Biology subjects

Zhu, J.

Publications and source records attributed to Zhu, J..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

RNA polymerase-mediated regulation of intrinsic antibiotic resistance and bacterial cell division

Rifampin is a frontline antibiotic that inhibits the RNA polymerase of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Unlike most antibiotics, rifampin has an unusual ability to shorten the duration of treatment needed to cure TB that is not simply explained by its antimicrobial potency. We sought specific secondary effects of rifampins inhibition of Mtb RNA polymerase that may mediate this activity. We discovered that rifampin elicited a cell division arrest that was mediated through its inhibition of RNA polymerase. This arrest resulted in a downstream inhibition of the MtrAB two-component regulatory system, a mediator of intrinsic antibiotic resistance in Mtb. This inhibition is broadly conserved in other bacteria and represents a novel form of antimicrobial activity, termed adjunctive sensitization, that can mediate synergy and may contribute to rifampins unusual treatment shortening activity.

microbiology↗

bioRxiv2025

ROCK2 inhibition has a dual role in reducing ECM remodelling and cell growth, while impairing migration and invasion

The Rho-associated coiled-coil containing protein kinases 1/2 (ROCK1/2) are key signalling proteins involved in the regulation of the actin cytoskeleton and control a variety of cellular processes. This includes cell proliferation, stemness, cell migration and invasion as well as actomyosin contraction and extracellular matrix (ECM) remodelling. Due to a lack of ROCK2 specific inhibitors, previous pharmacological studies of ROCK function have relied on pan-ROCK1/2 inhibition. Here, we use the ROCK2 specific inhibitor, GV101, in the context of breast cancer (BC) models to uncouple the effects of ROCK2 pharmacological inhibition on both epithelial and stromal fibroblast cell populations. We demonstrate that ROCK2 inhibition with GV101 reduces fibroblast-mediated remodelling of pre-existing and de novo synthesised ECM resulting in a reduction in biomechanical stiffness, while also limiting epithelial cell growth in 2D and 3D settings. We also demonstrate that ROCK2 inhibition exposes epithelial cell vulnerability to fluid flow-induced shear stress. Furthermore, using 3D co-cultures we reveal that GV101 reduces single-cell migratory capacity, while the disruption of stromal ECM architecture is sufficient to impede collective cell migration and invasion. Finally, we assessed ROCK2 expression in human BC patient tumours revealing that ROCK2 expression is up-regulated during BC progression and that high ROCK2 expression correlates with poor patient outcome in the triple-negative subtype of BC. Together, these results demonstrate that ROCK2 specific inhibition disrupts key functions in both epithelial cell and stromal fibroblast compartments warranting further assessment of ROCK2 in highly proliferative, fibrotic or metastatic diseases, such as BC. HighlightsO_LIFibroblast-mediated remodelling of pre-existing and de novo synthesised extracellular matrix is reduced upon ROCK2 specific targeting. C_LIO_LIROCK2 inhibition impairs epithelial cancer cell growth and colony formation in 2D and 3D contexts, while also limiting single-cell migration and cell survival upon fluid flow-induced shear stress. C_LIO_LIROCK2 targeting during fibroblast-mediated ECM remodelling is sufficient to disrupt collective cell migration as well as 3D invasion into organotypic fibroblast-contracted collagen matrices. C_LIO_LIROCK2 expression is up-regulated during breast cancer progression and high expression correlates with poor patient outcome in triple-negative breast cancer. C_LI

cell biology↗

bioRxiv2025

A positive feedback loop between sensory and octopaminergic neurons underlies nociceptive plasticity in Drosophila larvae

Adaptive modulation of nociceptive behaviour based on prior experience is essential for responding effectively to environmental threats. In Drosophila larvae, nociceptive escape behaviours are robust and stereotyped, yet emerging evidence suggests this can be modulated by experience and internal state. Here, we demonstrate that repeated activation of nociceptive sensory neurons enhances both the likelihood and intensity of nocifensive rolling, reflecting a form of behavioural sensitization. This heightened responsiveness is accompanied by a sustained increase in activity within nociceptive sensory neurons, suggesting that plasticity arises, at least in part, within the sensory compartment. We identified the neuromodulator octopamine as a critical regulator of the sensitization: signalling through the octopamine receptor OAMB is required to sustain elevated nociceptive gain, and feedback from one of octopaminergic neurons class, the ventral unpaired median (VUM) neurons, amplifies sensory neuron output. Together, these findings reveal an experience-dependent positive feedback loop in the nociceptive system, where neuromodulatory circuits tune behavioural output.

