Biology subjects

Yang, X.

Publications and source records attributed to Yang, X..

At least 217 records · Page 12Linked to original sources

bioRxiv2025

ARHGEF17 Deficiency Induces Endothelial Dysfunction and Intracranial Aneurysm Formation via RhoA/ROCK2/MLC Signaling Pathway

BACKGROUNDGenetic susceptibility is a major determinant in intracranial aneurysm (IA) formation and rupture, yet the underlying mechanisms linking genetic variation to vascular dysfunction remain largely unknown. We have identified mutations in ARHGEF17, a guanine nucleotide exchange factor that regulates RhoA activation and cytoskeletal organization, as potential risk variants for IA. Given ARHGEF17s regulatory role in endothelial barrier integrity and actin remodeling, we hypothesized that ARHGEF17 deficiency promotes IA pathogenesis through dysregulation of the RhoA/ROCK2/MLC signaling axis, leading to endothelial dysfunction and vascular wall instability. METHODSCRISPR-Cas9-mediated ARHGEF17 knockout (ARHGEF17-/-) mice and morpholino-based ARHGEF17-deficient zebrafish were established to assess the in vivo vascular effects of ARHGEF17 loss. An intracranial aneurysm model combining elastase injection and deoxycorticosterone acetate (DOCA)-induced hypertension was used to evaluate aneurysm incidence, rupture rate, and survival. Structural remodeling of the Circle of Willis (CoW) was assessed by Victoria Blue, EVG, and Picrosirius Red staining, as well as immunofluorescence for -SMA, OPN, CD31, and inflammatory markers. Complementary in vitro studies were performed in HUVECs using lentiviral ARHGEF17 silencing (three shRNAs of varying efficiency) to examine endothelial proliferation, migration, tube formation, and barrier function (TEER). Activation of RhoA/ROCK2/MLC signaling was quantified by G-LISA and Western blotting. The ROCK inhibitor Y-27632 (10 M) was applied to determine pathway dependence. RESULTSARHGEF17-/- mice exhibited a significantly higher incidence and rupture rate of intracranial aneurysms, accompanied by fragmentation of elastic fibers, loss of collagen organization, vascular smooth muscle cell dedifferentiation, and robust inflammatory activation in the CoW. Zebrafish lacking ARHGEF17 showed frequent intracranial hemorrhage and compromised vascular wall integrity, further confirming ARHGEF17s role in cerebrovascular stability. In ECs, ARHGEF17 knockdown impaired proliferation, migration, tube formation, and barrier integrity in a silencing-efficiency-dependent manner. Mechanistically, ARHGEF17 deficiency activated the RhoA/ROCK2/MLC pathway, leading to increased phosphorylation of MLC and MYPT1 and disorganization of F-actin and junctional proteins. Pharmacological inhibition with Y-27632 restored endothelial function, normalized cytoskeletal structure, and re-established junctional continuity, indicating a ROCK2-dependent mechanism. CONCLUSIONSOur findings establish ARHGEF17 as a critical regulator of cerebrovascular integrity and identify RhoA/ROCK2/MLC mediated cytoskeletal remodeling as the mechanistic link between ARHGEF17 deficiency and aneurysm pathogenesis. Loss of ARHGEF17 compromises endothelial barrier function, triggers vascular inflammation, and promotes aneurysm formation and rupture. Importantly, ROCK inhibition rescues endothelial dysfunction, highlighting the RhoA/ROCK2/MLC axis as a promising therapeutic target for ARHGEF17 mutation-associated intracranial aneurysms.

neuroscience↗

bioRxiv2025

Genetically Engineered Cell Membrane-Coated Nanodrug for Targeted Treatment of Thyroid Cancer

