Biology subjects

Fang, Y.

Publications and source records attributed to Fang, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Pulmonary colonization of Candida albicans drives breast cancer lung metastasis via candidalysin

The intratumoral mycobiome is emerging as a key modulator of cancer progression, with specific fungal taxa as potential biomarkers. However, whether and how mycobiomes colonizing distant organs contribute to tumor evolution remains largely unexplored. Here, we identify selective enrichment of Candida albicans in breast cancer lung metastases. Mechanistically, the fungal virulence factor candidalysin activates pulmonary mast cells, which release chemotactic mediators that expand immunosuppressive populations and suppress cytotoxic lymphocyte activity, remodeling the lung into a metastasis-permissive microenvironment. Analysis of clinical isolates and isogenic mutants further demonstrates that candidalysin secretion levels dictate metastasis-promoting potential. Informed by these findings, we developed a combination regimen that concurrently eliminates fungal colonization, stabilizes mast cells, and reverses the immunosuppressive microenvironment, thereby significantly curtailing metastatic progression. Collectively, our study establishes pulmonary C. albicans colonization as a driver of breast cancer lung metastasis and provides a mechanistic framework for targeting mycobiome-host interactions in metastatic disease.

cancer biology↗

bioRxiv2026

Common and Sex-Biased Muscle Transcriptomic Aging Signatures Across Diverse Species

Sex differences in lifespan are widespread yet inconsistent across the animal kingdom. In mammals, XX females outlive XY males in over 60% of species, while this pattern reverses in birds, where ZZ males have a higher life expectancy. These sex differences raise the question of whether sex-biased aging biomarkers (age-associated molecular signatures that reflect biological aging processes) can be identified based on transcriptomic data and whether such markers are shared across taxa. To identify sex-biased aging biomarkers, we analyzed sex-specific skeletal muscle transcriptomes (RNA-seq) from young and old individuals of six species spanning major evolutionary lineages. Four female-biased and 18 male-biased aging biomarkers were identified across all species. Three shared aging biomarkers were also identified in both sexes of all species: Na Channel, Heat Shock Protein 70 (HSP70), and Secreted Protein Acidic and Rich in Cysteine (SPARC). Particularly, age-associated changes in the HSP70 family are suggestive of a shared decline in proteostasis, a hallmark of aging observed across both model and non-model organisms. Furthermore, using an Ornstein-Uhlenbeck (OU) model applied to orthogroup phylogenies, we identified lineage- and sex-dependent expression shifts in shared aging biomarkers. In addition, sex-biased orthogroups revealed age-associated alterations in muscle structure and function in females, whereas mitochondrial and metabolic pathways were predominantly changed in males, indicating divergent mechanisms in muscle aging between sexes. Together, these findings identified a set of transcriptional aging signatures, both shared and sex-biased, that are detectable across diverse evolutionary lineages, providing insight into shared and divergent molecular mechanisms underlying aging.

genomics↗

bioRxiv2026

Adolescent prodromal phenotypes of psychiatric disorders: insights from a novel DISC1-perturbed monkey model

Neurodevelopmental deficits frequently lead to mild but significant adolescent social and cognitive changes, representing prodromal manifestations of adult-onset psychiatric disorders in a cross-disease manner. Although experimental medicine utilizes animal models to address the mechanisms, rodent brains lack critical structures for human higher brain functions such as the dorsolateral prefrontal cortex. To fill this translational gap, we generated monkeys with an impaired DISC1 gene locus, targeting the multifunctional protein essential for neurodevelopment and involved in transdiagnostic mental health risks. Here we analyze the F0 animals by minimizing mosaicism. At ages equivalent to human adolescence, these monkeys exhibited blunted responsiveness to social stimuli and increased internal drives, mirroring altered social behaviors in the prodromal stage in humans. Resting-state functional MRI data indicated disrupted global functional connectivity and reorganization of network topology, marked by a shift in the dominance of brain hubs from prefrontal regions to sensory areas. This primate model provides a unique platform for studying psychiatric disorders, such as schizophrenia, across the developmental trajectory.

neuroscience↗

bioRxiv2026

Combining an autoactivated cGAS mutant with membrane-tethered IL-12 via mRNA lipid nanoparticles promotes systemic tumor control

