Biology subjects

Zhao, M.

Publications and source records attributed to Zhao, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Discrete depolarisations of chordotonal organ neurons propagate toward the soma and are independent of the sensory TRP channels NompC and Nanchung-Inactive.

The electrophysiological process of auditory transduction in insects remains largely conjecture due to the unknown role of ion channels localised to the cilia, but experimental evidence supports either NompC or Nan-Iav as the auditory mechanotransduction ion channel. Here, we knocked down two key genes that code for the two candidate sound-activated ion channels using dsRNA-mediated RNA interference. We measured sound-evoked activity of the auditory nerve and intracellular electrical currents from the ciliated ending of individual auditory receptors. We found that the sound-evoked nerve activity was reduced in nompC, nan and ift88 knockdown. Using whole-cell patch clamp recordings we found that nompC and nan knockdown resulted in reduced sound-evoked transduction current. Stochastic depolarisations hypothesised to be mediated from one of the candidate mechanotransduction ion channels, either NompC or Nan-Iav, where not affected by knockdown of either channel. The discrete depolarisations are therefore mediated through another unidentified ion channel. We test the hypothesis that discrete depolarisations are graded action potentials that travel toward the soma through noise analysis of the transduction current and analysis of discrete depolarisations to voltage-steps. As a positive control we also knocked down ift88, a protein essential for transporting proteins, including ion channels, along the cilium and found both the transduction current and the discrete depolarisations decreased. Key pointsO_LIInjection of dsRNA decreased RNA of nompC and nan C_LIO_LISound-evoked nerve activity is reduced for RNAi-mediated knockdown of nompC and nan C_LIO_LINompC and Nan both contribute to the transduction current C_LIO_LIThe stochastic discrete depolarisations are not due to NompC or Nan-Iav ion channel but to a third unidentified ion channel. C_LIO_LINoise analysis of the transduction current and the discrete depolarisations suggests they are graded action potentials that travel in the direction of the soma. C_LIO_LIKnockdown of ift88 reduced both the transduction current and discrete depolarisations. C_LI Significance StatementInsects are important to understand, economically, agriculturally and medically. However, we still do not understand fundamental aspects of how insects detect their own body movements, vibrations and sound. These senses are detected by insect chordotonal organs, specialised miniaturised mechanoreceptors that convert movements into electrical signals through specialised ion channels. Previous experimental work has advocated either NompC or Nan-Iav as the mechanosensitive ion channel. Here, for the first time, we reduced the expression of both nompC and nan and measured the sound-evoked transduction current directly from neurons in a specialised auditory chordotonal organ. In contradiction to previous studies, we show that both ion channels contribute to the transduction current and find that electrical signals termed "discrete depolarisations" travel toward the soma.

neuroscience↗

bioRxiv2026

Neuropeptide Y4 receptor activation delays autoimmune diabetes by reprogramming β-cell stress and immune tolerance

Type 1 diabetes (T1D) involves immune-mediated destruction of pancreatic {beta}-cells, yet current disease-modifying therapies mainly target immunity without enhancing {beta}-cell resilience. We show selective neuropeptide Y4 receptor (Y4R) agonism protects {beta}-cells while reshaping islet immunity across T1D models. Multi-modal localisation using cell sorting, qPCR, RNAscope and fluorescent ligand competition demonstrated predominant Y4R expression and functional accessibility on mouse and human {beta}-cells. Selective Y4R agonism was non-toxic and did not impair islet network integrity, Ca{superscript 2} dynamics, glucose-stimulated insulin secretion or systemic glucose tolerance. Y4R activation conferred cytoprotection against inflammatory cytokines, streptozotocin, lipotoxicity and ER stress, reducing caspase-3/7 activation and {beta}-cell loss whilst sustaining insulin release and promoting proliferation in both mouse and human islets. Bulk RNA-seq revealed a coordinated {beta}-cell resilience programme characterised by reinforced identity and insulin processing, KEAP1-NFE2L2-driven antioxidative and proteostatic activation, and suppression of EIF2 signalling and associated biosynthetic and ER stress pathways. Concurrently, Y4R agonism dampened pathogenic chemokine and cytokine networks, including CXCL10, CCL3/4/7 and IL-6, while preserving IL-2 and Foxp3 signals, thereby limiting CD8 T cell, CD4 T cell and macrophage chemotaxis toward cytokine-stressed islets. Reduced immune-cell recruitment was conserved in a fully human immune-islet system, where Y4R activation significantly attenuated IL-2-activated human PBMC migration and invasion toward cytokine-stressed human islets. In a stringent NY8.3 CD8 T cell adoptive-transfer model, systemic Y4R agonism significantly delayed diabetes onset. These data position Y4R as a {beta}-cell-centric therapeutic target coupling intrinsic resilience with local immune modulation, offering a complementary approach for {beta}-cell preservation in T1D and islet replacement therapies. Graphical abstractThe selective Y4 receptor agonist K22 binds {beta}-cell-enriched NPY4R in mouse and human islets, activates a {beta}-cell resilience programme that preserves insulin secretion under inflammatory and metabolic stress, and simultaneously dampens islet chemokine output, thereby limiting innate and adaptive immune-cell recruitment and delaying autoimmune diabetes onset. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/736290v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@7efd48org.highwire.dtl.DTLVardef@1268860org.highwire.dtl.DTLVardef@c38a81org.highwire.dtl.DTLVardef@1ba3e6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

