Biology subjects

Zhong, M.

Publications and source records attributed to Zhong, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Adjacent Z-DNA contributes to the formation of homologous DNA triplex

Whether the homologous parallel triplex (HP-triplex, formed by dsDNA and a homologous ssDNA) acts as an intermediate prior to DNA recombination remains controversy, owing to the intrinsic instability and lake of experimental data. Here, we report a HP-triplex that is stable at least at 35 oC under protein-free conditions. Two complementary circular ssDNAs were first hybridized at a 1:1 ratio to form an LR-chimera containing both Z-DNA and B-DNA. Then the circular homologous ssDNA (T-rich) was found to easily hybridize with this LR-chimera to form the HP-triplex (strand ratio of 2:1), involving both left- and right-handed triplex parts under the topological constraint. The third strand locates in the major groove and forms hydrogen bonds with both bases in each base pair of dsDNA without obvious strand exchange. Our data indicate that the third-strand ssDNA may first bind to the B-DNA region, followed by association with the Z-DNA region to assemble the full triplex structure. Structural simulations and analyses reveal that topological constraint imposed by the circular architecture raises the energy barrier for strand displacement, thereby stabilizing this triplex. In summary, the dynamic HP triplex can be stabilized via a Z B junction structure that mimics the in vivo one formed by negative supercoiling. These findings demonstrate that HP-triplex may act as an intermediate for DNA recombination, anti-gene strategy, and other interactions between dsDNA and homologous ssDNA or RNA.

molecular biology↗

bioRxiv2026

GluD1 Modulates GluN2B-containing NMDAR Function and Plasticity at Subicular Synapses

Dysregulation of the delta-type glutamate receptor GluD1 and N-methyl-D-aspartate receptors (NMDARs) is implicated in neuropsychiatric disorders including schizophrenia and intellectual disability, and GluD1 modulates NMDAR response in hippocampal neurons. However, the precise mechanisms by which GluD1 influences specific NMDAR subtypes remain undefined, representing a critical gap given the reliance of synaptic plasticity and cognition on NMDAR composition. GluN2A- and GluN2B-containing NMDARs are essential for synaptic long-term potentiation (LTP) and contextual learning and memory. Here, we used CRISPR/Cas9 to generate GluD1 knockout (KO) in cultured hippocampal neurons and observed a selective decrease in GluN2B-containing NMDAR responses. In acute hippocampal slices, GluD1 KO similarly reduced GluN2B-containing NMDAR currents at ventral CA1[->]subiculum synapses and impaired LTP at these synapses. In vivo, region-specific GluD1 deficiency in the ventral subiculum disrupted long-term contextual memory, indicating a critical role for GluD1 in cognitive processes. These findings demonstrate that GluD1 is indispensable for preserving GluN2B-containing NMDAR function, synaptic plasticity, and memory, providing molecular insight into how GluD1 regulates NMDAR subtypes implicated in synaptic dysfunction in neuropsychiatric disorders. Understanding this mechanism will guide the development of therapeutic strategies that selectively target GluD1-dependent modulation of NMDAR subtypes in brain disease.

neuroscience↗

bioRxiv2026

Conformational dynamics of exopolysaccharides underlie biofilm matrix mechanics in Vibrio cholerae

Polysaccharides remain the least understood biomacromolecules, particularly in terms of the relationship between their chemical structure and physical properties. On the other hand, polysaccharides often serve as the main structural components in biofilms: surface-attached aggregates of bacterial cells encased within a mechanically resilient extracellular matrix. The large chemical space explored by bacteria within biofilms provides excellent opportunities to establish the structure-function relationship for polysaccharides. In this paper, we systematically characterize various polymer properties of Vibrio polysaccharide (VPS), the major exopolysaccharide in biofilms formed by Vibrio cholerae, the causative agent of pandemic cholera. Using a combination of shear rheology, dynamic and static light scattering, and small-angle X-ray scattering, we measure the viscosity, molecular weight, persistence length, radius of gyration, and hydrodynamic radius of this chemically unique biopolymer. Combining all-atom and coarse-grained simulations, we show how the conformational flexibility of a single glycosidic linkage within each VPS monomer can lead to dramatic compaction of the entire polymer chain and nonclassical entanglement behavior. Our comprehensive quantification represents a rare endeavor for bacterial biofilms, whose matrix composition and physical properties remain largely nebulous; it also represents a significant step towards a detailed understanding of the molecular origins of biofilm mechanics.