Local tumor therapies rarely induce systemic immunity capable of controlling metastatic disease. Here, we engineer an mRNA lipid nanoparticle (LNP) platform to coordinate innate immune sensing and T cell activation in situ through co-delivery of an autoactivated cyclic GMP-AMP synthase mutant (cGASR241E) and membrane-tethered IL-12 (IL-12TM). cGASR241E mRNA LNPs autonomously generated cyclic GMP-AMP in vivo, activating host STING signaling and initiating antitumor responses. Co-administration with IL-12TM mRNA LNPs promoted localized cytokine production, reduced regulatory T cells, and restored effector function in tumor-infiltrating T cells. This combination elicited systemic antitumor immunity and suppressed distal tumors across multiple mouse models. The therapeutic efficacy required CD8+ T cells and IFNg; signaling in host, supporting a model in which innate DNA sensing is coupled to IL-12-mediated T cell functional reinforcement. In addition, the combination enhanced responsiveness to PD-L1 blockade. Together, these findings establish a clinically translatable strategy to integrate cGAS-STING activation with cytokine-driven T cell programming to drive systemic tumor control.

cancer biology↗

bioRxiv2026

An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements

Transposable elements (TEs) constitute a substantial fraction of the human genome and contribute to genomic and epigenomic regulation. However, TE-related knowledge remains fragmented across the literature and databases, with inconsistent identifiers hindering integration and reuse. Here, we present TE-Dee (Transposable Element Data Exploration Engine), a curated resource that harmonizes literature-derived TE relationships with TE annotations, tissue-specific expression, and GTEx v11 eQTL associations. TE-Dee contains 10,387 entities and 9,583 curated relationships from 2,308 publications, 1,505 leaf-level TE classification records, and 11,334,060 instance-level observations generated by intersecting 640,456 reference TE intervals with significant variant-gene associations across 50 GTEx tissue categories. By linking molecular knowledge to genomic, transcriptomic and genetic evidence, TE-Dee provides reusable data for investigating TE biology, gene-regulatory and disease-related mechanisms, and a structured corpus for training and benchmarking data-driven and artificial intelligence models. TE-Dee is available at https://bis.zju.edu.cn/tedee/.

bioinformatics↗

bioRxiv2026

Rational Design of 5' UTRs for Optimized mRNA Expression and Cost-Effective, Rapid Analysis of Capped mRNA

In vitro-transcribed (IVT) messenger RNA (mRNA) therapeutics require rigorous quality control of 5' capping efficiency and 3' poly(A) tail length, both of which constitute critical quality attributes (CQAs). Current analytical workflows for these CQAs rely on hybridization with nucleic acid probes and biotin-based affinity purification, which constrain throughput and increase per-assay cost. Here, we report a rationally designed 5' untranslated region (5' UTR) that sustains high translational efficiency while enabling probe-free, one-step purification for rapid quantification of capping efficiency and poly(A) tail length distribution. This approach exploits a strategically engineered 5' UTR incorporating a purine-only RNase A-resistant fragment terminating at a single pyrimidine cleavage site, together with a translation-enhancing element comprising an N6-methyladenosine (m6A) deposition motif and an 18S rRNA complementarity sequence. This dual-function design accommodates GA-rich sequence segments without compromising mRNA translational output. Compared with conventional probe- and biotin-dependent workflows, the present method substantially reduces cost and processing time and is compatible with simultaneous detection of segmented AmGn poly(A) tail variants. This integrated platform provides a simplified, probe-free and construct-universal for high-throughput in-process control (IPC) of mRNA therapeutics.

bioengineering↗

bioRxiv2026

A kinetic-aware approach to infer metabolic variations and flux using transcriptomics and metabolomics data

