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Liu, N.

Publications and source records attributed to Liu, N..

At least 19 recordsLinked to original sources

Mesoscale Soft Robotics for Mechanically Perturbing and Functionally Monitoring Responses in Human Organoids

Human organoids represent promising models for studies of significance to the biology and medical communities. Of the existing approaches for monitoring organoids, none offers the ability to apply programmable mechanical forces while simultaneously recording multi-modal physiological responses, of relevance to phenomena spanning from traumatic brain injuries to cardiac rhythm disorders. Here, we present a mesoscale soft robotic organoid interface that enables programmable delivery of forces to organoids of diverse shapes, and to map electrophysiological activity and mechanical responses. The platform combines actuation elements with integrated sensors for quantitative measurement and control. Studies using this technology reveal that spheroidal cortical organoids exhibit distinct responses to mechanical trauma, including silencing, recovery, and changes in neuronal firing patterns. Additional experiments on cardiac ring tissues demonstrate that sustained stretching induces beat-to-beat rhythm variability and altered conduction. The results establish a framework for investigating force-triggered transitions between physiological and disease-like states in human tissue models.

bioengineering↗

Matrix stiffness shapes immunometabolic states and response to PD-1 blockade in gastric cancer

The extracellular matrix of solid tumors exhibits spatially heterogeneous stiffness, yet how matrix stiffness shapes antitumor immunity in gastric cancer (GC) remains unclear. Here, we integrated anti-PD-1 clinical cohorts, GC specimens, single-cell and spatial transcriptomic analyses, a syngeneic mouse model, and tunable-stiffness hydrogels to clarify the immunological consequences of matrix stiffness. High matrix stiffness was associated with collagen accumulation and immune exclusion, while higher stiffness-associated transcriptional scores were related to poorer response to PD-1 blockade. Matrix softening markedly reshaped the immune microenvironment and enhanced the efficacy of PD-1 blockade. Mechanistically, stiff matrices promoted F-actin remodeling and YAP nuclear enrichment, driving LDHA-dependent glycolytic reprogramming in GC cells that further impaired the effector function of CD8 T cells. Intriguingly, matrix softening was accompanied by enhanced IFN-{gamma}-responsive PD-L1 expression in GC cells, consistent with adaptive immune resistance that may contribute to the limited antitumor effects of matrix softening alone. These findings suggest that matrix remodeling alleviates spatial and metabolic constraints on antitumor immunity, providing a preclinical rationale for combining matrix softening with PD-1 blockade in GC.

cancer biology↗

Decoding super-enhancer regulatory grammar and pathogenic gain-of-function variants directly from DNA sequence

Super-enhancers (SEs) drive cell-identity gene expression, yet their identification relies on epigenomic profiling (e.g., H3K27ac ChIP-seq), precluding discovery in unprofiled cellular states and leaving their underlying sequence grammar unknown. Here, we present Borzoi-SE, a deep learning framework built upon the genomic transformer Borzoi that formulates SE discovery as hierarchical, cell-type-resolved genomic object detection directly from long-range sequence across 90 human lineages. Base-resolution attribution recovers lineage-defining master transcription factors across cell types. Within SEs shared across lineages, it reveals lineage-dependent motif usage, suggesting that the same regulatory regions can support distinct cell-type-specific programs. Using in silico ablation, Borzoi-SE decoded the functional hierarchy of the {beta}-globin super-enhancer, prioritizing hypersensitive site 2 (HS2) as the dominant constituent, which we experimentally verified via CRISPR interference. Trained without variant-effect labels, Borzoi-SE identified gain-of-super-enhancer variants in different tissues. At the CHRM2 locus, a single-nucleotide variant created a de novo glucocorticoid receptor (GR) motif that recruited activated GR and potentiated adjacent MEF2 regulatory syntax, nucleating a cardiac super-enhancer. Orthogonal multi-omics and population-genetic evidence linked this variant to increased CHRM2 expression and variation in resting heart rate and PR-interval duration. Borzoi-SE establishes a general framework for decoding SE regulatory grammar and prioritizing causal non-coding variants directly from sequence.

genomics↗

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

Cause-excluded Effect Evaluation: a framework for the faithful assessment of genetic perturbation target identification