biophysics↗

bioRxiv2026

Spatial Glyco-Codes Define Human Liver Pathology and Progression

Glycosylation is a fundamental process regulating cellular function, tissue organization, and disease progression. However, comprehensive glycan profiling at single-cell spatial resolution remains largely inaccessible, particularly in clinical archival tissues. Here we develop spatial-GPT, a multimodal platform for simultaneous profiling of glycans, proteins, and/or transcripts in archival formalin-fixed paraffin-embedded (FFPE) tissues. Using a panel of 30 DNA-encoded lectins recognizing major mammalian glycan motifs and structural classes, sequencing-based spatial-GPT (DBiT-GPT) mapped the spatial glycome, proteome, and transcriptome across 16 human liver specimens encompassing steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC), leading to identification of spatial glyco-codes - combinatorial glycan states associated with distinct cellular identities, tissue features, and pathological processes. Unexpectedly, glyco-codes alone were sufficient to resolve major cell types, disease states, and HCC subtypes, revealing a previously unappreciated level of biological information encoded within the tissue glycome. Spatial glycomics uncovered tumor-like glyco-codes in premalignant regions, suggesting that glycan reprogramming may precede overt malignant transformation. Using imaging-based single-cell spatial glycan-protein profiling (CODEX-GP), we track glyco-codes across the whole-tissue architecture of 3 representative HCC samples. We further examined the glyco-codes across more than 300 patient specimens and quantified cell-type- and disease-specific glyco-codes as well as glycan-defined immune-evasion, T-cell-exhaustion, and steato-fibrotic niches. Together, these findings establish spatial glyco-codes as a previously unrecognized layer of tissue organization that encodes cellular identity, tissue function, and disease progression. The ability of glyco-codes to distinguish major liver pathologies across independent patient cohorts further highlights their potential as a new class of molecular histopathology biomarkers.

pathology↗

bioRxiv2026

Cardiovascular Benefits of Menopause Hormone Treatment is Age-Dependent

BackgroundHormone therapy (HT) has not consistently reduced atherosclerotic cardiovascular disease (ASCVD) events in post-menopausal women, yet the underlying mechanisms remain poorly understood. MethodsFemale Ldlr-/- mice with established atherosclerosis were subjected to surgical menopause and treated with 17{beta}-estradiol (E2) following lipid normalization. Studies were performed in aging and young mice. To determine whether inflammation mediates the age-dependent response to HT, a cohort of aging mice underwent transplantation with Ifn{gamma}-/- bone marrow (BM) before hormone treatments. Metabolic parameters, HDL function, systemic inflammation, atherosclerotic burden, liver metabolic and oxidative stress signaling, and hepatic estrogen receptor signaling were evaluated. ResultsIn aging mice, menopause E2 treatment failed to reduce established atherosclerosis as shown in sham operated mice during lipid normalization. Instead, E2 treatment increased circulating IFN{gamma} and IL-6, impaired HDL antioxidant and cholesterol efflux functions, and promoted inflammatory and vulnerable plaque phenotypes. Suppression of inflammation through Ifn{gamma}-/-BM transplantation restored HDL function and significantly reduced atherosclerosis in E2-treated aging mice. In contrast to aging mice, young mice exhibited reduced systemic and plaque inflammation, improved HDL functions and atherosclerosis following E2 treatment. Liver RNA sequencing and qPCR validation identified activation of inflammatory, oxidative stress, and lipid metabolic pathways in aging E2-treated mice, which were largely attenuated following Ifn{gamma}-/-bone marrow transplantation as well as in young mice. Compared to young mice, aging mice presented hepatic estrogen receptor remodeling characterized by reduced estrogen receptor (ER) expression and increased G-protein coupled estrogen receptor (GPER) expression. Constitutive GPER activation was accompanied by induction of NOX1-dependent oxidative stress, which was further exacerbated by E2 treatment, leading to persistent inflammation. ConclusionsThe cardiovascular effects of estrogen therapy are fundamentally age dependent. Aging shifts estrogen signaling toward hepatic oxidative stress and inflammation through increased GPER. While E2 treatment preserves both metabolic and cardiovascular protection in young mice, aging exacerbates GPER-NOX1-mediated oxidative stress, resulting in impaired HDL function and persistent residual ASCVD risk. These findings identify inflammation-driven, non-lipid mechanisms as potential therapeutic targets to improve cardiovascular outcomes during hormone therapy in postmenopausal women.