Assessing metabolic variations and flux quantities enable systematic understandings of metabolic shifts, reprogramming, adaptation and interactions in human diseases. However, omics-based estimation of metabolic flux and its variation remains challenging due to several fundamental limitations: the need for disease and tissue context specific metabolic model; nonlinear enzyme kinetic model that links enzyme and substrate changes to reaction flux; partial, unpaired, and snap-shot measurements across omics modalities; and uncertainty in computational prediction. Here, we present Michaelis-Menten model-based Flux Estimation Analysis (mmFEA), a Monte Carlo framework for estimating condition-specific flux changes by integrating paired or unpaired metabolomics and transcriptomics (or proteomics) data. mmFEA separates each reaction-rate change into enzyme- and substrate-associated components and assess reaction rate using Michaelis-Menten kinetics equation. A baseline metabolite saturation rate is introduced by integrating protein language model predicted kinetic parameters and human baseline level metabolic concentration to enable kinetic-aware integration of unpaired substrate and enzyme level measurements. Distribution of metabolic flux and variations between conditions are further computed using MCMC sampling by treating Michaelis-Menten-derived marginal flux distribution as prior and coherency in flux balance as likelihood. To benchmark mmFEA, we generated an in-house multi-omics data set including transcriptomics, metabolomics, metabolic activity functional assay, and CRISPR screening data using pancreatic cancer cell line system treated by APEX1 inhibitors. We demonstrated that mmFEA could accurately capture experimentally observed metabolic changes and achieved a better performance than all baseline methods. Our analysis revealed the necessity in using both substrate and enzyme modality and kinetic aware model in metabolic flux assessment. Further analysis using independent pancreatic cancer cohorts further validated the robustness of mmFEA, supporting integration of condition-linked unpaired data. Pan-cancer and spatial multi-omic applications demonstrated the use of mmFEA for resolving context-dependent metabolic variation when direct flux measurements are unavailable. Together, mmFEA provides a mechanistically grounded framework for estimating relative metabolic flux changes and their uncertainty from heterogeneous omics data.

systems biology↗

bioRxiv2026

Hypomagnetic field inhibits seed germination via ROS signaling and reprogramming transcriptome in Arabidopsis thaliana

The geomagnetic field (GMF) is a ubiquitous yet poorly understood environmental factor that affects plant growth and development. It has been suggested that the blue-light photoreceptor cryptochrome (CRY) functions as a critical magnetic-field sensor in birds and insects through the radical-pair mechanism (RPM). However, whether CRY acts as a bona fide transducer of GMF signals and what are the downstream cascades remain largely elusive in plants. To address these key issues, we generated hypomagnetic field (HMF) via Helmholtz coils and passive magnetic shielding to investigate the GMF deprivation effects in Arabidopsis thaliana. HMF significantly delays the germination speed without altering the final germination rate, suggesting that HMF specifically modulates germination kinetics rather than seed viability. Time-resolved transcriptomic profiling revealed a coordinated transcriptional shift characterized by downregulation of growth-promoting genes and concurrent upregulation of defense-related genes under HMF. This biphasic transcriptional reprogramming coincides with a significant increase of reactive oxygen species (ROS), linking redox perturbation to the germination delay. Consistently, supplementation with ROS-scavenging antioxidants (e.g., reduced glutathione and ascorbic acid) rescues both germination speed and the misregulated expression of a subset of HMF-responsive genes, suggesting the central role of ROS in mediating HMF bioeffects. Genetic analysis using cry1 cry2 double mutants further indicated that HMF-induced germination delay operates through both CRY-dependent and -independent signaling pathways, suggesting the involvement of additional magnetosensitive modules beyond the canonical CRY-based RPM. These findings suggest that the GMF acts as a positive environmental cue that fine tunes the growth-defense trade-off through a redox-dependent signaling.

plant biology↗

bioRxiv2026

Innate immune stress pathway activation underlies heterochromatin dysfunction pathology

Heterochromatin loss disrupts nuclear architecture, gene regulation and repetitive element silencing, and is associated with diverse human diseases. However, mechanisms linking heterochromatin dysfunction to pathological phenotypes remain unclear. Using genetic interaction screening and genomic analyses in C. elegans, we identify secondary activation of the Intracellular Pathogen Response (IPR), an innate immune stress pathway, as a major contributor to heterochromatin mutant phenotypes. Constitutive IPR activation phenocopies slow growth and indirect transcriptional changes observed in these mutants. Depletion of genetic enhancers further increased, whereas suppressor RNAi attenuated IPR activation, with direct heterochromatin targets remaining substantially deregulated. Notably, many suppressors encode active chromatin components, and mild reduction of RNA polymerase II activity ameliorates growth defects in C. elegans HP1 mutants and human HP1-deficient cells. Our findings reveal secondary stress response activation as an important mechanism linking heterochromatin dysfunction to pathology and identify transcriptional dampening as a potential therapeutic strategy for mitigating these effects.

genetics↗

bioRxiv2026

ACAN regulates VSMC mitochondrial homeostasis through the YAP1/TAZ pathway and contributes to the onset and progression of aortic dissection

