Biology subjects

Xia, J.

Publications and source records attributed to Xia, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Developing High-Yield and Safe Therapeutic EVs by Ablating Tissue Factor-Mediated Toxicity

The clinical translation of extracellular vesicles (EVs) as next-generation drug delivery vehicles is currently stalled by two interrelated challenges: the difficulty of manufacturing EVs at an industrial scale ("the yield problem") and the risks of toxicity associated with systemic administration of high doses ("the safety ceiling"). In this comprehensive study, we present a two-pronged genetic engineering strategy to overcome these limitations. First, we discovered that overexpression of glycosylphosphatidylinositol (GPI)-anchored proteins, such as CD55 and CD59, significantly enhances EV production in HEK293T and Expi293F cells. By engineering a truncated CD55 variant (TR3) that retains the GPI-anchor but lacks functional domains, we developed the ExoBoost cell line, which boosts EVs yield by approximately 50-fold without altering vesicle morphology. Second, we observed acute toxicity in mice following intravenous administration of high-dose ExoBoost EVs, with symptoms resembling venous thromboembolism. Through comparative analysis of EVs derived from other cell types, including keratinocyte stem cells (KSCs) and mesenchymal stem cells (MSCs), we identified Tissue Factor (TF/F3) as the critical causative agent of this lethal response. Moreover, we completely abolished this toxicity by generating a F3-knockout cell line (ExoBoost2.0) using CRISPR/Cas9, thereby raising the safe dose to as high as 1.5E12 particles per mouse, as quantified by nano flow-cytometry (nFCM). Finally, using a novel CD46-nanoluciferase reporter system, we demonstrated that high-dose administration of these safe EVs saturates hepatic and splenic clearance pathways, leading to a dramatic increase of systemic EVs accumulation, particularly in hard-to-target tissues such as the brain ([~]10,000-fold) and muscle ([~]1,000-fold). Additionally, repeated high-dose administration of ExoBoost2.0 EVs did not upregulate inflammatory cytokines or production of IgG and IgM. In summary, these findings establish a scalable, safe, and highly biocompatible EVs platform, potentially revolutionizing the drug delivery system in clinical application.

bioengineering↗

bioRxiv2025

A Combinatorial mRNA Therapy for Treating Rheumatoid Arthritis and Osteoarthritis by Inhibiting Inflammation and Promoting Cartilage Regeneration

Rheumatoid arthritis (RA) and osteoarthritis (OA) are debilitating joint disorders with distinct etiologies but share common pathological features of chronic inflammation and progressive cartilage damage. Current therapeutic options are largely palliative and yet fail to achieve desired effect. In this study, we developed a combinatorial mRNA therapy using a rationally engineered lipid nanoparticle (LNP) containing a novel ionizable lipid for enhanced cartilage penetration upon intra-articular administration. This LNP co-delivers mRNAs encoding two complementary therapeutic proteins: interleukin-1 receptor antagonist (IL-1Ra) for inflammation attenuation and a C-terminal truncated derivative of angiopoietin-like 3 (ANL3) for cartilage regeneration. In pre-clinical models including collagen-induced arthritis mice, TNF-transgenic mice with spontaneous RA and destabilization of medial meniscus (DMM) surgical OA model, this "one-shot" combinatorial therapy significantly ameliorated disease severity, reduced synovitis and bone erosion, and potently promoted the regeneration of hyaline-like cartilage. Mechanistically, transcriptomic profiling of joint specimens revealed that the combinatorial therapy concurrently suppressed inflammatory pathways and extracellular matrix degradation pathways, meanwhile upregulating anabolic genes facilitating chondrogenesis. Collectively, our study establishes a versatile and synergistic mRNA therapy that offers a potent disease-modifying immunomodulatory strategy capable of addressing the long-standing unmet needs in arthritis treatment.

immunology↗

bioRxiv2025

Neonatal BCG Vaccination Engages the Vasculature to Elicit γδ T Cell-Mediated Protection against Tuberculosis