physiology↗

bioRxiv2026

Decoding Spatial Programs in Human Glioblastoma Through Surprisal Information-Theoretical Analysis

Glioblastoma (GBM) is a highly heterogeneous and invasive brain tumor in which complex interactions among tumor cells, immune cells, and neurons shape disease progression and therapeutic resistance. Resolving spatial patterns programs in glioblastoma (GBM) requires analytical approaches that go beyond variance-driven embeddings. Here, we applied thermodynamic surprisal analysis, an information-theoretic decomposition framework, to spatial transcriptomic sequencing from human GBM specimens to identify orthogonal constraint modes that capture dominant and previously hidden spatial programs. Surprisal analysis revealed structured patterns in the data that are not highlighted by standard approaches such as PCA or cell type deconvolution, including immune-activation-associated signatures as well as spatial programs consistent with synapse remodeling. Coupling surprisal decomposition with spatial ligand-receptor interaction analysis, NICHES, along with multiplexed protein imaging connected these spatial hidden modes to reveal potential communication networks. Together, these results position surprisal analysis as a powerful, complementary strategy for interrogating spatial tumor architecture, enabling discovery of non-obvious spatial programs and interactions that are obscured by variance-based methods.

systems biology↗

bioRxiv2026

Decoding and Targeting Coordinated CDKN1A and CDKN2A Senescence Programs in ECM-Dominant Cardiovascular Pathologies

Cellular senescence is a hallmark of aging and an emerging therapeutic target; however, its role as a context-specific driver of disease remains incompletely defined, and senolytic therapies have shown inconsistent clinical benefit. Here, we identify extracellular matrix (ECM)-dominant pathologies as a major class of senescence-driven disease, characterized by inflammation, matrix degeneration, and progressive tissue dysfunction. Using integrated single-cell transcriptomics, spatial profiling, and multiplex imaging across human specimens and murine models, we demonstrate that senescent fibroblasts, rather than canonical myofibroblasts, constitute the principal disease-driving cell state in myxomatous mitral valve disease (MMVD) and related conditions. These cells exhibit coordinated CDKN1A inflammatory and CDKN2A ECM-remodeling programs that form a feed-forward circuit linking immune activation to matrix disorganization and functional decline. Senescence extends beyond fibroblasts to endothelial and immune compartments, establishing a multicellular senescent milieu that reinforces intercellular crosstalk and disease progression. Senolytic treatment (dasatinib plus quercetin or fisetin) restores ECM architecture and improves cardiac function, outperforming pathway-specific anti-inflammatory and antifibrotic approaches. Cross-disease analyses further reveal conservation of this coordinated CDKN1A/CDKN2A senescence programs across multiple ECM-dominant cardiovascular diseases, including aortic aneurysm and calcific valve disease. Notably, in vivo single-cell transcriptomic profiling following multiple senolytic treatments provides whole-transcriptome resolution of context-dependent cellular responses. Collectively, these findings establish context-specific senescence as a central organizing mechanism in ECM-dominant diseases and support a shift from generalized anti-aging strategies toward precision senolytic prevention or therapy. Given that valvular and aortic diseases affect millions and increase markedly with age to a prevalence comparable to major cancers, these results indicate a potential solution to a substantial and underrecognized clinical burden.