neuroscience↗

bioRxiv2025

A GCN1-independent activator of the kinase GCN2

Mutations of EIF2AK4, which encodes the eIF2 kinase GCN2, cause a severe inherited form of pulmonary hypertension called pulmonary veno-occlusive disease (PVOD). Some pathogenic variants of GCN2 are amenable to pharmacological reactivation by low concentrations of ATP-pocket binding inhibitors. Kinase inhibition at modestly elevated concentrations limits the clinical utility of these drugs against PVOD. We therefore performed an in cellulo chemical screen for GCN2 activators and identified three structurally distinct compounds with low micromolar stimulatory activities. Unlike previously described GCN2 activators, one of these molecules activated GCN2 independently of GCN1. Modelling supported by structure activity screens suggested it binds within the ATP-pocket of GCN2, but unlike existing ligands does not protrude inward into the allosteric pocket or outward into the solvent. This overcomes a key requirement of other GCN2 activators.

cell biology↗

bioRxiv2025

StruCloze: A Unified Framework for Backmapping and Inpainting of Biomolecules

Atomistic resolution is essential for understanding biomolecular structure and function, yet coarse-grained (CG) models remain indispensable for simulating large and dynamic systems. Reconstructing accurate all-atom structures from CG representations, particularly across varied CG schemes and biomolecular types, remains a fundamental challenge. Moreover, flexible or disordered regions may well suffer from failure in structure modeling, making inpainting missing regions another challenging task. Here, we present StruCloze, a deep learning framework for reconstructing atomistic structures from CG models and inpainting missing regions for both proteins and nucleic acids. StruCloze generalizes across various CG levels and biomolecule types on single pretraining, with minimal fine-tuning required for optimal performance on specific representations. It achieves state-of-the-art accuracy in reconstructing both protein and nucleic acid structures, demonstrates superior transferability and speed compared to existing methods. Leveraging masked learning strategy, StruCloze also excels at inpainting structurally missing regions in structures, offering a practical tool for structural refinement and integrative modeling. Our framework provides a general solution for bridging reduced or incomplete representations with full atomistic detail of biomolecular structures, enabling rapid local structure prediction and further analysis on system dynamics.

bioinformatics↗

bioRxiv2025

Whole genome sequence-based characterization of foodborne Staphylococcus aureus isolated from pork in 2018 and 2023.

This study characterizes the genomic epidemiology of 111 Staphylococcus aureus isolates collected from retail meat in Beijing and Copenhagen during 2018 and 2023 using whole-genome sequencing. Our analysis identified concerning antimicrobial resistance patterns, with methicillin-resistant S. aureus (MRSA) prevalence rising from 19.51% to 24.13% over the study period. The livestock-associated CC398 lineage (27.03% of isolates) demonstrated strong correlations with tetracycline resistance (tetM) and persisted as the dominant clone in Beijing, increasing from 33.33% to 40.91% prevalence. In contrast, we observed the rapid emergence of community-associated CC8 strains in Denmark, reaching 71.43% prevalence by 202327. Virulence profiling revealed MSSA strains frequently carried enterotoxin genes (seg/sei in 55.8% of isolates), while mobile genetic elements like SCCmec IV in ST59-t437 contributed significantly to pathogenicity. Phylogenetic analysis delineated five major clades and highlighted the expansion of multidrug-resistant CC398 strains in Beijing. These findings demonstrate the dynamic evolution of S. aureus at the human-animal interface and emphasize the urgent need for integrated One Health surveillance systems to track resistance gene dissemination. Future research should prioritize investigating zoonotic transmission pathways and the role of horizontal gene transfer in driving the convergence of virulence and resistance traits in foodborne pathogens.

genomics↗

bioRxiv2025

Role of Macrophage PARP1 in the Regulation of Crosstalk between Adipose Immune Cells and Adipocytes during Diet-induced Obesity