The Bacillus Calmette-Guerin (BCG) vaccine remains the only approved vaccine against tuber-culosis (TB). Although its efficacy against pulmonary TB in adults is limited, BCG provides re-markable protection against miliary TB when administered during infancy. Despite more than 100 million infants worldwide receiving BCG annually, the mechanisms underlying its neonatal protective effects remain poorly defined. Here, we demonstrate that subcutaneous neonatal BCG vaccination (BCG-sc) induces a marked expansion of {gamma}{delta} T cells producing IL-17 and IL-22, which mediated protection against subsequent Mycobacterium tuberculosis (Mtb) experimental infection. A similar expansion of {gamma}{delta} T cells was observed in a longitudinal cohort of infants, from birth to three months of infants followed after intradermal BCG vaccination. Mechanistical-ly, BCG-mediated protection in neonates was linked to its early vascular dissemination through the distinct structure of neonatal skin, resembling the protective effects of intravenous BCG in adults. Moreover, neonatal BCG-sc vaccination generated a distinct BCG-induced microbiome signature, characterized by enrichment of Prevotellaceae, Tannerellaceae, and Bifidobacteriaceae, which was associated with protection. Together, these findings identify {gamma}{delta} T cells as key mediators of early-life BCG-induced immunity and highlight the role of the gut-lung axis in long-term protection against TB from infancy into adulthood.

immunology↗

bioRxiv2025

Encoding and Decoding of Brain Dynamic Functional Connectivity for ADHD Diagnosis

Recent studies have demonstrated strong associations between the changes in dynamic functional connectivity (FC) and both behavioral and cognitive functions. The sliding window technique is the most widely used method for evaluating dynamic FC; however, it faces two key challenges: distributional shifts across windows and high dimensionality, as FC is computed across windows of the entire time series. To address these issues, we propose BRAINMAP (Bi-level Representation using Attention for INterpretability with Mamba-Aided Prediction) to model the dynamic FC of the brain. BRAINMAP employs the Optimal Transport technique to correct distributional shifts across sliding windows and leverages Graph Neural Networks (GNNs) in conjunction with a hybrid approach that integrates an attention mechanism and the Mamba block to effectively capture spatiotemporal features for functional MR images. Finally, we introduce a novel Top-K sliding window feature selection algorithm to induce sparsity in dynamic FC. We conducted an extensive evaluation of our model for diagnosing Attention Deficit Hyperactivity Disorder (ADHD) using three resting-state fMRI datasets: ADHD-200, UCLA, and CNI-TLC, which comprise a total of 447 subjects with ADHD and 845 typically developing controls. Our architecture outperformed existing state-of-the-art dynamic FC models in ADHD detection, achieving improvements ranging from 3% to 12% across the three datasets. We demonstrate that our proposed model produces robust biomarkers, most notably the connection between the dorsal attention network and the visual network. Using an association study, we further establish the clinical relevance of the identified biomarkers.

neuroscience↗

bioRxiv2025

Longitudinal Analysis of Matched Patient Biospecimens Reveals Neural Reprogramming of Cancer-Associated Fibroblasts Following Chemotherapy in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC), the most common subtype of pancreatic cancer, is a deadly disease with a complex tumor microenvironment (TME). How chemotherapy alters the TME, and whether these changes drive chemoresistance, is poorly understood. We examined matched pre- and post-treatment tissue specimens and found near-universal enrichment of axonal guidance genes in cancer-associated fibroblasts (CAFs) after treatment. These CAFs were enriched near sites of perineural invasion, coinciding with regions of increased tumor cell proliferation, and were enriched in tumor areas distant from nerves after chemotherapy. Metastatic recurrence lesions had the highest prevalence of these CAFs versus primary tumors and untreated metastasis. These CAFs showed elevated non-canonical Wnt mediators and axonal guidance genes, which complemented matching cognate binding partners in tumor epithelial cells, suggesting a role in tumor-stroma crosstalk. Our findings implicate fibroblast-derived axonal-guidance genes in promoting PDAC invasion and point to a promising target for this disease. Statement of SignificanceTherapeutic resistance remains a major challenge in pancreatic cancer. Our findings shed light on the changes in the complex tumor microenvironment in response to chemotherapy and identify fibroblasts high in axonal-guidance genes that may drive tumor progression and chemoresistance, thus uncovering a potential avenue for targeting pancreatic cancer.