Cell Biology↗

bioRxiv2026

Candida albicans reprograms host inosine metabolism to drive immunosuppressive macrophage polarization and gastric cancer carcinogenesis

Gastric cancer (GC) is strongly associated with changes in the gastric microbiome. However, the direct contribution of individual pathogenic species to tumor initiation and progression remains poorly defined. Here, we identified Candida albicans (C. albicans), a fungus that ranks as the most significantly enriched taxon in GC tissues, can directly promote gastric carcinogenesis. We found that when C. albicans alone was colonized into the gastric mucosa of mice, it induced the complete sequence of GC-associated preneoplastic lesions, including chronic gastritis, mucinous metaplasia, and atypical hyperplasia, with 16% of colonized animals progressing to low-grade intraepithelial dysplasia. In K19-C2mE transgenic mice, a model of spontaneous GC formation, infection with C. albicans significantly accelerated GC formation, with synergistic effects observed upon co-infection with the well-known gastric carcinogen, Helicobacter pylori. Mechanistically, C. albicans upregulated inosine levels in both gastric tissues and circulation. This inosine promoted polarization of macrophages toward an M2-like phenotype by activating the adenosine A2a receptor (A2aR), creats an immunosuppressive microenvironment that protects GC cells from the tumoricidal effects of anti-tumor immunity. Depletion of M2 macrophages or pharmacological inhibition of A2aR attenuated C. albicans-mediated tumorigenesis. Clinically, elevated inosine levels correlated with prior C. albicans exposure and poorer outcomes of GC patients. Our findings establish C. albicans as a direct pro-tumorigenic pathogen in GC and highlight the inosine-A2aR-M2 macrophage axis as a promising target for therapeutic intervention.

cancer biology↗

bioRxiv2026

Modeling Meibomian Gland Development and Dysfunction: A Mouse-Derived Organoid System Reveals Hippo-YAP as a Critical Regulator

The developmental program governing meibomian gland (MG) morphogenesis and proliferation remains poorly understood, largely due to the lack of physiologically relevant model systems. Here, we established a novel high-fidelity, three-dimensional organoids model derived from mouse meibomian gland (mMGO) epithelium. Transcriptomic and phenotypic analyses demonstrated that mMGOs faithfully recapitulate postnatal gland development in vivo, including dynamic transcription program, branching morphogenesis, lineage differentiation, and functional lipid accumulation. Leveraging this model, we identified the Hippo-YAP pathway as a pivotal regulator of MG epithelial proliferation and homeostasis for the first time. YAP inhibition severely impaired organoids growth, while pharmacological inhibition of Hippo pathway with XMU-MP-1 enhanced proliferation and progenitor clonogenicity. Crucially, in inflammation-induced atrophic organoids, XMU-MP-1 treatment rescued YAP nuclear localization and stimulated regrowth and functional restoration. Our study provided new mechanistic insights and a robust organoids platform for MG development research, and nominated targeted Hippo pathway inhibition as a promising strategy to reverse glandular atrophy in meibomian gland dysfunction.

developmental biology↗

bioRxiv2026

SpaCir-VDJ: a broadly compatible circularization strategy for spatial immune repertoire profiling

Deciphering the spatial organization of immune clonal lineages is critical for understanding the evolution of adaptive immune responses. However, mainstream spatial transcriptomics platforms struggle to reconcile cost-effective short-read sequencing with the simultaneous and efficient capture of V(D)J sequences. To address this gap, we developed SpaCir-VDJ, an approach that utilizes a "multiplex PCR enrichment plus library circularization" strategy to integrate spatial barcodes and V(D)J CDR3 regions into a compact circular template optimized for standard short-read sequencing. This workflow is accompanied by an automated computational pipeline designed for circular-library data parsing, sequence reconstruction, spatial barcode deconvolution, and high-fidelity clonotype calling. In human lymphoid tissues, SpaCir-VDJ delineated germinal center (GC)-associated clonal organization and isotype-linked somatic hypermutation (SHM) patterns. Notably, lineage-based spatial analyses inferred inter-GC clonal redistribution events, suggesting that GCs in the analyzed samples may not be fully isolated reaction units. Functional perturbation provided orthogonal support for candidate SHM regulators identified by spatial analysis, with knockdown of MDM4, LYN, EAF2, and H2AFY each leading to reduced SHM. Finally, in gastric cancer, SpaCir-VDJ localized dominant BCR lineages within tertiary lymphoid structures and tumor-margin plasma cell-rich regions, with lineage patterns consistent with extension toward the tumor interior. We further observed a significant positive correlation between cumulative tumor mutations and spatial TCR diversity, consistent with a spatial association between local mutational burden and T-cell remodeling within the tumor microenvironment. Collectively, SpaCir-VDJ provides a scalable and cost-effective framework for interrogating the spatiotemporal dynamics of immune microenvironments.