Identifying which gene drives a desired cell-state transition is a foundational inverse problem in target discovery and cell-state engineering, yet far less developed than forward prediction. We show that prevailing benchmarks inflate performance through two artefacts: training leakage, where test-perturbation cells are seen during fitting, and evaluation leakage, where the perturbed gene's own expression change exposes the answer. Here, we introduce Cause-excluded Effect Evaluation (CEE), a framework that separates train and test perturbation targets, removes target-gene self-effects from expression profiles and scores candidates in downstream response space. With CEE, we find that simple structure-based methods consistently outperform complex deep learning models across 16 single-cell perturbation datasets, revealing that the recoverable signal is governed by low-rank and additive structure in perturbation responses rather than by model complexity. Our work disentangles evaluation artefacts from genuine predictive capacity and offers a design principle for developing perturbation target identification methods.

bioinformatics↗

Extracellular cGAMP transmission exacerbates neuroinflammation in aging and multiple sclerosis

Neuroinflammation drives neurodegeneration and cognitive decline in aging, but the signals that spread this inflammation across the CNS remain unclear. Here, we show in mice that advanced age and experimental autoimmune encephalomyelitis (EAE) both result in elevated cytosolic mtDNA in microglia, which stimulates the production and export of cGAMP from these cells. Meanwhile, ENPP1, the dominant cGAMP hydrolase in the brain and spinal cord, is downregulated in both EAE mice and MS patients, releasing the brake on extracellular cGAMP accumulation. In Enpp1H362A mice, which selectively lack cGAMP hydrolysis activity, unrestrained extracellular cGAMP worsens EAE-associated paralysis and drives premature aging phenotypes including impaired motor coordination (rotarod, pole test) and reduced exploration (open field test) in a manner dependent on STING. Single-cell RNA sequencing pinpoints microglia, astrocytes, and inhibitory neurons as the principal cGAMP responders that activate STING-dependent interferon-stimulated gene induction in response to elevated extracellular cGAMP. Mechanistically, microglia import cGAMP through the LRRC8A:C channel, while astrocytes and neurons import cGAMP via the glutamate antiporter system xc-, reinforced by SLC1A2-mediated glutamate uptake in astrocytes and SLC38A1/2-fueled glutamine-to-glutamate synthesis in neurons. In isolated primary astrocytes and neurons, high intracellular glutamate and system xc--driven redox demands favor cGAMP uptake, raising the possibility that neurotransmitter cycling and redox burden shape cellular vulnerability to cGAMP immunotransmission in vivo. Together, these findings position ENPP1 as a protective brake on neuroinflammation in aging and MS, nominating cGAS inhibition and CNS ENPP1 enhancement as therapeutic strategies.

cell biology↗

NSD2 deficiency disrupts the epigenetic landscape of cochlear hair cells to enhance ECM expression and to perturb cochlear hair cell function

Mammalian cochlear hair cells (HC) are crucial for hearing, and histone modifications may play an important role in HC maturation and functions. However, whether and how NSD2, a histone H3 lysine 36 (H3K36) dimethyltransferase, affects cochlear HC maturation remains unclear. Here, we established an HC-specific Nsd2 knockout mouse model and discovered that the loss of NSD2 results in severe structural defects in stereociliary bundles and profound hearing impairment. Integrated multi-omics profiling revealed that NSD2 deficiency leads to a decreased expression of H3K36me2, which in turn alters genome-wide chromatin accessibility and gene expression. Mechanistically, NSD2 deficiency triggers the aberrant upregulation of extracellular matrix (ECM) genes at the transcriptional level, causing excessive collagen accumulation and compromising tissue structure. Crucially, ECM intervention can mitigate NSD2-deficiency mediated hearing damage. Our study reveals an epigenetic mechanism by which NSD2 regulates cochlear HC maturation through inhibition of chromatin remodeling-induced ECM accumulation, and provides a potential new therapeutic direction for hearing impairment.

cell biology↗

Circulating apoB-containing lipoproteins constituted blood-borne innate immune barrier limits ZIKV dissemination and congenital infection risk