cancer biology↗

bioRxiv2025

Phylogenomics of Rhinogobius gobies reveal northern-southern divergence and trait evolution in China

The goby genus Rhinogobius represents a prominent radiation of freshwater fishes in East Asia, with China serving as its evolutionary hotspot harboring over 39 endemic species. Despite their ecological dominance in riverine ecosystems, phylogenetic relationships among mainland Chinese Rhinogobius species remain poorly resolved due to limited sampling and morphological conservatism, particularly in meristic traits traditionally used for classification. To address these knowledge gaps, we employed a nuclear gene enrichment approach to target 4,434 single-copy nuclear loci across 26 species spanning all major river basins in eastern and southern China. Our phylogenomic analyses based on sequence of 2,137 cleaned-up loci (477,822 bp) recovered a robust topology dividing Rhinogobius into three primary lineages: an early-diverging of R. similis sister to two major clades, the northern vs. southern clades exhibiting strong geographic structuring. Fossil-calibrated molecular dating placed the crown age of Rhinogobius at [~]9.33 million years ago (Ma) during the late Miocene, with a pivotal north-south divergence at [~]5.96 Ma coinciding with major paleo-drainage reorganizations in East Asia. Ancestral state reconstruction revealed that the southern clade uniquely evolved unstable first dorsal fin formula and near-universal presence of predorsal scales. By integrating the most extensive geographic and taxonomic sampling to date with phylogenomic data, this study establishes: (1) a revised evolutionary timeline for Rhinogobius diversification linked to East Asian geomorphological history, (2) diagnostic morphological characters for major clades, and (3) a robust phylogenetic framework to guide future taxonomic revisions and conservation efforts for this ecologically significant group. HighlightsO_LIPhylogenomics resolves north/south split in Chinese Rhinogobius gobies. C_LIO_LIFossil-dated 9.3 MYA origin of Rhinogobius and rapid divergence at 5.96 MYA. C_LIO_LISouthern lineages exhibit more predorsal scales and unstable first dorsal fin formula. C_LIO_LIFirst genomic backbone for species revision and adaptation study. C_LI

zoology↗

bioRxiv2025

Engineering of Pseudomonas putida KT2440 for Broad-Chain-Length 3-Hydroxy Fatty Acid Biosynthesis

3-Hydroxy fatty acids (3-HFAs) are versatile intermediates for bio-based polymers, fuels, and surfactants, and are advancing circular economy manufacturing. We built an acyl- CoA ligase-deficient chassis of Pseudomonas putida KT2440, thereby blocking 3-HFA activation and preventing its use as carbon source. This strategy decoupled synthesis from catabolism and enabled 3-HFA accumulation. We then compared two different routes for modifying the free 3-HFA composition. 1. In a direct route, overexpressing native PhaG produced C8, C10, C12, and C14 3-HFAs, achieving a total titer of 0.73 g/L in shake flasks. Functional analyses under our tested conditions support a re-assignment of PhaG: rather than acting primarily as a 3-hydroxyacyl-ACP:CoA transacylase, it functions mainly as a thioesterase, liberating free 3-HFAs from hydroxyacyl-ACP. 2. In an indirect route, overexpressing RhlA variants generated hydroxyalkanoyl-alkanoates (HAAs) that were converted to free 3-HFAs by endogenous esterase(s): RhlA from Pseudomonas aeruginosa PAO1 favored C8-C12 and yielded 0.47 g/L 3-HFAs, whereas RhlA from Burkholderia plantarii PG1 favored C10-C14 with 0.14 g/L, of which 80% was C14. Finally, we demonstrated process feasibility by up-scaling the PhaG pathway in a stirred-tank reactor. These results establish modular, stable, chassis-compatible routes for tailoring 3-HFA chain-length distributions, thereby providing a foundation for scalable, bio-based monomer supply in a circular economy.