immunology↗

bioRxiv2026

Dysregulation of Hippo Signaling Pathway as a Convergent Mechanism Underlying Choroid Plexus Defects in Bipolar Disorder

Bipolar disorder (BD) is a prevalent and highly heritable psychiatric condition. Developmental mechanisms are implicated but the specific molecular origins remain unclear. The choroid plexus (ChP), which regulates cerebrospinal fluid (CSF) and brain homeostasis, has been implicated in BD, but its role is poorly understood. Here, we identify aberrant expansion of ChP in human cortical (hCOs) and ChP organoids (hChPOs) derived from, and in vivo structural magnetic resonance imaging (sMRI) scans of, individuals with BD compared to healthy comparison individuals. Single-cell transcriptomics revealed a lineage bias toward ChP fate in BD hCOs, accompanied by structural enlargement observed in both BD hChPOs and ChP in sMRI scans from individuals with BD. Comprehensive transcriptomic profiling implicates early hyperactivation of the Hippo signaling pathway in neural progenitor cells as a convergent mechanism driving ChP overgrowth. Whole-genome and genome-wide association study analyses highlight recurrent genetic variants in Hippo regulators, including STK4 and YAP1, suggesting genetic priming. BD hChPOs exhibit disrupted epithelial junctions and altered in vitro CSF secretion. These findings position the ChP as a genetically and developmentally predisposed to pathology in BD and highlight organoids as a platform for translational discovery in diagnostics and therapeutics.

developmental biology↗

bioRxiv2026

Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches

Immunosenescence, the age-associated decline in immune function, is a key feature of human aging. In human lymphoid organs, however, the specific immune cell populations that acquire senescence-associated phenotypes during aging and how they influence the surrounding tissue microenvironment remain poorly understood. A spatially resolved map of these senescence-associated immune states in human lymphoid tissues could help clarify their relationship with aging and their potential contributions to the progressive decline of immune function. Here, we integrated single-cell and spatial multi-omics to systematically characterize age-related senescence in human lymph nodes (LNs). Single-cell transcriptomics of lymphoid tissues from donors aged 18 to 100 years old identified 34 immune and stromal cell types and revealed age-associated upregulation of senescence signatures in specific populations. Spatial proteomic profiling of 99 LN sections from 51 donors (18-86 years) using high-plex immunofluorescence ([~]20 million cells) mapped senescence markers (p16, p21, HMGB1, -H2AX) at single-cell resolution, revealing diverse senescent-like cell types ("senotypes") and a stepwise shift from extrafollicular to germinal center (GC) localization with age. Notably, we observed focal clonal-like senescence in GC B cells in older donor LNs. Spatial transcriptomics, epigenomics, and metabolic imaging of selected samples further elucidate the multi-omics signatures and underlying mechanisms of functional impairment, metabolic remodeling, and distinct regulatory programs in senescent-like GC B cells. This study presents a comprehensive spatial atlas of senescence-associated immune states in human lymph nodes, revealing cell-type-specific and spatial heterogeneity that may contribute to immunosenescence and the decline of immune function during aging.

immunology↗

bioRxiv2026

Cross-Species Multi-Omics Profiling Identifies Conserved Activated Valvular Interstitial Cell Population Driving Myxomatous Mitral Valve Degeneration