The Two-Component System CrdRS Mediates Sub-inhibitory Antibiotic-Induced Biofilm Formation in Helicobacter pylori via Bidirectional Regulation of Transporters PlpA and GlnP

Biofilm formation by Helicobacter pylori is a major driver of antibiotic tolerance and treatment failure, yet the signaling pathways that trigger biofilm development under sub-inhibitory antibiotic pressure remain poorly understood. Here, we show that sub-MIC levels of metronidazole, amoxicillin, and ciprofloxacin potently induce dense H. pylori biofilms. Through transcriptomic and genetic analyses, we identify the two-component system CrdRS as a central signaling hub that orchestrates this response via the bidirectional regulation of two ATP-binding cassette (ABC) transporters. Phosphorylated CrdR binds to AC-rich promoter motifs to directly activate plpA, which encodes a substrate-binding protein that drives exopolysaccharide secretion and matrix assembly. Concomitantly, CrdR represses glnP, which encodes an inner-membrane permease, thereby relieving transcriptional inhibition of the L-asparaginase gene ansB. This derepression triggers aberrant reactive oxygen species (ROS) accumulation, which promotes oxidative stress-dependent biofilm maturation. Through phenotypic analysis of crdRS deletion mutants, phosphorylation-defective point mutants (CrdRD53A and CrdSH173A), and exogenous hydrogen peroxide (H2O2) induction, we demonstrate that CrdRS specifically responds to antibiotic-induced stress signals in a manner genetically separable from ROS sensing. Collectively, our findings establish a dual-mechanism model in which CrdRS orchestrates antibiotic-induced biofilm formation by simultaneously controlling matrix production and intracellular ROS generation. Notably, glnP expression was significantly lower in clinical multidrug-resistant isolates than in drug-sensitive ones, whereas plpA showed the opposite trend. These findings provide a mechanistic foundation for developing CrdRS-targeted strategies to combat biofilm-associated H. pylori infections.

microbiology↗

bioRxiv2026

Human cardiomyocytes with trisomy 21 exhibit heightened susceptibility and immunological response to SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is associated with significant cardiovascular complications, including myocardial injury and long-term cardiac dysfunction. Individuals with Down syndrome (trisomy 21) exhibit increased susceptibility to severe COVID-19 outcomes, yet the cardiomyocyte-intrinsic mechanisms underlying this vulnerability remain poorly understood. To investigate genotype-specific responses to SARS-CoV-2 infection, we generated induced pluripotent stem cell-derived cardiomyocytes from individuals with trisomy 21 and their euploid, sex-matched biological relatives. Cardiomyocytes were inoculated with SARS-CoV-2, and viral susceptibility was assessed by immunofluorescence. Bulk RNA sequencing was performed under baseline and infected conditions to define transcriptional programs associated with viral response. Trisomy 21 iPSC-CMs exhibited increased susceptibility to SARS-CoV-2 infection, with greater viral protein expression and a higher proportion of infected cardiomyocytes compared to controls. Baseline transcriptomic analysis revealed no significant differences in canonical viral entry factors including ACE2 and TMPRSS2, suggesting that differential susceptibility is not driven by entry receptor availability. Following infection, both trisomy 21 and euploid control groups activated conserved antiviral pathways; however, trisomy 21 cardiomyocytes displayed a markedly amplified transcriptional response, with substantially greater numbers of differentially expressed genes. Upregulated pathways included interferon signaling, NF-{kappa}B activation, cytokine and chemokine signaling, and innate immune responses, while downregulated pathways were enriched for cardiomyocyte structural integrity, calcium handling, and metabolic processes. Notably, inflammatory and cytokine-related transcripts were significantly more elevated in trisomy 21 cells, consistent with an exaggerated immune response. These findings provide mechanistic insight into the increased cardiovascular risk observed in individuals with Down syndrome and highlight dysregulated immune signaling as a potential therapeutic target in this high-risk population.