Objective: Aortic dissection (AD) is a serious, life-threatening cardiovascular crisis. While vascular proteoglycans normally buffer hemodynamic stress, their aberrant accumulation in the AD aorta predisposes to rupture. Aggrecan (ACAN) is among the most frequently elevated proteoglycans in this setting, yet its pathogenic relationship to AD remains undefined. This study aimed to investigate the role of ACAN in AD and identify potential therapeutic targets. Approach and Results: We employed human tissues, animal models, and cell cultures. Western blotting and immunohistochemistry (IHC) were performed on aortic samples from AD patients and controls to assess contractile markers, MMPs, ACAN, and SOX9. In vivo, AD was induced in mice using {beta}-aminoisobutyric acid (BAPN) and Ang II, with AAV-mediated ACAN knockdown in VSMCs. Histological staining confirmed model validity and enabled assessment of AD incidence, mortality, and protein expression changes. In vitro, human aortic vascular smooth muscle cells (HAVSMCs) were stimulated with Ang II, and SOX9 and ACAN were silenced via siRNA to evaluate the functional impact of ACAN downregulation. In human AD aortas, elevated ACAN and its upstream transcription factor SOX9 drove VSMC phenotypic switching and ECM degradation. In mice, ACAN knockdown corrected AD-induced medial structural disruption, elastin fragmentation, and collagen deposition, markedly reducing incidence and mortality while curbing excessive mitochondrial fission and rescuing functional integrity. ACAN silencing attenuated Ang II-induced mitochondrial damage in HAVSMCs via the RNA-seq-identified YAP1/TAZ pathway, and Verteporfin restored homeostasis. Conclusion: ACAN is aberrantly expressed in AD and murine aortas. ACAN downregulation delays disease progression by preserving mitochondrial homeostasis and function via the YAP1/TAZ pathway.

pharmacology and toxicology↗

bioRxiv2026

Large Language Models Predict Human Social Behavior via Interpretable Mechanisms

The development of large language models (LLMs) offers promising opportunities for predicting human behavior across diverse contexts. However, most prior work has emphasized behavioral imitation, with limited attention to transparent or interpretable models of the cognitive mechanisms underlying human decisions. In this study, we introduce MindEvolve, an autonomous workflow designed to predict behavior in social interactions by generating interpretable symbolic models of cognition. We systematically evaluate the modeling capabilities of multiple LLMs across a battery of socioeconomic games covering four core domains of social cognition: economic preferences, social preferences, social reasoning (theory of mind), and recursive planning. The symbolic models proposed by the LLMs are assessed by expert human evaluators for interpretability and theoretical coherence. Our results show that while most LLMs robustly capture economic and social preferences in relatively simple strategic settings, and in some cases generate novel models that integrate broader knowledge than those proposed by human experts, their capacity to model more complex psychological processes remains limited. However, a subset of state-of-the-art models demonstrates promising performance in capturing higher-order reasoning processes such as theory of mind and recursive planning. Together, these findings highlight the emerging potential of LLMs not only to imitate behavior, but to generate interpretable, mechanistic accounts of human social decision-making. Our results provide a roadmap for advancing LLM-based cognitive modeling toward human-expert-level theory construction.

neuroscience↗

bioRxiv2026

Shank3 mutation disrupts affective touch encoding in the dorsal medial prefrontal cortex of Beagle dogs

Individuals with autism spectrum disorder (ASD) often show aversion to affective touch (AT). However, the neural mechanism of this abnormality in cortices remains poorly understood probably due to the lack of effective animal models. Here, we used a canine model to address this issue by leveraging the intimate dog-human interactions. In a newly-designed heterospecific AT paradigm, we found that dogs carrying mutations in Shank3, a high-risk gene for ASD, avoided human AT. In vivo single-unit recording analysis showed that AT-evoked oscillations in the dorsal medial prefrontal cortex (dmPFC) were significantly altered in Shank3 mutant dogs. Shank3 mutation also reduced the number of neurons encoding AT in the dmPFC. Importantly, the aversion to AT and altered neural processing in Shank3 mutants were largely rescued by a GABAA receptor antagonist pentylenetetrazole. Together, these findings provide neural mechanisms for abnormal AT processing in ASD and suggest potential biomarkers for therapeutic strategies.

neuroscience↗

bioRxiv2026

Delayed Tagging of ED-A Fibronectin-Mimetic Peptide in an RGD-Decorated Synthetic Matrix Induces Fibroblast-to-Myofibroblast Transition