Adipose tissue consists of heterogeneous cell populations, including macrophages, which play a key role in maintaining adipose tissue homeostasis. We previously identified PARP1 as a critical regulator of proadipogenic gene expression in preadipocytes and proinflammatory gene expression in macrophages. To investigate the role of macrophage PARP1 in regulating adipose tissue homeostasis, we generated myeloid lineage-specific Parp1 knockout mice (Parp1 KOLysM). When subjected to a high fat diet for 12 weeks, the Parp1 KOLysM mice exhibited an obese phenotype accompanied by white adipose tissue (WAT) dysfunction, characterized by altered metabolite profile, pronounced adipocyte hypertrophy, and increased macrophage infiltration. Coculture of primary preadipocytes with the conditioned medium from bone marrow-derived macrophages (BMDMs) isolated from Parp1 KOLysM or control mice demonstrated that macrophage PARP1 depletion inhibited LPS-induced proinflammatory gene expression in BMDMs, but enhanced differentiation of preadipocytes into mature adipocytes. Single cell RNA-sequencing using CD45+-sorted WAT resident immune cells showed that macrophage PARP1 depletion increased the fraction of macrophages and NK cells, altered gene expression in both cell populations, and promoted intercellular communications. Taken together, our studies demonstrate a key role for macrophage PARP1 in the maintenance of adipose tissue inflammatory and metabolic homeostasis. Macrophage PARP1 depletion promotes cell-cell crosstalk among macrophages, fat cells, and other immune cell populations in adipose tissue, which cooperatively drives the development of obesity. SignificanceIn this study, we characterized a role for macrophage PARP1 in regulating adipose tissue homeostasis. Depletion of PARP1 in macrophages enhances cell-cell crosstalk among immune cells and fat cells, which exacerbates adipose dysfunction and drives obesity and adverse metabolic outcomes.

molecular biology↗

bioRxiv2025

UniCure: A Foundation Model for Predicting Personalized Cancer Therapy Response

Predicting drug efficacy across diverse patient contexts remains a major challenge in oncology, as models trained on cancer cell lines often fail to capture patient-specific biology. Emerging biological foundation models and patient-derived technologies offer a promising solution. Here, we present UniCure, the first pre-trained foundation model integrating both omics and chemical foundation models (UCE and Uni-mol) to predict transcriptomic responses to drugs across diverse cellular and tissue contexts, enabling personalized cancer therapy and drug prioritization at the individual level. Rather than encoder/decoder used in traditional models, UniCure utilizes parameter-efficient fine-tuning (PEFT) techniques for optimizing the training process, a novel FlexPert module for modeling flexible drug-cell interactions, and a Maximum Mean Discrepancy (MMD) loss for learning unpaired data. Trained on over 1.8 million perturbation RNA-seq profiles over 22,000 compounds, 166 cell types, and 24 tissues, UniCure achieves high accuracy in predicting both dose-dependent responses and drug combination effects, demonstrating strong generalization across bulk and single-cell transcriptomic data. In particular, fine-tuning on our patient-derived tumor-like clusters and real-world data of 800 profiles enables UniCure to generate individualized therapeutic predictions on patients tissue samples. In addition, UniCure enables patient stratification based on the predicted drug responses, providing a new way for subtyping patients. UniCures drug prioritization was validated across over 1000 patients from pan-cancer cohorts and supported by experiments of candidate therapeutics. By enabling the potential to screen millions of compounds per patient at scale, UniCure represents a biologically grounded tool that could advance personalized precision oncology and accelerate drug discovery.

bioinformatics↗

bioRxiv2025

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica, respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica. Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches.

genomics↗

bioRxiv2025

X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models

The rapid expansion of massively parallel sequencing technologies has enabled the development of foundation models to uncover novel biological findings. While these have the potential to significantly accelerate scientific discoveries by creating AI-driven virtual cell models, their progress has been greatly limited by the lack of large-scale high-quality perturbation data, which remains constrained due to scalability bottlenecks and assay variability. Here, we introduce "Fix-Cryopreserve-ScRNAseq" (FiCS) Perturb-seq, an industrialized platform for scalable Perturb-seq data generation. We demonstrate that FiCS Perturb-seq exhibits high sensitivity and low batch effects, effectively capturing perturbation-induced transcriptomic changes and recapitulating known biological pathways and protein complexes. In addition, we release X-Atlas: Orion edition (X-Atlas/Orion), the largest publicly available Perturb-seq atlas. This atlas, generated from two genome-wide FiCS Perturb-seq experiments targeting all human protein-coding genes, comprises eight million cells deeply sequenced to over 16,000 unique molecular identifiers (UMIs) per cell. Furthermore, we show that single guide RNA (sgRNA) abundance can serve as a proxy for gene knockdown (KD) efficacy. Leveraging the deep sequencing and substantial cell numbers per perturbation, we also show that stratification by sgRNA expression can reveal dose-dependent genetic effects. Taken together, we demonstrate that FiCS Perturb-seq is an efficient and scalable platform for high-throughput Perturb-seq screens. Through the release of X-Atlas/Orion, we highlight the potential of FiCS Perturb-seq to address current scalability and variability challenges in data generation, advance foundation model development that incorporates gene-dosage effects, and accelerate biological discoveries.