Cell Biology↗

bioRxiv2026

A feedback control for restraining autoimmune γδ T cells: reprogramming into ILC1s

{gamma}{delta} T cells are promising mediators of cancer immunotherapy, yet their potential to drive autoimmunity remains incompletely understood. Here, we identify a feedback mechanism in which innate-like V{gamma}1.1V{delta}6.3 T cells are reprogrammed into ILC1-like cells, thereby restraining autoimmune pathology. We define a previously unrecognized ILC1 subset whose development depends on an intact Tcrd locus. These cells predominantly harbor productive V{gamma}1.1 and V{delta}6 rearrangements, consistent with their origin from V{gamma}1.1V{delta}6.3 T cells. Mechanistically, TCR signaling induces Id3, which suppresses E protein-dependent activation of T cell-specific genes, including that encoding V{delta}6.3. Id3 ablation drives robust expansion of V{gamma}1.1V{delta}6.3 T cells and severe autoimmunity, characterized by tissue infiltration, autoantibody production, enhanced T follicular helper cell differentiation, and accumulation of germinal center and age-associated B cells. Together with previously described exocrine dysfunction, these features resemble human Sjogrens disease. Consistent with this, we observed in the salivary glands of Sjogrens disease patients an increased frequency of CD4-CD8- T cells enriched for {gamma}{delta} T cells, including subsets functionally analogous to murine V{gamma}1.1V{delta}6.3 cells. Collectively, these findings uncover a TCR-Id3-dependent reprogramming pathway that limit the pathogenic potential of harmful {gamma}{delta} T cells.

immunology↗

bioRxiv2026

Differentiation of Bacterial, Fungal, and Algal Communities on Coastal Concrete Versus Drainage Pipes and the Coexistence of Corrosion and Healing Potentials

Coastal concrete structures and drainage pipes are prone to microbially influenced deterioration. However, differences in microbial communities and their corrosion/healing potentials between these habitats remain unclear. Here, we compared bacterial(16S), fungal (ITS) and algal(18S) communities on coastal concrete(C) and drainage pipe(P) surfaces. Fungal and algal -diversity were significantly higher in P than in C, while bacterial diversity did not differ. {beta}-Diversity strongly separated bacterial and algal communities between habitats, but not fungi. A shared core "seed bank" of 575 bacterial, 520 fungal and 40 algal ASVs was identified. Students t-test revealed that P enriched oligotrophic degraders (Sphingomonas) and acid-producing fungi (Arxiella, Bisifusarium), whereas C selected for halotolerant EPS-producing bacteria (Tunicatimonas, Muricauda) and the extremotolerant alga Coelastrella. db-RDA linked these differences to salinity, NH4+-N, NO3--N, and COD. Functional prediction indicated a shift from metabolism pathways in C to signaling in P. Co-occurrence networks revealed cross-kingdom competition and within-kingdom cooperation, especially among algae. Importantly, both habitats harbored microorganisms with documented corrosion and healing potentials, but under natural conditions, net deterioration dominated, microbial healing is hardly to counteract the negative effects. This study provides a functional taxonomic framework for understanding and managing concrete microbiomes in coastal and sewer infrastructure. ImportanceConcrete is the most widely used construction material, and its deterioration in coastal and sewer environments poses significant economic and safety challenges. Microorganisms play a dual role in concrete durability -- they can both corrode and heal concrete, but the net outcome under natural conditions is poorly understood. Most studies have focused on bacteria alone, overlooking the contributions of fungi and algae, and few reports on the of coastal concrete which also exist the microbially influenced concrete corrosion (MICC) similar to sewer. Here, we simultaneously analyzed all three microbial kingdoms on coastal concrete and drainage pipes. We found that while concrete surfaces harbor a diverse "seed bank" of microorganisms potentially involved in both corrosion and healing, under natural conditions, net deterioration dominated, indicating microbial healing is hard to counteract the negative effects from the environment and microbial. Our work provides a functional framework to guide the development of microbiome-based strategies for enhancing concrete durability, such as activating rare healing taxa in drainage pipes or selecting for endogenous healers in marine environments.

