Biology subjects

Zhu, W.

Publications and source records attributed to Zhu, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

An RNA regulates iron homeostasis and host mucus colonization in Bacteroides thetaiotaomicron

Symbiotic bacteria in the human intestinal microbiota provide many pivotal functions to human health and occupy distinct biogeographic niches within the gut. Yet the molecular basis underlying niche-specific colonization remains poorly defined. To address this, we conducted a time-resolved dual RNA-seq experiment to simultaneously monitor the transcriptional co-adaptations of human commensal Bacteroides thetaiotaomicron and human gut epithelial cells in an anaerobe-epithelium co-culture system. Comparative transcriptomic analysis of mucus-associated versus supernatant Bacteroides populations unveiled small RNAs (sRNAs) that are differentially regulated between spatially segregated subpopulations. Among these, we identified IroR as a key sRNA that facilitates B. thetaiotaomicron adaptation to the mucus-rich, iron-limiting niche, partly by modulating expression of bacterial capsule genes. This work provides new insights into the spatiotemporal dynamics of gut colonization and underscores a previously underappreciated role for bacterial sRNAs in shaping mutualistic interactions between the human microbiota and the gut epithelium.

microbiology↗

bioRxiv2025

No more than three PlpE non-overlapping epitopes trigger significant antibody production in individuals vaccinated with the Pasteurella multocida epitope-chimeric proteins

Current vaccine research still confronts multiple challenges, and epitope-focused vaccine design serves as an effective technical approach to address these issues. Antigens harbor multiple epitopes; however, the number of epitopes capable of triggering significant antibody responses in vaccinated individuals remains undefined. This study aimed to determine the number of non-overlapping epitopes--designated "effective epitopes" hereafter--that trigger significant antibody production in vaccinated individuals when presented in distinct PlpE epitope-chimeric proteins. Herein, chimeric proteins incorporating varying numbers of PlpE non-overlapping B-cell epitopes were generated. By analyzing serum antibody responses in vaccinated individuals, the number characteristic of PlpE effective epitopes was elucidated. The total number of PlpE effective epitopes in vaccinated individuals was 2.6 (95%CI: 1.909-3.201) for full-length PlpE, and 1.2 (95%CI: 0.5426-1.857), 0.9 (95%CI: 0-1.820), and 0.2 (95%CI: 0-0.5016) for the PlpE chimeric proteins (PlpE-VP60P, PlpE-BcfA, PlpE-PtfA), respectively. With an increase in the number of PlpE non-overlapping epitopes incorporated into the chimeric proteins, the number of PlpE effective epitopes exhibited a trend of initial increase followed by a decrease. Ultimately, the average total number of effective epitopes across all PlpE chimeric proteins did not exceed 3, with the highest number 2.1 (95%CI: 1.572-2.628). In conclusion, the number of PlpE non-overlapping epitopes on an antigen, that trigger significant antibody responses in each vaccinated individual, is very limited. IMPORTANCEEpitopes underpin the antigenicity of protein antigens. Although the concept of antigenic epitopes has been proposed over 50 years, our understanding on epitopes remains incomplete. Multiple antigenic epitopes can be identified on a single antigen, while the number of these epitopes that function in vaccinated individuals remains unclear--a gap hindering the rational design of vaccines. In previous studies, we identified 6 non-overlapping epitopes of Pasteurella multocida PlpE. Herein, we found that the total number of non-overlapping epitopes--capable of significantly triggering antibody production--that are present in PlpE chimeric proteins does not exceed 3 per vaccinated individual. This finding offers important insights for rational vaccine design: given the highly limited number of non-overlapping epitopes that function in vaccinated individuals, only a limited number of epitopes can be grafted onto scaffold proteins. Epitope-focused vaccine design must therefore account for competitive interactions between epitopes on the new antigen.

immunology↗

bioRxiv2025

Genome-wide SNVs revealed reticulate evolutionary history of an Eurasia-African songbird radiation