Synthetic hydrogels with bioactive ligands have been utilized to develop 3D models to gain mechanistic insight into how discrete extracellular matrix (ECM) cues direct cell fate. While the RGD motif is ubiquitously present in healthy and diseased tissues, the EDGIHEL (EDG) sequence is present only in the extra domain A-containing fibronectin (ED-A FN), which is transiently deposited in the provisional matrix in the wound bed. Here, we explore the potential of covalently tethered EDG in conjunction with RGD to promote fibroblast-to-myofibroblast transition (FMT). Normal human lung fibroblasts (NHLFs) were maintained in bioorthogonally constructed, hyaluronan-based hydrogel (BOHAGel) with tethered RGD ligands. When EDG was introduced on day 0 during cell encapsulation, cellular expression of Toll-like receptor 4 (TLR4) was upregulated, and a pro-inflammatory matrix remodeling response was observed, but myofibroblast differentiation was not detected. To mimic the transition from a healthy to an injured state, we leveraged the temporal tunability of BOHAGel by supplementing cell culture media with trans-cyclooctene (TCO)-tagged EDG after cells were primed in the RGD environment for 8 days. As the TCO species diffused through the hydrogel, EDG was instantaneously coupled to the network through immobilized tetrazine functionalities. Delayed introduction of profibrotic EDG motifs increased mRNA levels of the myofibroblast marker (ACTA2), ECM proteins (COL1A1, COL3A1, FN1), and transforming growth factor beta1 (TGFbeta1) downstream targets (VEGFA, CTGF), as well as matrix remodeling enzymes (MMP2, TIMP1). These changes were accompanied by the formation of alpha-SMA stress fibers, confirming complete FMT. Delayed EDG conjugation also enhanced and reinforced alpha1 integrin expression. Importantly, removing the RGD signal from the gel failed to induce myofibroblast differentiation. Collectively, our results suggest that FMT depends on ligand identities and the timing of their emergence in engineered matrices.

bioengineering↗

bioRxiv2026

Adaptive energetic tuning of nucleolar phase separation regulates rRNA transport

Eukaryotic cells adjust biochemical pathways in response to environmental stressors, stalling energetically costly processes such as protein synthesis and ribosome biogenesis. Ribosome biogenesis occurs within the multiphase nucleolus that contains three layers roughly corresponding to ribosomal RNA (rRNA) transcription, processing, and assembly. While nucleolar perturbations induced by drug treatments and optogenetic nucleolar gelation alter nucleolar stability and hinder ribosome biogenesis, it remains unclear whether nucleolar properties are actively tuned in response to metabolic and growth cues. Here, we show that nucleolar phase separation is adjusted to physiological needs. Live-cell imaging of endogenously tagged NPM1 reveals a tight relationship between NPM1 partitioning and nutrient availability. In nutrient-deprived conditions, NPM1 levels in the nucleolus increase, indicative of stabilized phase separation and a more gel-like state. Indeed, we show that rRNA diffusion decreases and the nucleolar meshwork contracts. Furthermore, this change corresponds to decreased rRNA processing, suggesting that reduced transport properties prevent the release of immature ribosome subunits from the nucleolus. Mechanistically, we show that these changes are driven by ATP levels, which broadly affect the energetically expensive process of ribosome biogenesis. Upon restoration of ATP levels by nutrient reintroduction, nucleolar composition returns to normal within minutes, suggesting active regulation. Taken together, our findings reveal that the biophysical properties of the nucleolus are not fixed, but are actively remodeled by cellular energy levels, linking phase separation dynamics to metabolic control of ribosome biogenesis.

biophysics↗

bioRxiv2026

Coronary Artery Disease Transcriptomics Reveals Two Drivers of the Endothelial Cell SR-BI Expression and LDL Transport that Underlie Atherosclerosis