Following establishment of primary viremia, flaviviruses require prompt penetration through vascular endothelium to achieve systemic dissemination, yet most infections remain asymptomatic or self-limited. Canonical defenses, including complement and phagocyte clearance, cannot fully explain this containment, suggesting an additional blood-borne antiviral barrier. Here, we identify apoB containing lipoproteins as potent restriction factors against Zika virus (ZIKV), a devastating danger of global pregnancy. By displaying surface accessible phosphatidylserine (PS), they competitively occupy host PS receptors and block entry by viruses exploiting apoptotic mimicry, including flaviviruses, Ebola, and chikungunya virus. In vivo, increasing apoB lipoproteins enhances serum antiviral activity and limits systemic ZIKV dissemination. This barrier extends to the maternal fetal interface, where elevated maternal LDL attenuates vertical transmission and fetal abnormalities. Its efficacy is modulated by gestational fluctuations in maternal LDL level and low abundance in fetal circulating LDL. Collectively, apoB containing lipoproteins form a constitutive blood-borne innate immune barrier that restrains apoptotic-mimicry viruses during the intravascular phase, limits viral dissemination and reduces congenital infection risk. This study provides a rationale for developing diet augmentation strategy to strengthen this innate barrier in at-risk individuals.

microbiology↗

Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems

Scientific software is often locked in its source language, callable from others but not natively extensible or built upon. We present Bio-Babel (biobabel.stanford.edu), an autonomous framework that rebuilds software natively in target ecosystems and makes it agent-callable, shipping each package with an agent-readable contract of its usage. Reconstructing a hierarchical, interdependent R-to-Python single-cell stack, Bio-Babel reproduced the originals faithfully and revealed pancreatic differentiation dynamic defects under graded SWI/SNF loss.

bioinformatics↗

Five novel ubiquitous totiviruses function as virulence-promoting symbionts in the obligate biotrophic fungus Puccinia triticina

Mycoviruses modulate fungal fitness and pathogenicity, yet their biological roles in obligate biotrophic phytopathogens remain poorly understood. Here, we report the first functional characterization of totiviruses in rust fungi, identifying five novel totiviruses, designated Puccinia triticina totivirus 1 to 5 (PtTV1?PtTV5), from the wheat leaf rust fungus Puccinia triticina (Pt). All five PtTVs possess the canonical genomic architecture of Totiviridae, including two overlapping ORFs and a conserved ?1 ribosomal frameshifting motif. Transcriptional profiling revealed that PtTVs are highly expressed during early Pt infection. PtTV-encoded proteins suppressed BAX-triggered programmed cell death in Nicotiana benthamiana, indicating immune-suppressive activity. Using BSMV-mediated host-induced gene silencing (HIGS), we showed that knockdown of PtTV transcripts significantly impaired fungal hyphal expansion and uredinial formation, concomitant with enhanced host H?O? accumulation. A survey of 90 Pt field isolates from four major wheat-growing regions of China revealed that PtTVs are ubiquitously distributed in natural rust populations. Collectively, these findings demonstrate that totiviruses function as virulence-promoting symbionts in Pt, establishing for the first time a functional link between totiviral infection and enhanced pathogenicity in cereal rust fungi and identifying candidate targets for RNAi-based disease control.

plant biology↗

Trehalose exerts cryoprotective effects on piglet testicular tissue

The cryopreservation of testicular tissue is crucial for maintaining male fertility; However, its efficacy is often compromised by oxidative stress and mitochondrial dysfunction. Trehalose, a natural cryoprotectant, demonstrates significant potential, yet its specific mechanisms, particularly in mitochondrial regulation, remain insufficiently characterized. This study aimed to investigate the cryoprotective effects of trehalose on testicular tissue from 18-21-day-old piglets, with a focus on mitochondrial metabolism. Samples were cryopreserved via a slow-freezing protocol in a modified standard solution containing 200 mmol/L trehalose. The protective effect was evaluated by measuring testosterone synthesis, blood testis barrier (BTB) and spermatogenesis. Additionally, protective outcomes were assessed by measuring cell viability, tissue morphology, reactive oxygen species (ROS) levels, apoptosis rates, and testosterone secretion following freeze-thaw cycles. Transcriptomic sequencing and bioinformatics analyses were conducted to elucidate the underlying molecular mechanism. Cryopreservation led to reduced testosterone synthesis and secretion, decreased levels of BTB-binding proteins, and impaired spermatogenesis. Results indicated that 200 mmol/L trehalose significantly improved cell survival, decreased apoptosis and ROS levels, and enhanced testosterone secretion. 200 mmol/L trehalose partially increased the expression of StAR and CYP11A1 genes associated with testosterone synthesis while it protected the tight junction proteins Claudin-11, ZO-1 and the gap junction protein Cx43. Consequently, it exerted a reproductive protective effect by increasing the expression of key spermatogenic regulators DDX25, HMGB2, acrosomal protein DYP19L2, and sperm tail proteins AKAP4 and CFAP44. Transcriptomic profiling demonstrated that trehalose predominantly restored the transcriptional expression of genes involved in the mitochondrial electron transport chain and oxidative phosphorylation pathways, including ND2, COX2, ATP8, ATP6, ND5, ND6 and CYTB. These findings indicate that trehalose primarily protects piglet testicular tissue during cryopreservation by enhancing mitochondrial function, thereby providing a molecular basis for optimizing cryopreservation protocols.