Thyroid cancer is the most common endocrine malignancy, particularly in patients with radioactive iodine-refractory differentiated thyroid cancer (RAIR-DTC), who have limited treatment options and poor clinical prognosis. In this study, doxorubicin (DOX) and sorafenib (SOR) were loaded into the photothermal conversion agent mesoporous polydopamine (mPDA), forming mPDS. Tumor cell membrane coating engineering resulted in the formation of mPDS@CAR-M, significantly improving tumor targeting. After internalization by tumor cells, the loaded drugs are rapidly released under near-infrared (NIR) laser irradiation. mPDS@CAR-M effectively inhibits tumor cell proliferation by enhancing oxidative stress, suppressing the PI3K-AKT-mTOR signaling pathway, and inducing cytotoxic autophagy. By activating harmful autophagy, mPDS@CAR-M further inhibits the epithelial-mesenchymal transition (EMT) process, reducing tumor cell migration capacity. In vivo experiments showed that mPDS@CAR-M significantly reduced tumor volume, with its therapeutic efficacy closely related to the expression level of the targeted surface antigen. Therefore, mPDS@CAR-M demonstrates significant potential in the treatment of RAIR-DTC, providing a novel direction for further clinical exploration.

cancer biology↗

bioRxiv2025

The past and potential antagonistic effects of fishing ban against nutrient loading control on eutrophication restoration in Lake Hongze

Integrated management strategies are often implemented to achieve comprehensive environmental restoration; however, the potential antagonistic effects among such measures are seldom examined. Fishing bans, aimed at enhancing fish biodiversity, may counteract the effectiveness of nutrient control measures in mitigating eutrophication. This study employs the PCLake model and structural equation modeling (SEM) to evaluate this hypothesis in Lake Hongze, the fourth largest shallow lake in China. The PCLake model was calibrated using observational data from Lake Hongze collected between 2016 and 2020. The calibrated model was subsequently applied in a hindcast analysis from 2020 to 2024 and a forecast simulation from 2025 to 2030 to assess the impacts of fishing bans. Combined with SEM path analysis, the results support the hypothesis that fishing bans can exhibit antagonistic effects on nutrient loading control by enhancing top-down regulation relative to bottom-up processes. Specifically, the fishing ban led to increased fish biomass, phytoplankton abundance, and nutrient levels over the past four years, while reducing the abundance of submerged macrophytes, zoobenthos, and zooplankton. Projections further indicate that such antagonistic effects would persist through 2030 if the fishing ban remains in place as planned. Additionally, model forecasts suggest that even with adjustments to the duration and intensity of fishing bans, antagonistic effects could be amplified under more stringent nutrient control scenarios. This study provides valuable insights into maximizing the net benefits of combined environmental management strategies through a systematic framework that evaluates both the effects and underlying processes of different interventions.

ecology↗

bioRxiv2025

ALDH2 Deficiency Drives Proliferative Mammary Morphogenesis and Epithelial Cell Stemness via Oxidative Stress and Estrogen Receptor Activation