Atherosclerosis is initiated by circulating low-density lipoprotein (LDL) cholesterol transfer into the artery wall, which is mediated by scavenger receptor class B, type I (SR-BI) in endothelial cells(1). Employing single-cell RNA sequencing in human coronary artery disease (CAD) samples, here we show that endothelial SR-BI expression is increased in atheroma, and in endothelial cells with a transcript signature indicative of responding to disturbed blood flow. In vivo in mice hypercholesterolemia and disturbed blood flow independently upregulate endothelial SR-BI; the flow-related upregulation initiates endothelial cell LDL uptake and atherogenesis. Guided by transcription factor networks, it is revealed that HIF-1 binding to human Scarb1 Intron 1 governs endothelial SR-BI transcription, and in mice HIF-1 drives hypercholesterolemia-related SR-BI upregulation and artery LDL uptake. Thus, the two major instigators of atherosclerotic lesion formation, hypercholesterolemia and disturbed blood flow, both upregulate endothelial SR-BI to drive the LDL transport that underlies the disorder. Targeting the processes regulating endothelial SR-BI potentially represents a new therapeutic strategy against CAD.

cell biology↗

bioRxiv2026

Bioorthogonal Tuning of Hydrogel Stiffness Promotes Zonal Redifferentiation of Passaged Chondrocytes

Generating bioengineered cartilage that recapitulates the depth-dependent phenotype, structure, and function of native articular cartilage remains a challenge. While cartilage is rich in aggrecan and type II collagen, proper function depends on depth-dependent protein expression. Superficial zone chondrocytes (SZCs) secrete proteoglycan-4 (PRG4) to lubricate the cartilage surface. Deep zone chondrocytes produce type X collagen (COLX) to support compressive loading and load transfer to subchondral bone. We previously demonstrated that passaged full-thickness chondrocytes (FTCs) and zonal chondrocytes can re-express cartilage and zone-specific markers following scaffold-free three-dimensional (3D) culture in redifferentiation media. However, in the absence of an instructive matrix, cells expressed low levels of zone-specific proteins and exhibited limited depth-dependent organization. We hypothesize that synthetic extracellular matrix with zone-specific microenvironmental cues will guide zonal differentiation. To this end, passaged primary bovine chondrocytes were encapsulated in a soft, hyaluronan (HA)-based, cell-adhesive, and protease-degradable hydrogel established via bioorthogonal tetrazine (Tz) ligation with norbornene (Nb). When supplemented with TGF{beta}3, FTCs deposited aggrecan and type II collagen with minimal type I collagen. Application of interfacial tetrazine ligation with trans-cyclooctene (TCO) during cell culture resulted in matrix stiffening, leading to upregulation of COLX expression. Conversely, SZCs cultured in soft hydrogels exhibited the greatest PRG4 expression. Establishment of a trilayered construct with region-specific stiffness via the diffusion-controlled reaction promoted PRG4 and COLX expression in defined zones. Together, these findings demonstrate that tunable HA-based hydrogels can enhance zone-specific chondrocyte phenotypes and promote the formation of zonally organized cartilage.

bioengineering↗

bioRxiv2026

Mass-transfer-constrained thermodynamics links fluid motion to the preferential use of hydrogen and formate in syntrophic propionate oxidation

Syntrophic propionate oxidation in methanogenic environments depends on interspecies electron transfer through hydrogen and formate, yet the physical factors governing the relative use of these carriers remain poorly understood. Here, we examined how fluid motion alters electron-transfer energetics and pathway expression in the obligate syntrophic propionate oxidizer Pelotomaculum schinkii grown in coculture with Methanospirillum hungatei. A mass-transfer-constrained thermodynamic model was used to estimate H2 and formate concentrations at the P. schinkii cell surface and calculate the corresponding Gibbs free-energy change of H2- and formate-mediated propionate oxidation under different mixing conditions and growth stages. Transcriptomic analysis was used to assess expression of electron-transfer pathways. Under unmixed conditions, formate-mediated propionate oxidation was more thermodynamically favorable than the H2-mediated pathway, consistent with highly expressed genes involved in formate production. Mixing altered coculture activity and pathway energetics. H2 was more sensitive to mixing and certain conditions shifted the energetic advantage toward H2. Expression of the major hydrogenases and formate dehydrogenases generally tracked these pathway-specific energetic changes. These results show that fluid motion reshapes the near-cell thermodynamic favorability and enables condition- and growth-stage-dependent use of alternative electron-transfer pathways. Fluid motion should therefore be considered an ecological and engineering control on syntrophic metabolism.

microbiology↗

bioRxiv2026

Desert hedgehog enhances endothelial resilience and prevents atherosclerosis by mitigating PAI-1 signaling