cell biology↗

Sepsis Subtypes in Blood and Liver Define Precision Strategy for CXCR2 Blockade

Sepsis is classified into distinct transcriptomic endotypes. Yet specific cellular drivers for those subtypes remain ambiguous. Although dysregulated CXCL8-CXCR1/2 signaling and neutrophil hyperactivation are implicated in severe endotypes, the therapeutic window and organ-specific consequences of CXCR2 antagonism remain unclear. To determine whether murine transcriptomic subtypes (MTSs) recapitulate human consensus transcriptomic subtypes (CTSs) and evaluate how subtype state dictates the efficacy and trade-offs of Danirixin in polymicrobial sepsis. We reanalyzed septic patients whole-blood CITE-seq data to characterize CXCL8- CXCR2 signaling. Using a severity-stratified murine polymicrobial model, we evaluated Danirixins efficacy. Endpoints included 7-day survival, cytokine profiling, and hepatic histology. Early (24-h) multi-compartment assessments of bacterial burden, NETosis, immune infiltration, and paired blood-liver bulk RNA sequencing informed MTS classification and mechanistic insights. Human CTS1 exhibited neutrophil and progenitor expansion, elevated CXCL8/CD11b expression, and reduced CXCR2, defining a hyperactivated, dysregulated myeloid state. Applying CTS-derived gene signatures to murine tissues identified three MTSs correlating with pathogen load and interleukin-6. Human CTS1 dysregulation was mirrored in murine MTS3. Crucially, Danirixin improved 7-day survival in MTS3 sepsis. Conversely, in MTS1, Danirixin attenuated systemic NETosis and hepatic injury but exacerbated bacterial dissemination, without improving survival. Murine transcriptomic subtypes translationally model human sepsis subtypes. In severely dysregulated host-response states (MTS3/CTS1), CXCR2 antagonism effectively mitigates maladaptive, neutrophil-driven immunopathology. However, in less severe subtypes, it compromises early bacterial containment. These findings therefore support for endotype-guided precision targeting of CXCR2 in sepsis. One Sentence SummaryTargeting CXCR2 improves sepsis survival only in a specific molecular subtype, showing that host traits dictate therapeutic outcomes.

systems biology↗

Destabilization of intratumor Tregs by CTLA-4 engagement confers anti-CTLA-4-driven immunotherapy

Immune checkpoint inhibitors (ICI) that are antibodies against CTLA-4 have achieved therapeutic effects on multiple types of cancers 1-4, but the mechanisms underlying the therapy remain incompletely understood. In contrast to the initial theory that the antibody blockades CTLA-4 on T cells is of central importance, it has recently been demonstrated that selective reduction of CD4+Foxp3+ regulatory T cells (Tregs) in the tumor microenvironment by the antibody plays a key role in the anti-tumor effects5-8, although this phenomenon remains under debate in human patients9-12. We show here that anti-CTLA-4 antibody engages CTLA-4 in Tregs specifically in the tumor tissues to reduce their stability and survival and weaken their suppressive function through upregulating TGF-{beta} signaling. This leads to the antibody-mediated - upregulation of CD4+ and CD8+ effector T cell anti-tumor immunity and consequently cancer immunotherapy. Specifically, anti-CTLA-4 antibody directly stimulates CTLA-4 in intratumor Tregs to enhance their TGF-{beta} receptor I (T{beta}RI)-mediated TGF-{beta} signaling13. This results in reduction of IL-2 receptor CD25 expression and downregulation of lactate metabolism in intratumor Tregs to reduce their stability and survival 14-16, and also compromises their suppressive function by inhibiting Foxp3 expression. This activity requires high levels of CTLA-4 expression in the intratumor Tregs and the presence of antibody Fc receptors in the tumor tissues. Strikingly, deletion of T{beta}RI specifically in Tregs completely prevents the reduction of intratumor Tregs and abrogates the anti-CTLA-4-mediated cancer immunotherapy. In contrast to intratumor Tregs, anti-CTLA-4 antibody treatment blocks CTLA-4 in the intratumor CD4+ Foxp3- and CD8+ T effector cells and in the peripheral Tregs to decrease their T{beta}RI expression and increase their expansion due to their relatively low levels of CTLA-4 in the same tumor bearing mice. Significantly, the engagement of CTLA-4 by anti-human CTLA-4 antibody (ipilimumab) also upregulates TGFBR1 but decreases Il2RA expression and lactate metabolism in human Tregs in vitro and in humanized mice in vivo, leading to suppression of tumor progression. We have provided additional mechanism underlying anti-CTLA-4-mediated anti-tumor effects through destabilizing intratumor Tregs by CTLA-4 engagement-mediated TGF-{beta} signaling. This could lay a theoretical foundation for designing optimal immunotherapy based on anti-CTLA-4 antibody in cancer patients.