microbiology↗

bioRxiv2026

FLASH reduces radiation-induced oral mucositis in a mouse model of Fanconi anemia

Patients with Fanconi anemia (FA) are particularly susceptible to developing squamous cell carcinoma of the head and neck due to impaired DNA repair pathways. However, their hypersensitivity to DNA damaging agents can limit effective treatment with standard radiotherapy due to severe side effects and complications. In pre-clinical models, ultra-rapid FLASH radiotherapy (FLASH) reduces radiation-induced toxicity in normal tissues while maintaining similar tumor control compared to conventional dose rate radiotherapy (CONV). Here, we investigated the safety of FLASH for treatment of the head and neck in a mouse model of FA. 129/Sv wild-type (WT) and Fanca-deficient (Fanca-/-) mice received single-dose oral cavity irradiation with electron beam FLASH or CONV to evaluate radiation-induced toxicity in non-tumor-bearing mice. Fanca WT and Fanca-/- mice were irradiated with 25 and 18 Gy, respectively, of FLASH (190 Gy/sec) or CONV (0.2 Gy/sec), with tongues harvested at 12 hours (hpi) and 10 days (dpi) post-irradiation. At 10 dpi, FLASH-irradiated tongues in both genetic backgrounds demonstrated reduced ulceration at the dorsal tongue surface compared to CONV-irradiated counterparts. Histopathological analysis of the tongue revealed lower mucositis severity scores with decreased epithelial thinning and ulceration in FLASH-irradiated tongues compared to CONV-irradiated ones. Analysis of {gamma}-H2AX foci formation at 12 hpi demonstrated fewer foci in WT mice treated with FLASH compared to CONV, with a similar trend observed in Fanca-/- mice. These findings suggest a potential normal tissue-sparing effect with FLASH and hold important clinical implications for the treatment of patients with Fanconi anemia and head and neck cancers.

cancer biology↗

bioRxiv2026

A paradoxical relationship between mitochondrial calcium regulation and retinal ganglion cell degeneration after axon damage

Retinal ganglion cells (RGCs) degenerate in optic neuropathies like glaucoma and traumatic optic nerve injury leading to irreversible vision loss. Higher levels of homeostatic Ca2+ and canonical Ca2+ regulated signaling promote RGC survival in animal models of glaucoma and optic nerve injury. Mitochondrial dysfunction is also a hallmark of degenerating neurons, including RGCs. Here, we investigate the intersection of mitochondrial function, Ca2+ homeostasis, and cellular resilience by performing an optic nerve crush model of RGC degeneration while monitoring and manipulating mitochondrial Ca2+ levels (mito-Ca2+). We find that mito-Ca2+ is predicative of RGC survival in that surviving RGCs are enriched for higher homeostatic mito-Ca2+ levels. Mitochondrial dysfunction was observed where mito-Ca2+ was reduced in RGCs after injury, regardless of survival. We then examined the importance of higher mito-Ca2+ in surviving RGCs by altering mito-Ca2+ levels and Ca2+ transit using pharmacological and AAV-mediated approaches. Paradoxically, treatment to decrease mito-Ca2+ increased survival to ONC. We then manipulated mito-Ca2+ permeability by altering the expression levels of the mitochondrial calcium uniporter (MCU) pore forming subunit that allows Ca2+ to enter mitochondria from the cytoplasm. Overexpressing MCU reduced RGC survival to injury, while shRNA knockdown of MCU increased RGC survival. These results reveal a complex relationship between mito-Ca2+ and RGC degeneration and suggest that well-surviving RGCs may be under chronic mitochondrial stress due to higher homeostatic mito-Ca2+ levels.

neuroscience↗

bioRxiv2026

An fMRI dataset of verbalized spontaneous thought with annotated transcripts and self-report trait measures