Alcohol consumption has been linked to breast cancer, partly due to the accumulation of toxic aldehydes like acetaldehyde, a carcinogenic byproduct of ethanol metabolism. ALDH2, a key mitochondrial enzyme, detoxifies acetaldehyde and other harmful aldehydes that drive oxidative stress, DNA damage, and hormonal dysregulation, key factors in carcinogenesis. Despite the possible link between alcohol consumption and breast cancer risk, little is known about how ALDH2 deficiency itself, independent of alcohol exposure, affects mammary gland biology and cancer susceptibility. Genetic variants leading to ALDH2 deficiency are highly prevalent in East Asian populations, where individuals carrying inactive ALDH2 alleles experience impaired aldehyde detoxification. While these individuals are at increased risk for alcohol-related cancers, the impact of ALDH2 deficiency on mammary gland development and homeostasis in the absence of alcohol exposure remains unexplored. To address this, we utilized a C57BL/6-based ALDH2 knockout (Aldh2-/-) mouse model to investigate its effects on mammary proliferation and development. Our findings revealed that Aldh2-/- mice exhibited hyperproliferative mammary glands, characterized by increased epithelial cell density, ductal expansion, and elevated Ki67+ cells. Flow cytometry analysis demonstrated a rise in luminal and basal epithelial subpopulations, alongside enhanced mammary epithelial stemness, as evidenced by increased mammosphere formation and colony-forming efficiency. At the molecular level, ALDH2 deficiency activated oxidative stress pathways, marked by elevated 8-OHdG, p38 MAPK, NF-{kappa}B, and Nrf2 signaling, alongside DNA damage responses involving p53 and H2A.X. Importantly, we also identified a previously unrecognized upregulation of RANKL in Aldh2-/- mammary glands, implicating the RANK/RANKL axis as a critical mediator linking aldehyde stress to NF-{kappa}B/p38 MAPK activation and enhanced mammary stemness. Furthermore, hormonal dysregulation was observed, with a significant increase in ER and PR expression and phosphorylation. Dysregulated ER signaling was further linked to enhanced erbB3 activation and downstream signaling, including the cyclin D1-pRb-E2F1 axis. Our results suggest that the accumulation of endogenous aldehydes, independent of alcohol exposure, profoundly alters mammary morphogenesis, epithelial repopulation, and stemness. Mechanistically, this occurs through oxidative stress activation and DNA damage pathways, leading to metabolic changes and upregulation of estrogen receptor and receptor tyrosine kinase signaling. This study highlights for the first time the potential role of ALDH2 deficiency in increasing mammary tissue susceptibility to oncogenic factors and breast cancer risk.

cancer biology↗

bioRxiv2025

Genomic and Transcriptomic Insights into the Evolution and Parasitic Strategy of the Woody-Plant Nematode Pratylenchus vulnus

The root-lesion nematode Pratylenchus vulnus parasitizes a wide range of hosts including woody perennials such as walnut (Juglans regia) and grapevine (Vitis vinifera), significantly damaging roots and reducing yields. Here, we present a high-quality, chromosome-level genome assembly of P. vulnus (61.7 Mb across six chromosomes). Comparative genomic analysis revealed high collinearity in protein-coding genes between P. vulnus and the root-knot nematode Meloidogyne graminicola, indicating a closer evolutionary relationship with this sedentary endoparasite. Large chromosomal regions in P. vulnus lack synteny with other nematode genomes, have comparatively low GC content (<30%), and are enriched in genes with unique or lineage-specific functions. Transcriptome analysis highlighted dynamic, stage-specific expressions of genes involved in parasitism, development, and metabolism. Additionally, we identified an extensive repertoire of putative effector genes and characterized lineage-specific expansions of cell wall-degrading enzyme families. Overall, these findings provide insight into the genome organization, chromosome evolution, and parasitism-related gene repertoire in a woody-plant parasitizing nematode.

plant biology↗

bioRxiv2025

PD-1 signaling is essential for the early accumulation of HBV-specific CD8+ T cells during HBV infection

Background & AimsProgrammed cell death Protein 1(PD-1) is one of the key inhibitory receptors that regulates CD8 T cell exhaustion during chronic viral infection. However, the role of PD-1 in modulating effector T cell differentiation and function during early phase of hepatitis B virus (HBV) infection remains poorly defined. MethodsUsing adoptive transfer of wild-type or PD-1 KO HBV-specific TCR transgenic (C93-TCRtg) CD8 T cells, flow cytometry, and transcriptome sequencing, we systematically profiled early PD-1 dynamics in splenic and intrahepatic T cells and evaluated how PD-1 deficiency shapes anti-HBV T cell responses in acute self-resolving (AR) and chronic (CH) HBV mouse models. ResultsAcute HBV infection induced sustained PD-1 upregulation on intrahepatic/splenic CD8 T cells, which predominantly exhibited an effector phenotype. PD-1 cells displayed enhanced proliferation, cytotoxicity, and effector cytokine production compared to PD-1- counterparts. Adoptive transfer of PD-1 KO C93-TCRtg CD8 T cells resulted in significantly impaired early expansion in both spleen and liver during acute infection, accompanied by reduced granzyme B expression while maintaining IFN-{gamma}, TNF-, or IL-2 production. Transcriptomic analysis revealed that PD-1 deficiency was associated with the upregulation of apoptosis gene signatures. In chronic HBV infection, PD-1 KO cells failed to expand long-term and exhibited exacerbated exhaustion evidenced by a loss of IFN-{gamma} production. ConclusionsPD-1 is essential for the early expansion and survival of HBV-specific CD8 T cells during acute infection and does not suppress their effector cytokine function. Its absence impairs proliferation and promotes exhaustion of HBV-specific CD8 T cell in chronic infections. Impact and implicationsOur study redefines PD-1s role in acute HBV infection. Rather than merely constraining effector function, PD-1 is essential for the early expansion and survival of HBV-specific CD8+ T cells, acting as a safeguard against activation-induced apoptosis. The context-dependent functions position PD-1 as a critical rheostat calibrating the magnitude and quality of the antiviral CD8+ T cell response, with significant implications for immunotherapeutic strategies targeting this pathway in hepatitis B.