Phylogenomics has the power to uncover complex evolutionary hypothesis across taxa, thereby allowing important glimpses into the evolutionary history, such as incomplete lineage sorting (ILS) and introgression among closely related species. The Saxicola torquatus complex comprises several widely distributed insectivorous bird species across the Palearctic and Afrotropical realms. Nevertheless, the evolutionary history within this complex remains contentious, and previous findings suggest complication caused by cytonuclear discordance. Here, we conducted a phylogenomic analysis of nearly complete taxa within the complex using genome-wide SNVs to investigate potential causes of phylogenetic discordance across genomic regions and elucidate its evolutionary history. We detected multiple reticulate events during their diversification, leading to extensive phylogenetic discordance across the genome. The mitochondrial genome and W chromosome exhibited a consistent gene tree that conflicted with the species tree, with introgression being the most plausible explanation among several hypotheses. The Z chromosome was less affected by ILS/introgression and exhibited relatively stable local phylogenies compared to autosomes. Furthermore, we found that strongly introgressed regions were predominantly concentrated at the ends of smaller chromosomes, and the strength of introgression among species pairs showed consistently positive correlations, likely attributed to shared recombination hotspots in these regions. These findings stress the heterogeneous genomic landscape influenced by intricate evolutionary processes that endorse a reticulate evolution model for global speciation in the S. torquatus complex.

evolutionary biology↗

bioRxiv2025

Telomere replication stress-induced DNA damage response triggers inflammatory signaling via canonical and non-canonical STING pathways

Telomeres are protected by the shelterin complex, but they are also common fragile sites and are particularly susceptible to replicative stress. We found that depletion of telomeric repeat-binding factor 1 (TRF1), a key shelterin component essential for telomere replication, in mouse embryonic fibroblasts (MEFs) activated ATR- and subsequent ATM-dependent DNA damage responses. TRF1 loss increased the formation of micronuclei and cytosolic DNA, leading to ATR-dependent micronuclear rupture and activation of the cGAS/STING pathway. ATM activation enhanced STING K63 modification, thereby boosting the STING/NF{kappa}B pathway. Inhibition of ATM or cGAS reduced the expression of the pro-inflammatory cytokine IL6, with combined inhibition further suppressing IL6 levels. Depletion or inhibition of STING alone decreased production of IL6 and IFN{beta}, with no major reduction by combined ATM and/or cGAS inhibitors. These findings indicate that STING acts epistatically with ATM- and cGAS-mediated inflammatory responses. Overall, the telomere replication stress and dysfunction triggered by loss of TRF1 promotes inflammation through the ATR/cGAS/STING and ATM/STING pathways.

genomics↗

bioRxiv2025

Immunomodulatory effect of HLA-G Overexpressed Mesenchymal Stromal Cell in Cell-based Therapy for Myocardial Infarction

BackgroundOur previous study demonstrated that intravenous administration of mesenchymal stromal cells (MSCs) significantly increased local cell engraftment and improved heart function. We sought to investigate whether HLA-G1 overexpressed MSCs could further increase local transplanted cells engraftment and improve heart function. Methods and ResultsMice were randomized to receive intravenous administration of saline, human umbilical cord blood derived MSCs (hUCB-MSCs) 7 days prior to acute myocardial infarction (AMI), induced by ligation of the left anterior descending coronary artery. Then, intramyocardial transplantation of human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) was performed 30 minutes following AMI. Echocardiographic assessment was performed to assess heart function. In-vivo fluorescent imaging analysis were used to analyze cell engraftment. Flow cytometry of splenic regulatory T cells (Tregs) and natural killer (NK) cells was conducted to evaluate the immunomodulatory effect. Our result showed that systemic intravenous administration of hUCB-MSCs significantly increased systemic Tregs, decreased systemic NK cells, increased cell engraftment of intramyocardial transplanted hiPSC-CMs, culminating in improvement of heart function. Our in-vitro study showed that HLA-G1 overexpressed hUCB-MSCs modulated immune response by decreasing pro-inflammatory cytokines. ConclusionsSystemic intravenous administration of HLA-G1 overexpressed hUCB-MSCs modulated immune response and enhanced the survival of local transplanted hiPSC-CMs to improve heart function following AMI.

cell biology↗

bioRxiv2025

Transcriptome Reprogramming Associated with Autoimmunity Reveals Key Points of the Growth-Defence Trade-off in Arabidopsis thaliana

Growth and defence are inversely correlated processes requiring balance for optimal fitness. While each is well studied, their regulatory trade-offs are less understood. Using DANGEROUS MIX (DM) autoimmune plants with stunted growth in Arabidopsis thaliana, we investigated the balancing act. Transcriptome analysis of three DM cases and pathogen-treated seedlings identified two major modules representing defence and growth. These core modules, comprising 4,712 genes ([~]17% of the transcriptome), were sufficient for projecting the trade-off across immune transcriptome meta-datasets. Removing all three ADR1s, the helper NLRs, reversed the expression patterns of both modules and shifted the trade-off balance. ADR1s had a stronger impact on growth-associated RLK genes than on defence genes. Autoimmune plants also showed greater chromatin accessibility changes in growth loci than in defence loci. Our findings suggest an unexpected mechanism where immune signalling, partly mediated by ADR1s, actively suppresses growth genes, providing a strategy to regulate the growth-defence trade-off.