Spontaneous thought is pervasive in everyday human cognition, yet datasets capturing its neural dynamics under minimally interrupted conditions remain limited. The current dataset was acquired from a think-aloud functional MRI experiment in which 118 participants continuously verbalized their spontaneous thoughts during 10-minute scanning sessions. The raw MRI data and verbal transcripts with sentence-level timestamps were previously released and analyzed in our prior study examining neural activity associated with thought transitions. Building on that release, we additionally provide preprocessed MRI data, speech transcriptions with word-level timestamps aligned to image acquisition, large language model-generated ratings of transcribed thoughts across emotional and sensory dimensions, and self-report survey measures assessing personality, mental health, and cognitive abilities. Validation analyses demonstrated activation in expected cortical regions associated with speech production and sensory content identified from transcript annotations, agreement between language model and human ratings, and adequate internal consistency of survey measures, supporting the datasets overall quality. This dataset enables reuse for investigations of spontaneous thought, speech generation, and individual differences using naturalistic functional MRI data.

neuroscience↗

bioRxiv2026

ProteinFlux: accurate, rapid and scalable generative prediction of protein dynamics driven by post-translational modifications

The function of proteins, the building blocks of life, in health and disease depends not only on their 3D-conformational states but most importantly on the dynamic transition between states controlled by a wide array of post-translational modifications (PTMs). Recent major advances have been made in our ability to predict static 3D structures; however, understanding and predicting the impact of PTMs on protein conformational dynamics remains a major question and challenge in the field. Molecular dynamics (MD) simulation remains the major computational approach for studying protein dynamics. However, the high computational cost, lack of integration of PTMs as conditioning inputs and inefficient generation of continuous protein dynamics largely precludes PTM-regulated conformational dynamics and the study of slow conformational processes. To address this critical bottleneck, we developed ProteinFlux, a flow-matching generative framework that links PTM-conditioned conformational dynamics to evolutionary constraints encoded by PTM sites. Evolutionary information plays a critical role in capturing conformational dynamics beyond sequence identity, and PTM sites inherently encode evolutionary constraints critical to protein functional regulation. We therefore built FluxSite, a dual-modal PTM site predictor that integrates sequence evolutionary information and 3D structural features to generate a continuous conditional signal encoding conservation and functional importance for each predicted site. FluxSite achieves robust generalization across 18 PTM types and 30 disease-associated proteomes. ProteinFlux generates phosphorylation-conditioned, all-atom conformational trajectories across diverse protein fold classes, faithfully reproducing both thermodynamic properties such as free energy landscapes and kinetic features such as conformational transition pathways. It outperforms state-of-the-art predictors while achieving inference speeds several orders of magnitude faster than traditional MD. In addition, we introduce DynaMo-phos, a benchmark dataset of phosphorylated protein MD simulations. Together, ProteinFlux, FluxSite and DynaMo-phos provide a scalable, high-throughput platform for elucidating PTM-driven conformational mechanisms, with potential applications across allosteric drug design, functional annotation of disease-associated modifications and mechanism-guided therapeutic development.

bioinformatics↗

bioRxiv2026

Parallel Activation and Interference CRISPR (PAIR) with Sequencing Uncovers DNA Repair Networks Guiding Precision Cell Engineering

The dynamic balance of cellular homeostasis is often maintained by opposing regulatory pathways, yet most genetic screens interrogate them in one direction and therefore miss the bidirectional gene-gene interactions that shape complex phenotypes such as DNA damage response (DDR). Here, we present PAIR (Parallel Activation and Interference CRISPR), a bidirectional perturbation platform that enables simultaneous activation and suppression of distinct genes within the same cell using CRISPR activation (CRISPRa) and Cas13d RNA knockdown. Applying PAIR to the CRISPR/Cas9 induced DSB repair screen, we mapped gene-gene interactions across competing repair branches and identify synergistic perturbations, including NBN activation combined with suppression of end-joining factors, that shift repair outcomes toward homology-directed repair (HDR) and improve the precision of CRISPR-based gene editing. Using coupled PAIR with single-cell transcriptomic, we further demonstrated that NBN activation induces inflammatory and interferon programs, whereas co-suppression of end-joining factors buffers this response, revealing transcriptional states missed by conventional unidirectional perturbations. To translate these findings into non-viral chimeric antigen receptor (CAR) T cell engineering, we developed an mRNA-based strategy for parallel overexpression and knockdown of NBN-anchored DDR effectors in primary T cells, priming the T cells into a transient HDR-favored state that enhances the efficiency of CAR knock-in on the TRAC locus. Together, the PAIR system provides a general framework for studying opposing regulatory networks, uncovering hidden cell states, and guiding cell-state engineering through bidirectional perturbation.