genomics↗

bioRxiv2025

In vivo AAV9-SB-CRISPR screen identifies fatty acid elongase ELOVL5 as a pro-resolving mediator in lung inflammation

Timely resolution of inflammation is essential to prevent tissue damage and maintain homeostasis. Immunometabolism is critical for innate immunity and inflammation. However, how metabolic enzymes and metabolites contribute to inflammatory resolution remains largely unknown. To identify the key metabolic mediators of inflammation resolution, we generated an AAV9-Sleeping Beauty CRISPR library comprising 17090 sgRNAs targeting 2682 mouse metabolic genes. We then conducted an in vivo CRISPR screen in type II alveolar epithelial cells (AECIIs)-specifically expressing Cas9 mice and uncovered a very long chain fatty acid elongase, ELOVL5, that promoted the resolution of lung inflammation after influenza virus infection. Deficiency of Elovl5 in mouse lung epithelial cells impaired lung inflammation resolution and tissue repair phenotype both in vitro and in vivo. Mechanistically, ELOVL5 bound to STING, inhibiting TBK1 interaction and translocation to the Golgi. These effects ultimately reduced STING-mediated inflammation and promoted AKT1-mediated tissue repair. In addition, ELOVL5 decreased eicosanoid levels in AECIIs to promote lung inflammation resolution. Supplement with ELOVL5 downstream products reversed the increased expression of inflammatory cytokines caused by Elovl5 deficiency. These results support an unrevealed mechanism for polyunsaturated fatty acid metabolism in the resolution of innate inflammation and provide paths toward treating inflammatory diseases through manipulating cellular lipid metabolism.

immunology↗

bioRxiv2025

Undermining the cry for help: The phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria

During pathogen attack, plants recruit beneficial microbes in a "cry for help" to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonization through various mechanisms, including targeted host microbiota manipulation. Here, we characterize the Av2 effector of the vascular wilt fungus Verticillium dahliae as a suppressor of the cry for help. Inspired by in silico antimicrobial activity prediction, we investigated the antimicrobial activity of Av2 in vitro. Furthermore, its role in V. dahliae virulence was assessed through microbiota sequencing of inoculated plants, microbial co-cultivation assays, and inoculations in a gnotobiotic plant cultivation system. We show that Av2 inhibits bacterial growth, and acts as a virulence factor during host colonization. Microbiota sequencing revealed involvement of Av2 in suppression of Pseudomonas spp. recruitment upon plant inoculation with V. dahliae, suggesting that Av2 suppresses the cry for help. We show that several Pseudomonas spp. are antagonistic to V. dahliae and sensitive to Av2 treatment. We conclude that V. dahliae secretes Av2 to supress the cry for help by inhibiting the recruitment of antagonistic Pseudomonas spp. to pave the way for successful plant invasion.

plant biology↗

bioRxiv2025

Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice.

CHD8 mutations cause autism spectrum disorder, cognitive deficits, and macrocephaly. Chd8+/- mouse models exhibit macrocephaly and transcriptional pathology, with inconsistent findings regarding neurogenesis, neuron function, and behavior. Via stereology and single nucleus transcriptomics (snRNA-seq), we found increased Chd8+/- cortical volume was not explained by increase in neuron number. Differential expression (DE) was present across cortical cell types, with excitatory neurons exhibiting high DE burden and shared and subclass-specific DE signatures. Bulk RNA-seq DE of constitutive Chd8+/- and conditional Camk2a-Cre Chd8+/-mice identified shared transcriptional pathology. DE in synaptosomal versus nuclear mRNA identified overlapping DEGs, but also significant differences and exaggerated synaptosomal changes. Building on DE findings implicating glutamatergic neurons, we found Chd8+/-mice exhibited altered excitatory neuron spine density and dynamics, decreased GCaMP activity correlation, and sleep perturbation. Thus, Chd8 haploinsufficiency causes lasting excitatory neuron dysfunction, perturbs RNA regulation beyond transcription, and impacts neuronal properties, cortical microcircuits, and behavior.