synthetic biology↗

bioRxiv2025

Accurate processing of ultra-short immune signals by singlemacrophages

Accurately interpreting short-lived signals is challenging within noisy cellular microenvironments. It is not known if cells can distinguish different signaling molecules under transient exposure. Here, we explored the temporal limits of signal detection by single macrophages. Microfluidic experiments monitoring NF-{kappa}B dynamics showed that macrophages strongly respond even to 1-second pulses of cytokine and pathogen ligands. Information theory showed that short-pulse response is highly specific to the stimulating ligand, comparable to that under long-term stimulation. Macrophages were mainly sensitive to the duration of cytokines, and the dose of pathogen ligands. Stimulus duration altered the ranking of response strengths among different pathogenic ligands. Mathematical modeling showed that receptor cooperativity is crucial for robust responses to transient signals, while receptor pathway variability leads to accurate signaling in fluctuating environments. These findings demonstrate that dynamic transcription factor specificity is preserved across varying signal durations and uncover network-level mechanisms that accurately distinguish transiently encountered threats.

systems biology↗

bioRxiv2025

Evolutionarily Conserved and Divergent Mechanisms of Dual Ca2+ Sensors in Synaptic Vesicle Exocytosis

Neurotransmitter release at the C. elegans neuromuscular junction is governed by a dual Ca{superscript 2} sensor system composed of SNT-1 and SNT-3, which are functional analogs of synaptotagmin-1 and -7 (Syt1/Syt7) in mammalian central synapses. In this study, we investigated how SNT-1 and SNT-3 mediate fast and slow neurotransmitter release through their potential interactions with the SNARE complex and their polybasic motifs. AlphaFold 3 models of SNT-1-SNARE and SNT-3-SNARE complexes accurately recapitulated the canonical Syt1 C2B-SNARE primary interface (Zhou et al., 2015, Nature) and precisely identified conserved binding residues within the C2B domains, as well as in SNAP-25 and Syntaxin, highlighting the evolutionary conservation of this interaction. Electrophysiological analyses using targeted mutagenesis demonstrated that both SNT-1 and SNT-3 require C2B-SNARE interactions and polybasic motifs within their C2 domains to drive evoked fast and slow neurotransmitter release. Notably, SNT-1 and SNT-3 exhibited differential dependence on distinct regions of the C2B-SNARE interface and their respective polybasic motifs, suggesting that Ca{superscript 2}-triggered fast and slow release operate via distinct mechanistic strategies. Furthermore, we found that SNT-1 mediates spontaneous neurotransmitter release through multiple pathways, involving not only the primary C2B-SNARE interface but also additional putative SNARE-binding interactions. Together, our findings uncover both conserved and divergent mechanisms for synaptic exocytosis regulated by the dual Ca2+ sensors in C. elegans.

neuroscience↗

bioRxiv2025

SpatialESD: spatial ensemble domain detection in spatial transcriptomics

Spatial transcriptomics (ST) measures gene expression while preserving spatial context within tissues. One of the key tasks in ST analysis is spatial domain detection, which remains challenging due to the complex structure of ST data and the varying performance of individual clustering methods. To address this, we propose SpatialESD, a Spatial EnSemble Domain detection method that integrates results from different spatial domain detection methods to improve spatial domain detection. SpatialESD captures both direct co-occurrence patterns and multiscale indirect relationships between clusters, improving the robustness and accuracy of spatial domain detection. We evaluated SpatialESD on simulated datasets and multiple 10x Visium spatial transcriptomics datasets, including human brain, breast cancer, and ovarian cancer samples. The results show that SpatialESD consistently outperforms individual methods and the existing EnSDD ensemble method in terms of clustering accuracy and stability. Based on the identified domains, we further detected region-specific differentially expressed genes and performed trajectory and cell-cell interaction analyses. These results reveal spatial patterns of gene expression and cellular communication, offering insights into tissue organization and disease mechanisms. Overall, SpatialESD provides a reliable and effective solution for spatial domain detection in ST data and facilitates downstream biological discovery. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/675735v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1344724org.highwire.dtl.DTLVardef@12ab936org.highwire.dtl.DTLVardef@1e59d57org.highwire.dtl.DTLVardef@1bcd55f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Single-cell Genomic Copy Number Evolution Reveals Frequent Loss of the Y chromosome in Esophageal Adenocarcinoma