BackgroundPrimary mitral regurgitation resulting from mitral valve prolapse can lead to life-threatening complications, including arrhythmias, heart failure, and sudden cardiac death. Mitral valve prolapse is classically associated with myxomatous mitral valve degeneration, characterized by leaflet thickening, extracellular matrix disorganization, and progressive structural remodeling. Valvular interstitial cells, the predominant stromal population within the valve, maintain extracellular matrix homeostasis; however, their molecular heterogeneity, and state-specific contributions to disease pathogenesis remain incompletely defined. MethodsUsing a fibrillin-1 deficient mouse model and human tissue specimens we integrated single-cell RNA sequencing with spatial transcriptomic profiling to construct a comprehensive atlas of cellular composition and extracellular matrix organization across normal mitral valves, sporadic mitral valve prolapse, and Marfan syndrome-associated mitral valve prolapse. ResultsAnalyses revealed spatially organized cellular niches and substantial heterogeneity within the valvular interstitial cell population. Across murine and human datasets, we identified a conserved activated valvular interstitial cell population enriched for profibrotic extracellular matrix remodeling programs and preferentially localized to mechanically vulnerable leaflet tip regions. This population exhibited coordinated upregulation of collagen- and matrix-associated genes, metabolic signatures consistent with enhanced mitochondrial activity, and transcriptional features suggesting fibro-inflammatory signaling. ConclusionsWe identified a transcriptionally and spatially distinct activated valvular interstitial cell state conserved across species and disease etiologies that is strongly implicated in fibrotic remodeling during myxomatous mitral valve degeneration and provides a candidate therapeutic target.

molecular biology↗

bioRxiv2026

Machine learning-based image analysis of Parkinson's disease iPS-derived neurons predicts genotype and reveals mitochondria-lysosome abnormalities

Mitochondrial and lysosomal dysfunction are central features of Parkinsons disease (PD) across major genetic forms including PRKN, SNCA, and LRRK2. We applied cell morphomics, a machine-learning-based framework combining high-content imaging with quantitative feature extraction, to analyse mitochondrial and lysosomal morphology at single-cell resolution in iPS cell-derived cortical neurons from PD patients and healthy controls (13 lines total). Supervised machine-learning models distinguished PD neurons from controls with high accuracy (AUC = 0.87) and reliably separated individual genotypes. Feature importance and attribution analysis revealed genotype-specific organelle biases, with mitochondrial features dominating classification in PRKN neurons, balanced mitochondrial and lysosomal contributions in SNCA neurons, and a greater lysosomal contribution in LRRK2 neurons. Multi-class models retained strong performance, and findings were reproduced across two independent laboratories using different dyes and imaging conditions. These results demonstrate that morphomics provides a robust and scalable framework to quantify genotype-specific organelle abnormalities in PD neurons and supports its application for cellular stratification and biomarker discovery.

neuroscience↗

bioRxiv2026

Persistent Hypersensitivity after Repeat Concussion is Associated with Chronic Cognitive Dysfunction

Persistent sensory hypersensitivity is a common but under-recognized feature of post-concussion syndrome (PCS) following mild traumatic brain injury (mTBI), and may contribute to chronic cognitive complaints. However, the mechanistic relationship between long-term sensory dysregulation and cognitive dysfunction after repeat concussion remains poorly understood. Here, we used an experimental repeated closed-head injury (rCHI-5x), in young adult mouse model targeting the frontal cortex at 8-weeks of age to test whether chronic sensory processing abnormalities contribute to cognitive impairment under increased sensory load chronically at 8-10 weeks post-injury (4-months old). rCHI mice exhibited significant sensory dysfunction across multiple modalities, including increased tactile sensitivity, tactile avoidance, and impaired habituation to auditory startle, despite the absence of gross structural brain damage and preserved learning and memory under low-demand conditions. While spatial learning and working memory in the Barnes maze were intact, rCHI mice displayed increased perseveration and reduced cognitive flexibility. However, these cognitive deficits emerged only when auditory and tactile sensory distractors were introduced during testing, unmasking impairments that were not evident under baseline conditions. Within-animal statistical analyses found strong associations between the severity of sensory hypersensitivity, impaired sensory habituation, and deficits in cognitive flexibility in rCHI mice, but not in sham controls. These findings indicate that chronic sensory dysregulation following repeat mild concussion is not merely a secondary symptom, but a primary contributor to cognitive impairment under conditions of increased sensory load. Together, this work identifies persistent sensory processing and gating dysfunction as a key driver of PCS-related cognitive deficits and reveals that targeting sensory circuitry for therapeutic neuromodulation may offer functional rescue across multiple domains, extending beyond sensory symptoms to improve higher-order cognitive performance.