immunology↗

bioRxiv2025

Convergent utilization of APN receptor by hedgehog merbecoviruses

Dipeptidyl peptidase-4 (DPP4) and angiotensin-converting enzyme 2 (ACE2) are well-established receptors for merbecoviruses, yet the receptor usage of merbecoviruses of European and Asian hedgehogs (EriCoVs) remains unknown. Here, by testing hedgehog orthologs of known coronavirus receptors, we identify hedgehog aminopeptidase N (APN) as a functional receptor for EriCoVs. Analysis of 94 APN orthologs indicates that EriCoVs have a limited host range, primarily utilizing hedgehog APN and, to a lesser extent, APN from certain felids, shaped by specific determinants at the virus-receptor interface. Cryo-EM reveals an APN-binding mode distinct from those used by alpha- and deltacoronaviruses. Functional assays indicate that hedgehog transmembrane serine protease 2 (TMPRSS2) enhances spike activation and promotes pseudovirus entry. Neutralizing antibodies targeting RBD and APN were developed and could effectively block EriCoV pseudovirus entry and propagation. These findings reveal an unexpected convergent evolution of APN utilization among merbecovirus, establishing a foundation for risk assessment and countermeasure development. Graphic abstractConvergent utilization of hedgehog APN by EriCoVs O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/676546v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1ea334aorg.highwire.dtl.DTLVardef@cd53bforg.highwire.dtl.DTLVardef@352102org.highwire.dtl.DTLVardef@a1eed_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

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

Dual-LLM Adversarial Framework for Information Extraction from Research Literature

Information Extraction (IE) is a fundamental task in Natural Language Processing (NLP) that aims to automatically identify relevant information from unstructured or semi-structured data. Information extraction from lengthy research literature, particularly in multi-omics studies, faces significant challenges due to their complex narratives and extensive context. To address this, we present a novel dual-LLM adversarial framework in which one large language model (LLM) performs the extraction and another provides iterative feedback to refine the results. This process systematically reduces errors, enhances consistency across heterogeneous data sources, and converges toward more accurate outputs. We evaluated our approach against manual and single-LLM extraction, using LLMs as evaluators. Experimental results show that our adversarial framework outperforms these baselines, highlighting its effectiveness for extracting structured information from lengthy scientific texts.

bioinformatics↗

bioRxiv2025

A Universal Duplex Sequencing Approach for Accurate Detection of Somatic Mutations

Ultra-accurate detection of rare somatic mutations is critical for understanding mutational processes in human disease, aging, and environmental exposures, yet current methods are limited by error rates, restricted genome coverage, and high DNA input. We present UDSeq, a duplex sequencing protocol combining random fragmentation, efficient UMI ligation, and quantitative input control to achieve near-complete genome/exome representation from as little as 100 pg DNA. Benchmarking in human sperm estimates a UDSeq error rate of [~]2.5x10-9 per base pair. UDSeq captures mutational signatures from heterogeneous populations without clonal expansion, reproduces exposure-specific patterns in cell lines and rodent models, and enables cross-species profiling. Compared with prior duplex methods, UDSeq yields up to fourfold more usable duplex molecules, improves library conversion, and remains cost-effective. We include a step-by-step protocol with quality-control checkpoints for fragment size, ligation yield, library conversion, and duplication rate. UDSeq provides a scalable, low-input platform for accurate profiling of somatic mutagenesis.