immunology↗

Health-associated gut bacteriocins target TLR4 to suppress intestinal inflammation

The human microbiome maintains host immune homeostasis by secreting bioactive metabolites. However, extending beyond well-characterized metabolites, the functions of most microbiome-encoded peptides remain poorly defined. In this study, we developed a multi-cohort metagenomic framework to profile protective class II bacteriocins--unmodified, ribosomally synthesized peptides--that are enriched in healthy individuals but depleted in patients with inflammatory bowel disease (IBD). We have designated these health-associated bacteriocins as gutcins. Two gutcins, which lack canonical antimicrobial activity, potently attenuate intestinal inflammation in murine models. Cryo-electron microscopy (cryo-EM) reveals that one gutcin, named gutcin 03, directly engages the C-terminus of TLR4, blocking its dimerization and downstream inflammatory signaling. Guided by this structural interface, we generated truncated variants with enhanced potency, demonstrating the amenability of these simple peptides to rational optimization. Collectively, our findings reposition class II bacteriocins from antimicrobial agents to endogenous immunomodulatory effectors and establish a structural and mechanistic foundation for their development as next-generation therapeutics for inflammatory intestinal disorders.

microbiology↗

Multidimensional atlas of RNA-regulated proteins revealed by RNA-dependent thermal proteome profiling

RNA and proteins interact pervasively in cellular processes, yet the functional relevance of most RNA-binding proteins remains unknown. To address this, we developed RNA-dependent thermal proteome profiling (RTPP), a method that identifies RNA-regulated proteins (RRPs) by detecting changes in a proteins structural stability upon RNA binding, without requiring crosslinking or enrichment. Applying RTPP in HEK293T cells revealed 1,664 RRPs, including 257 previously undetected RNA-binding "orphans". One such orphan, SGK3, binds the lncRNA CASC15, facilitating its PtdIns(3)P binding, endosomal recruitment and kinase activity. We further generated a tissue-specific RRP atlas, identifying interactions unique to particular organs, including hippocampus-specific RRPs dysregulated in Alzheimers disease. Integrating RTPP with proximity labeling resolved RNA-binding heterogeneities across subcellular compartments. Live-cell RNase treatment also uncovered proteins associated with cell surface RNA, revealing that RO60 form nanoscale clusters with glycoRNA. RTPP provides a powerful approach to decipher functional RNA-protein interactions across multiple biological dimensions.

molecular biology↗

A Minimally Invasiveness Hybrid Brain-Computer Interface: A Distributed, Scalable and Evolvable Architecture for Whole Brain Access