neuroscience↗

bioRxiv2025

The Hippo Pathway Regulates Corneal Endothelial Regeneration

Corneal endothelial cells (CECs) have limited regeneration capacity in primates while display a potent restorative capability in some species such as rodents after wounding. The mechanism which determines the regenerative capability of CECs remains poorly understood. Here, we identify that the Hippo signaling pathway is inhibited and the downstream effector YAP is activated during CEC wound healing in rabbit and mouse. Knockdown of Yap1 and pharmacological inhibition of YAP suppresses CECs wound healing in rodents in both in vitro and in vivo models. XMU-MP-1, a specific small molecular inhibitor for Hippo signaling pathway, can promote the corneal endothelial regeneration in rodents and corneal endothelial proliferation in cultured primate CECs, as well as in vivo non-human primate CEC wounding model. These findings suggest that Hippo pathway serves as a conserved signal to regulate corneal endothelial regeneration among various species, providing a novel target for non-invasive treatment of corneal endothelium decompensation.

cell biology↗

bioRxiv2025

A coherent feed-forward loop fine-tunes KatG to maintain redox homeostasis in mycobacteria

Bacteria survive and reproduce in fluctuating environments by balancing their basic physiological needs, such as relying on iron-containing enzymes to detoxify reactive oxygen species (ROS) while conserving scarce iron. Understanding the regulatory networks that balance these conflicting needs is key to deciphering bacterial adaptability. Here, we identify a coherent feed-forward loop in mycobacteria that integrates the transcriptional regulator FurA3, the small RNA MrsI, RNA sponge FutR, and the catalase-peroxidase KatG. This circuit fine-tunes antioxidant responses according to iron availability. Under iron limitation, the iron-containing enzyme KatG is dually repressed by FurA3 transcriptionally and by MrsI post-transcriptionally, which conserves iron at the cost of antioxidant capacity. However, when iron deprivation coincides with oxidative stress, the circuit triggers an emergency response: H2O2 inactivates FurA3, relieving transcriptional repression of katG and futR, while induced FutR sequesters MrsI to post-transcriptionally derepress katG expression, enabling rapid KatG synthesis for effective peroxide detoxification. Our findings reveal a tightly regulated network that allows mycobacteria to balance iron homeostasis and oxidative stress defense, providing mechanistic insights into bacterial physiological trade-offs.

microbiology↗

bioRxiv2025

3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors

Uncovering the spatial and molecular landscape of precancerous lesions is essential for developing meaningful cancer prevention and early detection strategies. High-Grade Serous Carcinoma (HGSC), the most lethal gynecologic malignancy, often originates from Serous Tubal Intraepithelial Carcinomas (STICs) in the fallopian tubes, yet their minute size and our historical reliance on standard 2D histology contribute to their underreporting. Here, we present a spatially resolved, multi-omics framework that integrates whole-organ 3D imaging at cellular resolution with targeted proteomic, metabolomic, and transcriptomic profiling to detect and characterize microscopic tubal lesions. Using this platform, we identified a total of 99 STICs and their presumed precursors that harbor TP53 mutations in morphologically unremarkable tubal epithelium in all five specimens obtained from cancer-free organ donors with average-risk of developing ovarian cancer. Although these lesions comprised only 0.2% of the epithelial compartment, they displayed geographic diversity, immune exclusion, metabolic rewiring, and DNA copy number changes among lesions and normal fallopian tube epithelium discovered alterations in STIC-associated genes and the pathways they control. In sum, this platform provides a comprehensive 3D atlas of early neoplastic transformation, yielding mechanistic insights into tumor initiation and informing clinical screening strategies for detecting cancer precursors in whole organs at cellular resolution.

bioinformatics↗