plant biology↗

bioRxiv2025

Using Artificial Intelligence to Assess Cross-Species Transmission Potential of Influenza A Virus

Influenza A viruses (IAVs) pose pandemic threats through cross-species transmission, yet predicting their adaptive evolution remains challenging. We introduced Influenza A virus Adaptability to host X (FluAdaX), a deep learning framework that integrates a moving average-equipped gated attention mechanism using full-genome sequences. FluAdaX demonstrated robust host classification performance across endemic IAV strains, and outperformed traditional models in detecting avian-to-human transmission. Spillover score and adaptability score were introduced to evaluate host shift risk, which prioritized variants with elevated human adaptation potential, such as H7N9, H9N2 avian IAVs, and H1N1 swine IAVs. Besides HA and NA genes, PB2 and NS genes were found critical for zoonosis. Potential molecular markers associated with avian/human tropism were identified across PB2 and NS genes using XGBoost. FluAdaX provided a dynamic framework to decode IAV host adaptation, enabling real-time risk assessment of cross-species transmission of emerging IAV variants.

bioinformatics↗

bioRxiv2025

Inactivating a β1 subunit of SnRK1 promotes broad-spectrum disease resistance in rice

Rice is a staple crop for over half of the worlds population, and its sustainable production is vital to ensure global food security. However, rice is highly susceptible to several devastating fungal diseases1, including blast disease caused by Magnaporthe oryzae, sheath blight by Rhizoctonia solani, false smut by Ustilaginoidea virens, brown spot by Bipolaris oryzae, bakanae by Fusarium fujikuroi, and head blight by F. graminearum. The mechanisms underlying the susceptibility of rice to these fungal diseases remain unclear. Here, we report that the {beta} subunit of SnRK1, SnRK1{beta}1A, confers broad-spectrum susceptibility to these fungal diseases. Our findings reveal that diverse rice fungal pathogens have convergently evolved an effector, Gas2, which interacts with SnRK1{beta}1A to prevent its ubiquitination-mediated degradation and promotes its nuclear translocation. While SnRK1{beta}1A is expressed at low levels in healthy plants, its expression is markedly induced upon fungal infections, facilitating susceptibility by inhibiting SnRK11, the subunit of SnRK1, whose overexpression has been shown to enhance broad-spectrum resistance in rice2. Notably, rice lines with disrupted SnRK1{beta}1A are resistant to multiple fungal diseases without compromising growth and yield in the field. Together, this study demonstrates that broad-spectrum disease resistance in crops can be achieved by disrupting inducible susceptibility genes whose encoded proteins are targeted by effectors conserved in multiple pathogens.

plant biology↗

bioRxiv2025

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗

bioRxiv2025

Secondary structure transitions and dual PIP2 binding define cardiac KCNQ1-KCNE1 channel gating

The KCNQ1+KCNE1 potassium channel complex forms the slow delayed rectifier current (IKs) critical for cardiac repolarization. Loss-of-function variants in KCNQ1 and KCNE1 cause long QT syndrome types 1 and 5 (LQT1/LQT5), accounting for over one-third of clinical LQTS cases. Despite prior structural work on KCNQ1 and KCNQ1+KCNE3, the structural basis of KCNQ1+KCNE1 remains unresolved. Using cryo-EM and electrophysiology, we determined high-resolution (2.5-3.4 [A]) structures of human KCNQ1+KCNE1 in both closed and open states. KCNE1 occupies a pivotal position at the interface of three KCNQ1 subunits, inducing seven "helix-to-loop" transitions in KCNQ1 transmembrane segments. These structural rearrangements: 1) stabilize the closed pore and the conformation of the intermediate voltage-sensing domain, thereby determining channel gating, ion permeation, and single channel conductance; 2) enable a dual-PIP2 modulation mechanism, where one PIP2 occupies the canonical site, while the second PIP2 bridges the S4-S5 linker, KCNE1, and the adjacent S6, stabilizing channel opening; 3) create a fenestration capable of binding compounds specific for KCNQ1+KCNE1 (e.g., AC-1). Together, these findings reveal a previously unrecognized large-scale secondary structural transition during ion channel gating that fine-tunes IKs function and provides a foundation for targeted LQTS therapy development.

biophysics↗

bioRxiv2025

An Anaerobic Pathogen Rewires Host Metabolism to Fuel Oxidative Growth in the Inflamed Gut