Brain-computer interfaces face a fundamental trade-off between the signal fidelity and stimulation precision of noninvasive systems and the surgical burden and scalability of invasive systems. Non-invasive BCIs suffer from low signal quality and poor stimulation accuracy due to the skull barrier and the variability introduced by the scalp and skull. Existing invasive BCIs rely on traumatic surgical procedures or brain-penetrating electrodes, which limits their spatial extensibility, application, and patient acceptance. Here, we introduce a minimally invasive hybrid BCI architecture that uses the skull as a distributed interface layer rather than treating it solely as a barrier. The hybrid BCI comprises four integrated components: (1) the safe and smart micro-hole craniotomy; (2) distributed microelectrodes subcutaneously implanted in micro-holes in the skull with the distal end in contact with the dura; (3) an external bi-directional wearable headset for coupling, recording, stimulation, and channel selection; and (4) an AI-assisted planning and control agent. Animal studies have shown that micro-holes with a diameter of 300-800 m can be safely and conveniently prepared at any predefined locations across the skull without impairing the dura. In vivo experiments on rats demonstrate that the hybrid BCI with skull-implanted microelectrodes evidently increases resting-state spectral power and improves the signal-to-noise ratio of somatosensory and steady-state visual evoked responses compared to the scalp EEG; the computational modelling shows that distributed skull-dura microelectrodes can increase the intracranial electrical field strength and steer focused temporal-interference fields towards predefined deep brain targets. These findings will lay a solid foundation for future endeavors in wireless integration, safety evaluation and clinical benefits of the hybrid BCI. In summary, we propose the hybrid BCI as a distinct minimally invasive BCI paradigm with the great potential as a distributed, scalable, and upgradable neural interface that can expand the clinical application of minimally invasive BCI techniques.

bioengineering↗

Clinically derived micro- and nanoplastics uptake drives spatiotemporally confined metabolic stress revealed by bond-selective imaging

Although microplastics and nanoplastics (MP/NP) are pervasive environmental contaminants, our understanding of cellular toxicity remains incomplete, as adverse effects are often attributed to long-term intracellular accumulation, while the spatiotemporal onset of cellular damage remains poorly defined. Here, we employ chemical-bond-selective stimulated Raman scattering (SRS) microscopy and cell models that decouple continuous exposure from intracellular retention to directly visualize clinically derived MP/NP-cell interactions. Cellular stress occurs primarily during MP/NP exposure, accompanied by alterations in lipid droplet (LD) composition. In contrast, following extracellular removal, intracellularly retained MP/NP become largely inert, with recovery of lipid metabolism and cellular functions. Lipidomics identifies arachidonic acid (AA) as a key dysregulated metabolite, and SRS imaging further reveals transient, spatially confined AA enrichment in MP/NP-proximal LDs during uptake. Importantly, phospholipid coating of MP/NP attenuates LD alterations and cytotoxicity while preserving particle internalization, establishing uptake-driven metabolic stress, rather than long-term intracellular retention, as primary source of MP/NP-induced damage.

biophysics↗

Persistent Post-Inflammatory Matrix Stiffening Defines a Premalignant Mechanical Niche in Ulcerative Colitis-Associated Neoplasia

Patients with long-standing ulcerative colitis (UC) remain at risk for colorectal neoplasia even after overt inflammatory activity improves, suggesting that repaired mucosa may retain residual tissue-level abnormalities. Whether extracellular matrix remodeling leaves a persistent mechanical cue that contributes to early neoplastic remodeling is unknown. Here we identify post-inflammatory matrix stiffening as a premalignant mechanical niche in UC-associated neoplasia. In human colonic biopsies, collagen remodeling and atomic-force-microscopy-based mucosal stiffness increased from non-UC controls to UC and UC-associated dysplasia. A stiffness-associated transcriptional program was also enriched in histologically non-dysplastic mucosa from patients with UC-associated neoplasia. In mouse models, colonic stiffness increased along the colitis-to-tumorigenesis axis and remained elevated during apparent recovery, when epithelial permeability, junctional protein loss, crypt proliferation and nuclear {beta}-catenin accumulation persisted despite reduced disease activity. Stiffness-controlled intestinal epithelial cultures showed that stiff substrates were sufficient to disrupt ZO-1 organization and enhance {beta}-catenin redistribution, particularly under TNF- stimulation. Pharmacological matrix normalization with {beta}-aminopropionitrile partially restored barrier organization and attenuated early epithelial remodeling in vivo. Single-cell profiling identified a stiffness-associated MMP7-positive/YAP-active epithelial state that was enriched in collagen-rich regions and reduced after matrix softening. Inhibition of YAP or MMP7 attenuated stiffness-associated junctional disruption and {beta}-catenin redistribution. These findings suggest that inflammatory recovery and mechanical recovery can be uncoupled, and that persistent mucosal stiffening provides a tissue-level mechanism by which chronically injured UC mucosa may remain biologically vulnerable to premalignant epithelial remodeling.

Cancer Biology↗