genomics↗

bioRxiv2025

Experimenting with Two Recent Feature Selection Methods for High-Dimensional Biological Data

Feature selection in high-dimensional biological data, where the number of features far exceeds the number of samples, has long posed a significant methodological challenge. This study evaluates two recently developed feature selection methods, Stabl and Nullstrap, under a simulation framework designed to replicate regression, classification, and non-linear regression tasks across varying feature dimensions and noise levels. Our results demonstrate that Nullstrap consistently outperforms Stabl and other benchmarked methods across all evaluated scenarios. Furthermore, Nullstrap proved significantly faster and more scalable in high-dimensional settings, underscoring its suitability for large-scale omics data applications. These findings establish Nullstrap as a robust, accurate, and computationally efficient feature selection tool for modern omics data analysis.

bioinformatics↗

bioRxiv2025

Class A PBPs reinforce the septal cell wall following initial synthesis by SEDS-bPBP pairs during bacterial cytokinesis

Bacterial cytokinesis requires the coordinated action of septal peptidoglycan (PG) synthases to ensure efficient and accurate septum formation. Two major types of synthases contribute: SEDS-bPBP and bifunctional class A PBPs (aPBPs). How their activities are organized in space and time has remained unclear. Using Deinococcus radiodurans, which often contains both constricting and closed septa in the same cell, we show that septal PG synthesis proceeds through distinct steps at different regions. Primary synthesis at the leading edge by SEDS-bPBP pairs drives constriction, whereas aPBPs act later at the lagging edge and in closed septa to thicken the wall, enhance cross-linking, and reinforce septal integrity. At the single-molecule level, both synthase types move directionally to perform processive PG synthesis at distinct sites. We also observed spatiotemporal separation of SEDS-bPBP and aPBP synthases in Staphylococcus aureus, suggesting that secondary septal PG synthesis is a conserved mechanism securing successful cytokinesis.

microbiology↗

bioRxiv2025

Pentoxifylline, a Non-Antibiotic Drug, Promotes Adaptation of Clinical Isolates of Staphylococcus aureus via Modulating c-di-AMP Signaling

This study investigated how Staphylococcus aureus adapts under pentoxifylline (PTX) therapy through analyzing three phylogenetically related isolates (L1, L2, L3) from a bacteremia patient. Whole genome sequencing revealed L1 contained a 2400-bp insertion disrupting nupC, while L3 harbored mutations in the anti-Shine-Dalgarno sequences of 16S rRNA. Each isolate evolved distinct mechanisms to reduce c-di-AMP levels, accompanied by changes in survival ability and virulence. Molecular analysis demonstrated PTX noncompetitively inhibits GdpP phosphodiesterase, directly modulating cyclic diadenosine monophosphate (c-di-AMP) signaling. Our findings provide novel insights into how non-antibiotic medications shape bacterial adaptation through second messenger modulation, highlighting the complex trade-offs between stress resistance and fitness in clinical settings. ImportanceThis study reveals how pentoxifylline, a non-antibiotic drug, drives Staphylococcus aureus adaptation by modulating c-di-AMP signaling. Our findings highlight the unintended consequences of non-antibiotic medications on bacterial evolution, offering new insights for clinical treatment strategies to mitigate resistance development. HighlightsO_LIPTX noncompetitively inhibits GdpP, modulating bacterial c-di-AMP signaling C_LIO_LIS. aureus evolves distinct mechanisms to reduce c-di-AMP under PTX pressure C_LIO_LINon-antibiotic medications significantly shape bacterial adaptive trajectories C_LI

microbiology↗

bioRxiv2025

Adaptation of Perceived Animacy from Biological Motion: Evidence for a "Life Motion Detector"