bioengineering↗

bioRxiv2026

Automated Multimodal Correlative Registration for Organelle-Specific Molecular Imaging

Mapping subcellular drug distribution is essential for understanding trafficking and off-target effects. NanoSIMS enables chemical imaging of labeled therapeutics, but signal interpretation requires ultrastructural correlation with electron microscopy, a manual and laborious process. We present an automated AI-driven pipeline for correlating chemical and ultrastructural images, enabling multiscale, organelle-precise imaging of molecules in cells and tissues. The method integrates bidirectional optical flow, confidence-guided affine transformation, and automated template matching for cross-scale EM alignment. Morphology-rich ion channels (e.g., 32S) estimate transformations that propagate to sparse therapeutic signals (e.g., 79Br, 15N), overcoming low signal-to-noise challenges. We validate this framework across diverse cell and tissue types, tracking oligonucleotide and antibody therapeutics in vitro and in vivo to reveal cell-type- and organelle-specific distribution patterns. This work establishes a generalizable platform for automated multimodal registration and organelle-resolved subcellular pharmacology.

bioinformatics↗

bioRxiv2026

LNGCN: A Distance-Aware Dynamics Network for Protein-Protein Interaction Prediction

High-throughput PPI screening requires not only interaction discrimination but also stable, calibrated scores for candidate prioritization and efficient experimental allocation. Conventional graph neural networks may over-smooth deep residue representations, reducing score separation among high-confidence candidates. We therefore developed LNGCN, a distance-aware continuous-time graph framework for experimental PPI prioritization. LNGCN integrates residue-level structural graphs with liquid neural dynamics, uses radial distance to drive continuous graph evolution, and applies hierarchical calibration to convert raw outputs into prioritization scores. It performed robustly on balanced human, 1:10 imbalanced, and cross-species yeast bench-marks. On the imbalanced dataset, the top 5% of candidates achieved 85.1% precision. LNGCN also preserved residue-level representation diversity better than conventional GCN variants. In FGF23-FGFR1c--Klotho, SHP2 signaling, Tdk1 oligomer-dependent binding, and a TPR study, it enriched known partners near the ranking top, and experimentally supported novel interactions. Overall, LNGCN enables sustained enrichment of experimentally relevant PPI candidates.

bioinformatics↗

bioRxiv2026

β2-Adrenergic Signaling Switches from Cardioprotective to Cardiotoxic in Acute vs. Chronic Oxidative Stress

BACKGROUND AND PURPOSE{beta}-adrenergic receptors (AR) regulate both cardiac function and remodeling. Many studies suggest that, in addition to their effects on heart rate and contractility, {beta}1-ARs mediate cardiotoxic signaling, whereas {beta}2-ARs are generally cardioprotective. However, there is conflicting data on the role of {beta}2-ARs, differing dependent on the nature of the stress. Given the extremely common use of {beta}-blockers and agonists clinically, we sought to understand the differential cardioprotective/cardiotoxic effects of {beta}2-AR signaling dependent on timing (acute vs. chronic) and type of cardiotoxic stress. EXPERIMENTAL APPROACHWild-type (WT) and {beta}-AR knockout ({beta}1-KO and {beta}2-KO) mice were subjected to acute (15 mg{middle dot}kg-1 x 1 dose) or chronic (2 mg{middle dot}kg-1{middle dot}wk-1 x 7 wks) oxidative stress using doxorubicin (DOX). Survival, cardiac function and histopathology were assessed and differential signaling activation determined by Western blot and gene expression by RNA-seq. KEY RESULTSWe have shown that {beta}2-KOs manifest extreme cardiotoxicity with acute DOX (100% mortality within 30 min), supporting a strong cardioprotective role of {beta}2-signaling. In marked contrast, with chronic DOX, {beta}2-KO had enhanced survival (t[1/2] 54 d vs. 42 d in WT) and attenuated cardiac dysfunction. In {beta}2-KO, acute DOX activated stress MAPKs (p38, ERK and JNK), whereas chronic DOX did not; furthermore, in the absence of {beta}2-ARs, oxidative stress and lipid accumulation were reduced, genes regulating compensatory metabolic pathways (AMPK and insulin/PI3K) were upregulated, and genes regulating mitochondrial and contractile function were preserved, whereas they were downregulated in WT with chronic DOX. CONCLUSIONS{beta}2-AR signaling switches from being cardioprotective during acute oxidative stress, to cardiotoxic during chronic stress. Inhibition of {beta}2-AR signaling during chronic stress induces signaling and metabolic compensations that serve to reduce oxidative injury. This unexpected temporal switching has potential significant implications for all models of cardiovascular disease, as well as for the clinical use of subtype-specific {beta}-blockers. CLINICAL PERSPECTIVEO_ST_ABSWhat is new?C_ST_ABSO_LIOur finding that {beta}2-adrenergic receptor signaling can switch from being beneficial (cardioprotective) to detrimental (cardiotoxic) depending on the acuteness or chronicity of a cardiac stressor. C_LIO_LIIdentification of the mechanisms by which this temporal switch is mediated could lead to new drug development. C_LI What are the clinical implications?O_LIOur findings provide potential guidance in choosing between a {beta}1-specific vs. a {beta}1/2-non-specific drug when treating specific cardiovascular diseases based on their temporal characteristics. C_LIO_LIThe temporal protective/toxic switching that we describe could be a mechanism common to many other drugs, yet is rarely tested, suggesting the need for additional studies using temporal course as a factor. C_LI