BACKGROUNDAtherosclerotic cardiovascular disease remains the leading cause of death worldwide. Most current pharmacotherapies target conventional risk factors that promote atherosclerosis (e.g., hyperlipidemia) rather than intrinsic resilience factors that protect against atherosclerosis in the face of risk factors. Here, we investigated the role of desert hedgehog (DHH), a canonical ligand of the hedgehog signaling pathway, as a novel resilience factor that restrains endothelial mesenchymal transition (EndoMT) and protects against atherosclerosis. METHODSSingle-cell RNA sequencing (scRNA-seq) was performed on atheroprone and atheroprotective regions of the ApoE knockout mouse aorta to identify mechanoresponsive genes associated with atherosclerosis. Endothelial cell-specific Dhh knockout mice were subjected to partial carotid ligation and hypercholesterolemic conditions to investigate the role of endothelial Dhh in atherosclerosis progression. scRNA-seq, bulk RNA sequencing, endothelial lineage tracing, immunoprecipitation-coupled mass spectrometry, and surface plasmon resonance were used to in-vestigate the role and mechanism of DHH in EndoMT. Pharmacological interventions and recombinant DHH administration were performed in vivo to evaluate therapeutic potential of DHH targeting. DHH expression was also examined in human atherosclerotic arteries and serum samples from patients with coronary artery disease. RESULTSDHH protein expression was enriched in arterial endothelium from mice, porcine, and humans. However, DHH expression was significantly reduced in atherosclerotic arteries and serum from patients with coronary artery disease. scRNA-seq of atheroprone and atheroresistant region of mouse aorta identified Dhh as a novel mechanoresponsive gene enriched in aortic regions exposed to unidirectional laminar flow. Endothelial cell-specific Dhh knockout (DhhecKO) mice exhibited increased atherosclerotic lesion area, large necrotic cores, and reduced collagen content following partial carotid ligation. Similarly, under hypercholesterolemic conditions, both male and female DhhecKO mice showed aggravated atherosclerosis progression. scRNA-seq of DhhecKO mouse aortas revealed an increased proportion of endothelial cells undergoing mesenchymal transition, indicating enhanced EndoMT. These findings were corroborated by bulk RNA-sequencing of DHH depleted HUVECs and endothelial lineage tracing in inducible DhhecKO mice. Mechanistically, DHH directly interacted with plasminogen activator inhibitor type 1 (PAI-1) and suppressed PAI-1-induced EndoMT. PAI-1 promoted EndoMT in ECs through activation of canonical TGF-{beta} signaling (SMAD2/3) and noncanonical AKT/ERK1/2 signaling via interaction with low-density lipoprotein receptor-related protein (LRP1). Neutralization of PAI-1 or inhibition of LRP1, AKT/ERK1/2, or SMAD3 signaling abolished DHH deficiency-induced EndoMT. DHH competitively inhibited PAI-1 binding to LRP1, thereby attenuating downstream pro-EndoMT signaling. Intriguingly, treatment with PAI-1 inhibitor TM5275 mitigated endothelial Dhh deficiency induced EndoMT in vivo. Of translational relevance, recombinant mouse DHH protein administration reduced atherosclerosis progression, stabilized plaque, and decreased the expression of EndoMT markers in ApoE knockout mice. CONCLUSIONSDesert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 signaling. The present study implicates endothelial DHH as a potential therapeutic target for atherosclerotic cardiovascular disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/729715v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@194c8a3org.highwire.dtl.DTLVardef@1004d52org.highwire.dtl.DTLVardef@d47c73org.highwire.dtl.DTLVardef@368866_HPS_FORMAT_FIGEXP M_FIG C_FIG Desert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 binding to LRP1 and downstream AKT/ERK, as well as SMAD2/3 signaling. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIDHH was identified as a flow-responsive resilience gene that is downregulated by disturbed flow in endothelial cells. C_LIO_LIEndothelial-specific deletion of Dhh promoted endothelial-to-mesenchymal transition (En-doMT) and atherosclerosis. C_LIO_LIDHH directly interacts with PAI-1 and preclude PAI-1 mediated pro-EndoMT signaling. C_LI What Are the Clinical Implications?O_LIDHH maintains endothelial homeostasis during atherosclerosis. C_LIO_LITargeting endothelial DHH-PAI-1 axis may represent a potential therapeutic strategy to reduce EndoMT and limit plaque progression. C_LIO_LILower circulating DHH level may serve as a potential biomarker of endothelial dysfunction and plaque vulnerability in atherosclerotic disease. C_LI

biochemistry↗