Humans can readily perceive animacy from biological motion (BM) - the distinctive movement patterns of living entities. However, how the human brain extracts animacy information from BM remains largely unclear. The current study investigated this issue using visual adaptation, a non-invasive tool for revealing neural mechanisms underlying the selective processing of specific properties. Results showed that prolonged exposure to intact human walkers, compared to non-BM adaptors, biased the perception of subsequent walking stimuli towards less animate. This adaptation aftereffect persisted following adaptation to local foot motions carrying diagnostic kinematic cues, but was absent after exposure to static body forms, indicating the involvement of neuronal populations encoding animacy from BM based on motion signals. Moreover, adapting to pigeon movements also biased animacy perception for human motions, revealing a shared mechanism for encoding animacy from cross-species BM signals. These results support the existence of an inherent "life detection" system in the human brain, attuned to local foot motions and kinematic features prevalent in vertebrate movements, which may lay a foundation for perceiving life from motion across terrestrial species. Public significance statementsDiscerning whether a moving entity is animate is crucial for survival and for generating appropriate responses. This study explored how the human brain perceives animacy based on a prevalent movement pattern among vertebrates, namely, walking. Leveraging a non-invasive visual adaptation paradigm, five experiments demonstrated that pre-exposure to intact human walking, feet-only walking, and even intact pigeon walking motion sequences - but not static human forms - elicited significant adaptation aftereffects in animacy perception of human walkers. These findings support the existence of neural substrates encoding perceived animacy based on biological motion signals, particularly those carried by local foot motions and cross-species kinematic features. Such mechanisms may be integral to an inherent life detection system in the human brain.

neuroscience↗

bioRxiv2025

Interactions Between Dietary Metabolites and Regulatory Risk Variants for Human Colon Cancer

Interactions between genetic variants and environmental factors influence malignancy risk, including for colorectal cancer (CRC). Prevalent CRC susceptibility loci reside predominantly in noncoding regulatory DNA where they may interact with dietary influences to dysregulate expression of specific genes predisposing to neoplasia. The impacts of CRC protective and risk dietary metabolites, butyrate and deoxycholic acid, were thus studied on the transcription-directing activity of 3703 regulatory CRC-associated variants via massively parallel reporter assays (MPRA) in human colonic cells. 1595 variant-dietary metabolite interactions were identified, pointing to dysregulation of MED13L, NKD2, and several modulators of Wnt/{beta}-catenin signaling in potential CRC gene-environment interactions (GxE). Opposing impacts of butyrate and deoxycholic acid were also uncovered, indicating dietary influences may converge on common CRC risk loci and nominating FOSL1 and SP1 as mediators of these opposing responses. Coupling MPRA to relevant environmental factors offers an approach to extend insight into GxE in common human cancers.

genomics↗

bioRxiv2025

A Reproducible Supermicrosurgical Model of Cervical Lymphatic-Venous Anastomosis in a Transgenic Alzheimer's Mouse: Technical Translation, Proficiency, and a Validated Learning Curve

