and dynamic remodeling can emerge from a common mechanochemical feedback architecture.