To colonize their host and cause disease, enteric pathogens must deploy their virulence factors to establish distinct nutrient niches. How obligate anaerobic pathogens construct nutrient niches in the densely populated large intestine remains poorly understood. Enterotoxigenic Bacteroides fragilis (ETBF) is considered an obligate anaerobic bacterium and has been implicated in inflammation-associated diseases, including colitis and colorectal cancer. Here we show that ETBF uses its virulence factor, Bacteroides fragilis toxin, to reprogram colonic epithelial cell metabolism to colonize the inflamed gut. Bacteroides fragilis toxin activates colonic epithelial signaling and hijacks the host bile acid recycling pathway, inducing a metabolic shift in the epithelium from oxidative phosphorylation to glycolysis. This shift increases local concentrations of lactate and oxygen, nutrients that support an oxidative metabolism in ETBF. These findings reveal an unexpected strategy by which a pathogenic organism, previously considered to be an obligate anaerobic bacterium, generates and exploits an oxidative niche in the inflamed gut.

microbiology↗

bioRxiv2025

How Good is AlphaFold3 at Ranking Drug Binding Affinities?

Accurate affinity ranking of small molecules is pivotal for drug discovery. We investigate whether structure prediction models like AlphaFold3, pretrained on protein-ligand interactions, can address this task. Zero-shot evaluation of Protenix (an AlphaFold3-like model) demonstrates superior prioritization of active compounds over conventional scoring functions and state-of-the-art deep learning models. By further fine-tuning Protenix on structure-agnostic protein-ligand bioactivity data from ChEMBL and BindingDB, we develop AlphaRank that predicts pairwise affinity relationships. AlphaRank achieves prediction accuracy comparable to computationally intensive free energy perturbation (FEP+) workflows on standard benchmarks, while requiring substantially less computational resources. Our findings highlight the emergent potential of AlphaFold3-derived models in affinity ranking tasks and emphasize the necessity for targeted methodological exploration to fully harness their capabilities in drug discovery applications.

bioinformatics↗

bioRxiv2025

Alternating 2D and 3D Culture Reduces Cell Size and Extends the Lifespan of Placenta-Derived MSCs

Mesenchymal stem cells (MSCs) offer significant therapeutic potential, but traditional 2D culture on rigid substrates results in progressive cell enlargement and senescence, reducing proliferative capacity and therapeutic potency. This poses a major challenge for widespread clinical application. We explored a novel strategy for placenta-derived MSCs combining 2D expansion with 3D spheroid culture to address these limitations. Our research shows that culturing MSCs as 3D spheroids significantly reduces individual cell size and size distribution compared to 2D culture. Spheroid formation is feasible in chemically defined media with minimal cell death, and is enhanced by extracellular matrix protein supplementation. Although MSCs do not proliferate in 3D suspension, an alternating 2D/3D culture protocol, transitioning cells between 2D flasks and 3D spheroids after each passage, effectively slows MSC enlargement and senescence over long periods. This alternating method also preserves MSC immunomodulatory function, unlike continuous 2D culture which leads to its loss. For scalability, we developed an RGD-functionalized alginate hydrogel tube (AlgTube) system that mimics this alternating environment, supporting both adherent growth and chemically triggered spheroid formation. This alternating 2D/3D culture strategy and the scalable AlgTube platform provide a foundation for developing next-generation MSC manufacturing technologies to meet future clinical demands.

bioengineering↗

bioRxiv2025

Neural organoids protect engineered heart tissues from glucolipotoxicity by transferring versican in a co-culture system

Metabolic disorders could cause dysregulated glucose and lipid at the systemic level, but how inter-tissue/organ communications contribute to glucolipotoxicity is difficult to dissect in animal models. To solve this problem, myocardium and nerve tissues were modeled by 3D engineered heart tissues (EHTs) and neural organoids (NOs), which were co-cultured in a generalized medium with normal or elevated glucose/fatty acid contents. Morphology, gene expression, cell death and functional assessments detected no apparent alterations of EHTs and NOs in co-culture under normal conditions. By contrast, NOs significantly ameliorated glucolipotoxicity in EHTs. Transcriptomic and protein secretion assays identified the extracellular matrix protein versican as a key molecule that was transferred from NOs into EHTs in the high-glucose/fatty acid condition. Recombinant versican protein treatment was sufficient to reduce glucolipotoxicity in EHTs. Adeno-associated virus-delivered versican overexpression was sufficient to ameliorate cardiac dysfunction in a murine model of diabetic cardiomyopathy. These data provide the proof-of-concept evidence that inter-tissue/organ communications exist in the co-culture of engineered tissues and organoids, which could be systemically studied to explore potential pathological mechanisms and therapeutic strategies for multi-organ diseases in vitro.