The incidence of esophageal adenocarcinoma (EAC), an aggressive cancer, is rising in Western countries, and incidence is higher in men. To better understand the roles of DNA copy number evolution, tumor heterogeneity, and tumor microenvironment in EAC and its origins, we evaluated EAC, Barretts Esophagus (BE), and normal adjacent tissue using our previously developed ultra-sensitive, single-nucleus DNA copy number analysis (12,186 nuclei, 20 specimens) and single-nucleus RNA-sequencing (snRNA-seq; 87,027 nuclei, 32 specimens). Loss of Y (LOY) chromosome was rare in BE but markedly enriched in EAC. In genome unstable cells, complete LOY chromosome often coincided with X-chromosome duplication. We did not detect X-chromosome inactivation via XIST expression in cells with LOY, suggesting increased expression of X-chromosome genes and potential effects on tumor immune evasion. When considering patients clinical features, we identified distinct differences in tumor microenvironment by sex, age, and obesity status, particularly massively reduced immune cell composition in obese patients. Finally, our cell line models recapitulate LOY, and we identify the first candidate anti-LOY agent. Our findings highlight how LOY affects tumor subpopulations and shapes the tumor microenvironment during EAC progression.

cancer biology↗

bioRxiv2025

Integrative Multi-omics Deciphers the Assembly Rules of the Human Skin Microbiome and Highlights Lipid-Mediated Niche Partitioning

Understanding the ecological assembly mechanisms of microbial communities is critical for deciphering host-microbiota interactions, however, such processes remain poorly characterized in cutaneous ecosystems. By profiling a non-industrialized rural cohort, this study deciphers the assembly rules governing the human skin microbiome and reveals an evolutionarily conserved core microbiota structured by niche selection. Microbial -diversity peaks when C. acnes and M. osloensis reach equilibrium, supporting the Intermediate Disturbance Hypothesis. Host lipids, rather than aqueous compounds, emerged as the primary drivers of microbial niche partitioning. We further demonstrate that C. acnes and Malassezia restricta function as core metabolic engineers, expressing diverse lipases that hydrolyze triglycerides (TGs) into free fatty acids (FFAs), thereby maintaining skin surface lipid homeostasis ([~]85% TG + FFA). Notably, virtually all skin surface FFAs are microbially derived and function as "public goods", enabling cross-feeding that supports auxotrophic members and fosters mutualistic interactions. Importantly, in vitro coculture experiments confirm that C. acnes establish a survival niche for M. restricta. Our findings support a paradigm shift from a taxonomic to a functional understanding of the skin ecosystem, underscoring microbial lipid metabolism as a central orchestrator of ecological stability and a promising target for therapeutic intervention. O_FIG O_LINKSMALLFIG WIDTH=182 HEIGHT=200 SRC="FIGDIR/small/674196v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1274fa5org.highwire.dtl.DTLVardef@1ddfa07org.highwire.dtl.DTLVardef@49f917org.highwire.dtl.DTLVardef@807a14_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHIC ABSTRACTC_FLOATNO C_FIG

microbiology↗

bioRxiv2025

CREG1 restricts ALV-J replication via the mitochondrial dysfunction-driven activation of innate immunity and apoptosis

Despite the implementation of purification strategies to partially limit J subgroup avian leukosis virus (ALV-J) infection, the involvement of host factors in the underlying infection mechanism remains largely undefined. Here, we identify cellular repressor of E1A-stimulated genes 1 (CREG1) as a key regulator of mitochondrial function and a critical immune-related gene involved in ALV-J infection. The objective of this study was to explore the effects and underlying mechanisms of CREG1 in the context of ALV-J infection. Overexpression of CREG1 upregulates the expression of type I interferon (I-IFN) and certain interferon-stimulated genes (ISGs), thereby suppressing viral replication. Mechanistically, overexpression of CREG1 induces mitochondrial dysfunction, characterized by a decrease in mitochondrial membrane potential ({Delta}{psi}m), reduced adenosine triphosphate (ATP) production and respiratory chain activity, enhanced mitophagy, and increased release of mitochondrial DNA (mtDNA), which in turn triggers the activation of innate immune responses. Mitochondrial dysfunction further leads to the cytosolic release of cytochrome c and an increase in reactive oxygen species (ROS) levels, thereby triggering a robust apoptotic response. Moreover, the regulation of mitochondrial function by CREG1 depends on its interaction with the mitochondrial chaperone protein heat shock protein 1 (HSPD1), and their co-expression synergistically amplifies the antiviral response. In this study, we identify CREG1 as a potent antiviral gene and underscore the pivotal roles of mitochondria-mediated innate immunity and apoptosis during ALV-J infection. Author summaryDespite efforts to limit J subgroup avian leukosis virus (ALV-J) infection, the role of host factors in the infection process is still not fully understood. In this study, we highlight the cellular repressor of E1A-stimulated genes 1 (CREG1) as a crucial regulator of mitochondrial function and immune responses during ALV-J infection. We show that CREG1 overexpression enhances type I interferon (I-IFN) and interferon-stimulated genes (ISGs) expression, inhibiting viral replication. This is achieved through mitochondrial dysfunction, including reduced mitochondrial membrane potential, lower ATP production, and increased mitophagy and mitochondrial DNA release, which activate innate immunity. CREG1-induced mitochondrial dysfunction also triggers apoptosis by releasing cytochrome c and increasing reactive oxygen species (ROS). Furthermore, CREG1 interacts with heat shock protein 1 (HSPD1) to amplify its antiviral effects. Our findings establish CREG1 as a key antiviral gene and emphasize the importance of mitochondrial-mediated immune responses and apoptosis in ALV-J infection.