BackgroundCervical Lymphatic-Venous Anastomosis(LVA) holds therapeutic potential for Alzheimer disease (AD). However, a validated AD animal model for preclinical investigation remains lacking. This study aimed to establish and standardize LNVA, as a form of lymphatic-venous Anastomosis, in a murine AD model; to quantitatively assess its surgical learning curve; and to create a platform for mechanistic exploration and translational research. MethodsWe established and standardized a deep cervical lymph node-to-vein anastomosis (DC-LNVA), a specific type of lymphatic-venous anastomosis (LVA), in rodents. A two-stage training program was applied to a junior surgeon: 60 DC-LNVA procedures were performed in 30 small Sprague-Dawley rats (50-60g), followed by 20 bilateral anastomoses in 10 male 5XFAD mice. Surgical proficiency was evaluated using procedure time, UWOMSA scoring, and CUSUM analysis. Anatomical parameters were assessed with ImageJ. Anastomotic patency was confirmed via ICG lymphangiography. Intranasal Evans Blue was used to trace cranial distribution pathways. ResultsSD rats had significantly larger external jugular veins (0.376 {+/-} 0.013 mm vs. 0.228 {+/-} 0.011 mm) and DCLNs (1.359 {+/-} 0.084 mm2 vs. 0.333 {+/-} 0.022 mm2) than mice (P < 0.0001). Proficiency was achieved after 27 anastomoses in rats and 10 in mice. ICG confirmed 100% patency in 9 surviving 5XFAD mice. Evans Blue suggested a nasal-cranial pathway for tracer distribution. ConclusionWe developed and validated a cervical lymphatic-venous bypass (LVA) in transgenic AD mice. This platform complements existing loss-of-function approaches and offers a foundation for mechanistic and translational research into brain lymphatic clearance.

animal behavior and cognition↗

bioRxiv2025

The nucleotide analog bemnifosbuvir inhibits hepatitis E virus replication in preclinical models

BackgroundHepatitis E virus infections remain a global health concern. Immunocompromised patients are at an increased risk to develop chronic HEV infection and thereby severe liver disease. Current off-label regimens are suboptimal with treatment failure being reported. Therefore, there is an urgent need for an effective anti-HEV treatment. ObjectiveIn this study, we aimed to identify potent inhibitors of HEV replication. DesignWe developed a rapid, image-based screening platform based on a full-length HEV fluorescence reporter virus and screened a nucleotide/nucleoside analog library. The identified lead candidate was validated in authentic hepatocyte culture systems, as well as in a gerbil infection model. ResultsBemnifosbuvir (BEM), previously characterized as a nucleotide analog with activity against other RNA viruses, efficiently suppressed HEV replication in vitro and in vivo in a dose-dependent manner, with minimal cytotoxicity at effective concentrations. Combining BEM with ribavirin, the off-label drug given to chronic HEV patients, resulted in an additive antiviral effect against HEV. We found that HEV-3 remains susceptible to inhibition by BEM over an extended treatment period, reducing concerns about the rapid development of viral resistance. Importantly, BEM significantly reduced HEV viral loads and liver inflammation in a gerbil infection model. ConclusionsGiven BEMs favorable safety profile in preclinical and clinical settings, our results suggest investigating its efficacy in patients with chronic HEV infection.

microbiology↗

bioRxiv2025

Mediator Subunit MED16 Collaborates with UBP1-TFCP2 to Control Transcriptional Activation or Repression via Promoter Positional Specificity

The Mediator complex acts as a master transcriptional co-regulator, yet the mechanisms by which its individual subunits mediate gene-specific transcription remain incompletely defined. Here, we report that the Mediator subunit MED16 physically associates with the UBP1-TFCP2 heterodimer, which controls the context-dependent transcriptional activation or repression. Biochemical purification combined with mass spectrometry validated MED16 as a bona fide interactor of UBP1-TFCP2. Integrative transcriptomic analyses demonstrated that UBP1 recruits the Mediator complex through MED16 to activate a panel of silenced genes associated with lung homeostasis, angiogenesis and cell proliferation. By contrast, MED16-UBP1 co-occupancy at the HIV-1 transcription start site (TSS) represses viral transcription and sustains HIV latency by compromising pre-initiation complex assembly. Domain-mapping experiments revealed that MED16 must integrate into the intact Mediator complex to exert either activating or repressive function. Genomic analysis uncovered a positional regulatory logic: UBP1-TFCP2 binding motifs adjacent to the TSS promote transcription, while those overlapping the TSS elicit repression. Collectively, our work identifies an MED16-UBP1 regulatory module with dual transcriptional activity and highlights this signaling axis as a potential target for HIV-1 interventions.

biochemistry↗