cell biology↗

bioRxiv2026

Pan-cancer circular genomics identifies intratumoral Staphylococcus lugdunensis as a metabolic driver in bladder cancer

Intratumoral microbiota play key roles in cancer but are challenging to profile due to low biomass. We developed CIRCMIP, an enzymatic pipeline that eliminates linear DNA to enrich bacterial genomes, achieving 100-fold higher sensitivity than standard metagenomics. Applied to 312 pan-cancer specimens, CIRCMIP identified Staphylococcus lugdunensis as a signature bacterium enriched in early-stage bladder cancer (BLCA), where its presence predicts poor survival. Integrated modeling and lipidomics revealed that Staphylococcus lugdunensis colonization drives aberrant lipid metabolism with secretion of LPC14:0. Both Staphylococcus lugdunensis and LPC14:0 drive BLCA progression by promoting fatty acid uptake and {beta}-oxidation. Mechanistically, chemical proteomics revealed LPC14:0 as a direct PPAR{delta} ligand, binding via hydrogen bonds with Thr292/Thr289. This activation upregulates fatty acid transporters (CD36, FABP4) and metabolic enzymes (ACOX2), fueling malignant proliferation. Furthermore, CIRCMIP-derived biomarkers show robust diagnostic accuracy, establishing a new research paradigm and revealing the Staphylococcus lugdunensis-LPC14:0-PPAR{delta} axis as a therapeutic target in bladder cancer. HIGHLIGHTO_LICIRCMIP leverages DNA circularity to achieve 100-fold sensitivity in pan-cancer bacteriome profiling. C_LIO_LIStaphylococcus lugdunensis is a bacterial signature in early-stage bladder cancer that predicts poor patient survival. C_LIO_LIBacteria-derived LPC14:0 acts as a direct ligand for PPAR{delta} to drive host malignant metabolic reprogramming. C_LIO_LITargeting the Staphylococcus lugdunensis-LPC14:0-PPAR{delta} axis abrogates malignant progression in bladder cancer. C_LI

cancer biology↗

bioRxiv2026

Exercise-induced Sweat Promotes Wound Healing in Diabetic Foot Ulcers

Persistent hyperglycemia impairs wound healing in diabetic patients, and severe cases may even lead to disability or death. Glycemic control alone cannot effectively prevent the occurrence of diabetic foot ulcers, a serious complication of diabetes. However, safe, efficient, and cost-effective therapies remain unavailable and are urgently needed. Using a novel sports medicine paradigm, we predicted, based on reverse-transcriptomics, that exercise-induced sweat has the potential to promote would healing in diabetic foot ulcers. Subsequent animal experiments demonstrated that sweat can indeed promote re-epithelialization and collagen deposition, upregulate the expression of the proliferation marker Ki-67, the angiogenesis marker CD31, and -SMA, and significantly accelerate wound healing in a mouse model of diabetic foot ulcers. This study provides a new direction for sports medicine and offers a novel therapeutic strategy for patients with diabetic foot ulcers.