immunology↗

bioRxiv2025

Dynamic uterine microenvironment drives endometrial adenocarcinoma carcinogenesis and progression

Endometrial cancer (EC) development is driven by the interaction between the tumor and the microenvironment. However, the immune microenvironment dynamics during this process are not clear. Here, we applied single-cell RNA sequencing (scRNA-seq) to uterine blood samples collected at hysterectomy from 15 individuals encompassing four groups--benign controls, endometrial intraepithelial neoplasia (EIN), the transition from EIN to carcinoma, and EC. Uterine blood, obtained without prior enrichment, provides a liquid biopsy of the local tumor milieu, enabling high-resolution profiling of both immune and stromal cells in a minimally invasive manner. Our analysis revealed simultaneous immune and stromal remodeling in early premalignant lesions. Notably, even in the EIN, we observed significant immune cell reprogramming alongside the emergence of protumorigenic stromal-epithelial interactions. Importantly, we discovered predictive single-cell transcriptomic signatures derived from neutrophils that stratify patients according to disease state, highlighting the potential of tumor-educated innate immune cells as biomarkers. These findings yield candidate cellular and molecular signatures, particularly from neutrophils, that could enhance early EC detection and guide therapeutic strategies. Our work provides a proof-of-concept for leveraging local liquid biopsies in single-cell oncology, offering new insights into EC initiation and paving the way for noninvasive diagnostics on the basis of single-cell transcriptomic profiles.

cancer biology↗

bioRxiv2025

Scaling Molecular Representation Learning with Hierarchical Mixture-of-Experts

Recent advancements in large-scale self-supervised pretraining have significantly improved molecular representation learning, yet challenges persist, particularly when addressing distributional shifts (e.g., under scaffold-split). Drawing inspiration from the success of Mixture-of-Experts (MoE) networks in NLP, we introduce H-MoE, a hierarchical MoE model tailored for molecular representation learning. Since conventional routing strategies struggle to capture global molecular information--such as scaffold structures, which are crucial for enhancing generalization--we propose a hierarchical routing mechanism. This mechanism first utilizes scaffold-level structural guidance before refining molecular characteristics at the atomic level. To optimize expert assignment, we incorporate scaffold routing contrastive loss, ensuring scaffold-consistent routing while preserving discriminability across molecular categories. Furthermore, a curriculum learning approach and dynamic expert allocation strategy are employed to enhance adaptability. Extensive experiments on molecular property prediction tasks demonstrate the effectiveness of our method in capturing molecular diversity and improving generalization across different tasks.