cell biology↗

bioRxiv2025

Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS-chemokine-myeloid axis

Chromosomal instability (CIN), a characteristic feature of esophageal adenocarcinoma (EAC), drives tumor aggressiveness and therapy resistance, presenting an intractable problem in cancer treatment. CIN leads to constitutive stimulation of the innate immune cGAS-STING pathway, which has been typically linked to anti-tumor immunity. However, despite the high CIN burden in EAC, the cGAS- STING pathway remains largely intact. To address this paradox, we developed novel esophageal cancer models, including a CIN-isogenic model, discovering myeloid-attracting chemokines - with the chemokine CXCL8 (IL-8) as a prominent hit - as conserved CIN-driven targets in EAC. Using high-resolution multiplexed immunofluorescence microscopy, we quantified the extent of ongoing cGAS-activating CIN in human EAC tumors by measuring cGAS-positive micronuclei in tumor cells, validated by orthogonal whole-genome sequencing-based CIN metrics. By coupling in situ CIN assessment with single-nucleus RNA sequencing and multiplex immunophenotypic profiling, we found tumor cell-intrinsic innate immune activation and intratumoral myeloid cell inflammation as phenotypic consequences of CIN in EAC. Additionally, we identified increased tumor cell-intrinsic CXCL8 expression in CINhigh EAC, accounting for the inflammatory tumor microenvironment. Using a novel signature of CIN, termed CINMN, which captures ongoing CIN-associated gene expression, we confirm poor patient outcomes in CINhigh tumors with signs of aberrantly rewired cGAS-STING pathway signaling. Together, our findings help explain the counterintuitive maintenance and expression of cGAS-STING pathway components in aggressive, CINhigh tumors and emphasize the need to understand the contribution of CIN to the shaping of a pro-tumor immune landscape. Therapeutic strategies aimed at disrupting the cGAS-driven inflammation axis may be instrumental in improving patient outcomes in this aggressive cancer.

cancer biology↗

bioRxiv2025

Functional Neural Connectivity of the Mouse Brain using Photoacoustic Ultrasound Imaging

Brain connectomes are insightful models that describe the connectivity of different regions throughout the brain. These connectomes are traditionally generated through temporal correlation of blood oxygen level dependent (BOLD) signals detected by functional magnetic resonance imaging (fMRI). Photoacoustic ultrasound (PAU) can also detect oxygenation levels while being more accessible and cost effective than fMRI. We propose the use of PAU to generate brain connectomes as an alternative to fMRI. In this study we successfully developed a pipeline for processing PAU data from whole brain scans of mice models and found that the connectomes it produced were comparable to those generated by fMRI, particularly, in detecting connections previously documented in the literature. Our findings suggest that PAU is a promising alternative to fMRI for mapping brain connectome, offering advantages in sensitivity and accessibility, making it a valuable tool for future research on brain connectivity.

bioengineering↗

bioRxiv2025

SEL1L-HRD1 ER-Associated Degradation Facilitates Prohormone Convertase 2 Maturation and Glucagon Production in Islet α Cells

Proteolytic cleavage of proglucagon by prohormone convertase 2 (PC2) is required for islet cells to generate glucagon. However, the regulatory mechanisms underlying this process remain largely unclear. Here, we report that SEL1L-HRD1 endoplasmic reticulum (ER)-associated degradation (ERAD), a highly conserved protein quality control system responsible for clearing misfolded proteins from the ER, plays a key role in glucagon production by regulating turnover of the nascent proform of the PC2 enzyme (proPC2). Using a mouse model with SEL1L deletion in proglucagon-expressing cells, we observed a progressive decline in stimulated glucagon secretion and a reduction in pancreatic glucagon content. Mechanistically, we found that endogenous proPC2 is a substrate of SEL1L-HRD1 ERAD, and that degradation of misfolded proPC2 ensures the maturation of activation-competent proPC2 protein. These findings identify ERAD as a novel regulator of PC2 biology and an essential mechanism for maintaining cell function.

cell biology↗

bioRxiv2025

Optimizing Metagenome Analysis for Early Detection of Colorectal Cancer: Benchmarking Bioinformatics Approaches and Advancing Cross-Cohort Prediction

Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2,053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent dynamic patterns of microbial signatures are the fundamental for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability, advances the application of non-invasive approaches for the early screening and prevention of CRC.

bioinformatics↗