zoology↗

bioRxiv2026

ARID1A deficiency unleashes centromeric RNA transcription to drive chromosomal instability and boosts PKMYT1 inhibitor efficacy via RNA sensing

Cancer gene-associated mutations and molecular hallmarks of chromosomal instability (CIN) are unexpectedly common in histologically normal cells and tissues. These emerging findings challenge the binary distinction between "normal" and "cancerous" cells and suggest that early tumorigenesis may commence against a background of widespread yet largely tolerated genomic instability. However, it remains largely unexplored how a cancer gene-associated mutation can initiate the development of CIN-like states in non-malignant cells and drive tumor evolution. ARID1A, a chromatin remodeling factor, was identified as the most frequently mutated gene in both gastric normal epithelium and tumors. This distinctive molecular convergence presents an opportunity to elucidate the mechanisms by which a cancer-associated gene facilitates the initiation of early CIN phenotypes and develop effective antitumor strategies. In the present study, using primary human gastric organoids, we employed optical genome mapping (OGM) and live-imaging technologies to demonstrate that ARID1A depletion induced a wide spectrum of structural variants (SVs), copy number variants (CNVs), and chromosomal segregation errors, characteristic features of CIN at a very early stage of gastric tumorigenesis. Mechanistically, ARID1A bound centromere repetitive satellite DNA (satDNA) sequences. Its SWI/SNF-associated chromatin remodeling activity was required for suppressing satDNA transcription and the production of -SatRNA, through restricting RNAPII elongation. Consequently, ARID1A depletion led to overexpression of -SatRNA, and a higher incidence of sister chromatid exchange (SCE), a sensitive indicator of CIN. Importantly, the elevated -SatRNA expression in ARID1A-deficient cells further established a dual therapeutic vulnerability for G2/M checkpoint blockade, such as PKMYT1 inhibitor (PKMYTi), by concurrently aggregating CIN-induced cell death and activating self-dsRNA sensing-mediated innate immune response. Notably, PKMYTi markedly promoted -SatRNA expression, aberrant release of these self-derived dsRNAs into the cytosol and a robust activation of the RIG/MDA5-MAVS-depenent type-I interferon response in ARID1A-depleted cells. As expected, PKMYTi potentiated the efficacy of immunotherapy in ARID1A-deficient gastric tumors. Together, our findings reveal that ARID1A deficiency unleashes centromeric -SatRNA transcription, which sets the molecular stage for tumor evolution and targeted therapy by coordinately inducing CIN and self-dsRNA-induced innate immune responses.

cancer biology↗

bioRxiv2026

Extending the MARTINI 3 Coarse-Grained Forcefield to Polypeptoids

Polypeptoids (poly-N-substituted glycines) are synthetic peptidomimetic polymers with their sidechains attached to the backbone amide nitrogen rather than the -carbon in natural peptides. Peptoids display pronounced sequence-dependent conformational flexibility arising from the absence of backbone hydrogen bonding and slow cis/trans {omega}-dihedral isomerization. Despite growing interest in peptoid-based biomaterials, a coarse-grained (CG) model compatible with the modern MARTINI 3 framework is not yet available, limiting mesoscale simulation of peptoid structure and self-assembly. In this work, we develop the first MARTINI 3 compatible peptoid CG forcefield, covering 19 commonly used residue types. Extensive all-atom reference simulations employing parallel bias metadynamics (PBMetaD) were performed to ensure converged sampling of {omega}-dihedral transitions. Bonded parameters were derived from atomistic distribution functions via direct Boltzmann inversion (DBI), while nonbonded interactions were primarily adopted from the standard MARTINI 3 parameter library. The resulting CG model reproduces structural and thermodynamic properties in close agreement with all-atom simulations, while providing up to 57-fold enhanced computational efficiency. To facilitate its adoption by the research community, we have integrated all parameters and workflows to the MARTINI-based martinize2 tool, enabling automated generation of MARTINI 3 peptoid structures and topologies. This work establishes a transferable and computational efficient framework for simulating large-scale peptoid confirmations, assemblies, membrane interactions, and nanostructure formation, and supports the rational design of next-generation sequence-specific functional peptoid-based materials.

biophysics↗