genomics↗

bioRxiv2025

A caspase-1-cathepsin AND-gate probe for selectiveimaging of inflammasome activation

Caspase-1 is a key mediator of the inflammasome pathway, which is associated with several inflammatory disorders including obesity, diabetes mellitus (DM), cardiovascular diseases (CVDs), cancers and chronic respiratory diseases. Although substrate-based probes can be used to visualize the activity of caspase-1, none are selective enough for use as imaging agents. Here, we report the design and synthesis of a AND-gate substrate probe (Cas1-Cat-Cy7) that requires processing by both caspase-1 and cathepsins to produce a signal. Because both enzymes are only found together and active at the site of inflammasome activation, the resulting probe can be used to image caspase-1 mediated inflammation. We demonstrate that the probe produces selective signals in ex vivo biochemical and cellular assays and in a mouse model of acute inflammation.

biochemistry↗

bioRxiv2025

Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator

The androgen receptor (AR) is a critical driver of prostate cancer (PCa). To study regulators of AR protein levels and oncogenic activity, we created the first live cell quantitative endogenous AR fluorescent reporters. Leveraging this novel AR reporter, we performed genome-scale CRISPRi flow cytometry sorting screens to systematically identify genes that modulate AR protein levels. We identified and validated known AR protein regulators including HOXB13 and GATA2 and also unexpected top hits including PTGES3, a poorly characterized gene in PCa. PTGES3 repression resulted in loss of AR protein, cell cycle arrest, and cell death in AR-driven PCa models. PTGES3 is not a commonly essential gene, and our data nominate it as a prime PCa therapeutic target. Clinically, analysis of PCa data demonstrate that PTGES3 expression is associated with AR-directed therapy resistance. Mechanistically, we show PTGES3 binds directly to AR, forms a protein complex with AR in the nucleus, regulates AR protein stability in vitro and in vivo and modulates AR function in the nucleus at AR target genes. PTGES3 represents a novel therapeutic target for overcoming known mechanisms of resistance to existing AR-directed therapies in PCa.

cancer biology↗

bioRxiv2025

BRD4 binds the nucleosome via both histone and DNA interactions

BRD4, a bromodomain and extraterminal (BET) family transcriptional regulator of cell cycle progression, cell differentiation and cancer development, is believed to be recruited to chromatin via interactions between its tandem bromodomains (BD1 and BD2) and acetylated histone tails. Although extensive studies have explained how individual BRD4 bromodomains bind to acetylated peptides and how BET inhibitors interfere with such interactions, equivalent studies of full-length BRD4 protein with the nucleosome have been lacking. Our cryo-EM structure of the BRD4 short (BRD4-S) isoform bound to a nucleosome diacetylated on histone H4 shows how BRD4 BD1 engages both the H4 tail and nucleosomal DNA. Unexpectedly, our biochemical studies indicate that BRD4 uses basic regions outside of the bromodomains to bind nucleosomes tightly even in the absence of histone acetylation. Our results further show that histone H4 acetylation influences the conformation of the BRD4/nucleosome complex.

molecular biology↗

bioRxiv2025

Comparative assessment of co-folding methods for molecular glue ternary structure prediction