bioinformatics↗

bioRxiv2025

Measure Sodium Transport in Cells with NMR

Sodium ions (Na+) are fundamental to numerous physiological functions, such as maintaining electrolyte balance, enabling nerve impulse transmission, and facilitating muscle contraction. Dysregulation of Na+ transport across cell membranes is implicated in a range of health issues, including metabolic syndromes, neurological conditions, and cardiovascular diseases. However, current methods for assessing cellular Na+ activity often face limitations; they can be invasive or fail to capture dynamic changes. In this study, we introduce a non-invasive 23Na nuclear magnetic resonance (NMR) methodology designed to directly quantify the transport rate of sodium ions in living cells. Our technique integrates relaxation exchange spectroscopy (REXSY) with a multi-site exchange model, enabling the investigation of Na+ transport dynamics on a timescale of sub-seconds. A key advantage is its ability to differentiate between intracellular and extracellular Na+ pools based on the endogenous NMR relaxation difference, thereby avoiding the need for potentially disruptive exogenous reagents. Experiments conducted on human cell lines successfully demonstrated the techniques capacity to distinguish between various physiological states, such as when ion channels are pharmacologically blocked or activated. The resulting measurements of Na+ transport rates and intracellular Na+ fractions show a clear correlation with cellular metabolic activity, offering valuable quantitative markers for monitoring transmembrane ion dynamics in vitro.

cell biology↗

bioRxiv2025

piR-bmo-796514 Facilitates the Proliferation of Exogenous DNA Virus (Baculovirus) by Targeting the Host E3 Ubiquitin Ligase RNF181

PIWI-interacting RNAs (piRNAs), a class of 23-31 nucleotide non-coding RNAs, are known for silencing transposons and endogenous retroviruses that reside in animal genomes. However, the mechanisms by which host piRNAs affect exogenous viral infections, particularly those by DNA viruses, remain poorly understood. Here, we demonstrate that infection by Bombyx mori nucleopolyhedrovirus (BmNPV), a large DNA virus, induces significant upregulation of silkworm host piR-bmo-796514, which facilitates viral proliferation by suppressing the expression of E3 ubiquitin ligase RNF181. We further reveal that RNF181 exerts antiviral activity through ubiquitin-mediated degradation of Integrin 2b-like, a cellular membrane protein that interacts with viral GP64 protein to mediate BmNPV entry. This study unveils a previously unrecognized regulatory axis connecting host derived piRNAs with exogenous DNA virus infection, providing further mechanistic insights into the modulation of exogenous viral pathogenesis through the reprogramming of the piRNA pathway. Our findings not only advance the understanding of the immune escape mechanism of exogenous viruses but also provide new insights for the development of oligonucleotide antiviral drugs that target proviral piRNAs.

immunology↗

bioRxiv2025

Perivascular matrix densification dysregulates angiogenesis and activates pro-inflammatory endothelial cells

Fibrosis is central to numerous fatal conditions including solid cancers, pulmonary fibrosis, cirrhosis and post-infarct cardiac fibrosis amongst many others, thereby collectively contributing to 45% of all deaths in developed nations. The potential for fibrosis across most organ systems may stem from its connections to wound healing and the ubiquitous presence of vascular endothelium. Endothelial cells (ECs) and angiogenesis, cells and associated biological program central to wound healing, have been heavily implicated in many organ-specific fibroses, but the relationship between angiogenesis and fibrogenesis remains debated and little has been established in terms of how the EC phenotype governs tissue healing vs. fibrosis. Here, we examine a murine lung injury model enabling EC lineage tracing and observe the invasion of aberrant ECs from the bronchial microvasculature following lung injury along with concurrent densification of matrix fibers surrounding these vessels. To investigate the underlying mechanisms governing their appearance, we established a microphysiological system (MPS) of arteriole/venule-scale microvessels embedded within a tunable stromal mimetic matrix and find that heightened extracellular matrix fiber density activates ECs, drives endothelial to mesenchymal transition, and promotes aberrant tip EC (ATEC) invasion into the matrix. ATECs remain adherent to fibrotic matrix and possess a pro-inflammatory phenotype that secretes TGF-{beta}2. Notably, our studies establish that the formation of ATECs is gated by destabilization of endothelial adherens junction upon EC adhesion to fibrous matrix, and associated regulation of TGF-{beta} signaling that is mediated by a novel VE-cadherin - TGF-{beta}R2 axis. The current lack of effective anti-fibrotic therapies suggests potential critical involvement of other cell types such as ECs, and our findings suggest new contributions of ECs to fibrotic progression that may better inform future targets for novel anti-fibrotic therapeutics.

bioengineering↗