Molecular glues (MGs) represent an emerging therapeutic paradigm capable of inducing or stabilizing protein-protein interactions, with broad applications in creating neomorphic interactomes and targeted protein degradation. However, current discovery efforts remain largely confined to experimental screening, while in silico rational design of MGs persists as a formidable challenge. A critical step toward rational design lies in accurate ternary complex modeling. Given the scarcity of such complexes in the Protein Data Bank for training specialized predictive models, we tested the ability of recently developed co-folding models, including AlphaFold 3, Boltz-1, Chai-1, Protenix, and RoseTTAFold All-Atom in building the complex models. We systematically curated a dataset, named MG-PDB, with 221 non-covalent MG-engaged ternary complexes. MGBench were further introduced as a comprehensive benchmark set, which comprises 88 ternary structures excluded from co-folding models training data through rigorous time-based partitioning. Our benchmark results demonstrated that AlphaFold3 achieved the best overall performance among co-folding methods, in terms of both protein-protein interaction interface prediction (50.6% success rate) and MG-protein interaction recovery (32.9% success rate). However, our homology study showed that most of their successful predictions actually stemmed from memorization. Further analysis revealed three phenomena of current co-folding methods for MG ternary structure prediction. Firstly, these methods struggle to accurately model large interaction interfaces. Secondly, their predictive accuracy is notably reduced for domain-domain complexes compared to domain-motif interactions. Lastly, they face specific challenges in modeling MG degrader complexes with sufficient accuracy. We showcased they relied on the existing interaction patterns, and highlighted the need for further improved in novel E3 ligase systems. These findings reveal fundamental gaps in existing methods to learn atomic-level interaction rules for MG-engaged ternary complex modeling. MG-PDB and MGBench provide critical resources and mechanistic insights to advance computational MG discovery. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/655997v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@172b19borg.highwire.dtl.DTLVardef@ea4844org.highwire.dtl.DTLVardef@12ea246org.highwire.dtl.DTLVardef@9fb4bc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Mechanosensitive Endothelial METTL7A Regulates Internal m7G mRNA Methylation and Protects Against Atherosclerosis

BACKGROUNDInternal N7-methylguanosine (m7G) is a recently identified chemical modification of mammalian mRNA and a component of the epitranscriptome. While the epitranscriptome plays a key role in regulating RNA metabolism and cellular function, the specific contribution of internal m7G to cardiovascular health and disease remains unknown. Atherosclerosis preferentially develops at sites where disturbed blood flow activates endothelial cells, but whether internal m7G and its regulatory machinery influence endothelial mechanotransduction and atherogenesis is unclear. METHODSWe integrated epitranscriptomic profiling, human tissue analysis, genetically modified mouse models, and targeted nanomedicine approaches to investigate the role of Methyltransferase-like protein 7A (METTL7A), a putative internal m7G methyltransferase, in regulating the flow-sensitive endothelial transcriptome and atherosclerosis. Vascular endothelial cells were subjected to well-defined athero-protective and athero-prone flow waveforms in vitro and in vivo. METTL7A function was assessed using RNA sequencing (RNA-seq), liquid chromatography-tandem mass spectrometry (LC-MS/MS), crosslinking immunoprecipitation sequencing (CLIP-seq), RNA stability assays, and a CRISPR-Cas-inspired RNA targeting system (CIRTS). METTL7A expression in human coronary arteries with and without atherosclerosis was evaluated by RNA-seq and immunostaining. In vivo atherosclerosis studies were conducted in both global and endothelial-specific Mettl7a1 knockout mice. Endothelial METTL7A expression was restored using cationic polymer-based nanoparticles delivering CDH5 promoter-driven METTL7A plasmids or VCAM1-targeted lipid nanoparticles delivering N1-methylpseudouridine (m{superscript 1}{Psi})-modified METTL7A mRNA. RESULTSAthero-protective unidirectional flow significantly induced METTL7A expression, which promoted internal m7G methylation of endothelial transcripts, while other major epitranscriptomic marks and cap-associated m7G were not affected by METTL7A. METTL7A preferentially binds to AG-enriched motifs in protein-coding mRNAs and plays a key role in regulating KLF4 and NFKBIA transcripts, enhancing their internal m7G and stability and supporting vascular homeostasis. In contrast, endothelial METTL7A expression was significantly reduced by disturbed blood flow and in human atherosclerotic lesions. Global or endothelial-specific loss of METTL7A exacerbated disturbed flow-induced atherosclerosis in mice, independent of serum lipid levels. Restoration of endothelial METTL7A, via nanoparticle-mediated plasmid or m1{Psi} mRNA delivery, markedly reduced lesion formation in Mettl7a1-/- and ApoE-/- mice. CONCLUSIONSThese findings establish METTL7A as a previously unrecognized mechanosensitive methyltransferase that maintains endothelial homeostasis by stabilizing key anti-inflammatory transcripts, KLF4 and NFKBIA, through internal m7G methylation. Loss of METTL7A disrupts endothelial function and accelerates atherogenesis in response to disturbed flow. Therapeutic restoration of endothelial METTL7A, via targeted nanoparticle-mediated gene or m1{Psi} mRNA delivery, significantly lessens atherosclerosis. Collectively, these results uncover a novel epitranscriptomic mechanism governing vascular health and position METTL7A as a promising target for precision nanomedicine in atherosclerotic cardiovascular disease.

molecular biology↗