Biology subjects

Zhu, C.

Publications and source records attributed to Zhu, C..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Exploring endothelial cell environments across organs in spatially resolved omics data

Endothelial cells are ubiquitously present in the human body and line the luminal surface of blood and lymphatic vessels. The oxygen-dependence of cells impacts their proximity to blood vessels, and consequently, to endothelial cells depending on their functional properties and priorities. This paper presents cell-to-nearest-endothelial-cell distance distributions for various cell types using 399 spatially resolved omics datasets from 14 studies comprising 12 tissue types with a total of 47,349,496 cells. Additionally, we developed an open-source web-based interactive tool, Cell Distance Explorer, that allows researchers to interactively visualize cell graphs and linkages in 2D and 3D datasets. Finally, we present a hierarchical neighborhood analysis focused on the endothelial cell neighborhoods in small and large intestine datasets. This paper provides an open-access resource (datasets, tools, and analyses) to characterize and compare cell distances and cell neighborhoods in spatially resolved omics data.

bioinformatics↗

bioRxiv2025

Spatial transcriptomics reveals injury responsive compartments and coordinated immune fibrotic signaling in ANCA associated renal vasculitis

ANCA-associated vasculitis (AAV) often presents with rapidly progressive glomerulonephritis, yet how immune and stromal programmes are organised within kidney tissue remains unclear. We applied spatial transcriptomics to renal cortex biopsies from patients with AAV of varying disease severity and normal-histology controls, generating a spatial map that localizes disease programmes in situ. Four disease-responsive compartments--immune/interstitial fibroblasts (IM/Fib), glomeruli, myofibroblasts, and vascular compartments--showed distinct compartment-specific signatures that correlated with histopathology at the patient level. We also identify coordinated immune-fibrotic signaling linked to severity. Within IM/Fib, the CXCR4-CD74 receptor complex co-localised with IgM cells, and lumican (LUM) co-localised with collagen I/III; both were validated by immunofluorescence and associated with fibrotic injury. These tissue-anchored signatures constitute candidate diagnostic/prognostic biomarkers, and show the utility of this foundational spatial transcriptomics map to generate testable hypotheses which will guide validation in larger, stratified, treatment-annotated cohorts.

bioinformatics↗

bioRxiv2025

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families-- including the complete circadian toolkit--were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4{degrees}C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

evolutionary biology↗

bioRxiv2025

Scaling Personalized TMS: A Scalp-Based MRI-guided Alternative to Neuronavigation

BackgroundPersonalized transcranial magnetic stimulation (TMS) has shown promise in treating psychiatric and neurological disorders, but its accessibility is limited by reliance on costly and complex neuronavigation systems, particularly in resource-constrained clinical settings. ObjectiveTo develop and validate a scalp-based alternative to neuronavigation for personalized TMS targeting. MethodsWe developed a Continuous Proportional Coordinate (CPC) system-based approach for personalized TMS targeting and validated its performance through three operators across ten participants, using individualized DLPFC-SGC targets as an example. The validation framework included targeting consistency assessment, reproducibility evaluation, and cross-cortical generalizability analysis. ResultsThe CPC-based approach demonstrated comparable performance to neuronavigation, achieving 99.4% of its electric field strength (74.80 vs. 75.14 V/m; r = 0.962) and 93.9% of DLPFC-SGC functional connectivity (-0.216 vs. -0.230; r = 0.949), with high inter-operator reliability (ICC [≥] 0.903). Reproducibility analysis showed strong correlation between sessions (r = 0.948-0.957) with high reliability. Further simulations across 1,125 uniformly distributed cortical targets supported generalizability of this approach, with stable electric field preservation (99.07 {+/-} 1.54%) across different brain regions. ConclusionsThe CPC-based approach offers a practical alternative to neuronavigation, maintaining targeting accuracy and providing a more accessible option for personalized TMS implementation.

neuroscience↗

bioRxiv2025

Large-language-model-based antibiotic resistance gene prediction and resistomes mining in cyanobacterial blooms

The rapid spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a serious public health threat. Conventional ARG detection methods, including sequence-alignment and machine learning, are limited by high false-negative or false-positive rates, especially due to sequence diversity and class imbalance in metagenomic data. Moreover, few tools offer comprehensive solutions for ARG identification, classification, and functional annotation. To address these limitations, we developed ESMARG, a novel protein language model framework based on ESM1v, for accurate ARG identification, classification, and annotation. Trained with both ARG and abundant non-ARG sequences from real-world metagenomes to enhance robustness and reduce false positives, ESMARG significantly outperformed traditional alignment-based (BLAST, DIAMOND) and recent deep learning models (ARGNet, ARG-SHINE), achieving 0.998 precision, 0.939 recall, and 0.968 F1-score for ARG identification. Functional and mechanism classification modules also demonstrated high accuracy (0.986 and 0.987) and computational efficiency. We applied ESMARG to analyze 26 cyanobacterial aggregate (CA) metagenomes collected from Lake Taihu across a full annual cyanobacterial harmful algal bloom (CyanoHAB) cycle. A total of 110 ARGs, spanning 24 drug classes and multiple resistance mechanisms, were detected, with seasonal shifts in ARG abundance and composition. Strong correlations were identified between CA resistomes and microbial community structure, especially with cyanobacteria. Further, ARG abundance was shaped by both biotic factors--such as cyanobacterial dominance and bacterial functional profiles--and abiotic variables, including biochemical oxygen demand and water temperature. Our findings demonstrate the power of ESMARG for high-resolution ARG profiling and reveal complex ecological interactions between resistomes, microbiomes, and environmental factors in CyanoHAB. HighlightsO_LIDeveloped ESMARG model outperforms BLAST/other deep learning models in ARG detection C_LIO_LIARG showed seasonal dynamics in cyanobacterial metagenomes across algal bloom cycle C_LIO_LIARG was strongly correlate with microbiome structure and cyanobacteria dominance C_LIO_LIARG abundance was shaped by cyanobacteria, bacterial functions, BOD and temperature C_LI

bioinformatics↗

bioRxiv2025

Prior photon measurement density function constructed in a standard channel space for functional near-infrared spectroscopy

Photon measurement density function (PMDF) determines the measurement locations and their associated sensitivity to the hemodynamic fluctuations of an fNIRS channel, which is essential for pre-experiment optode arrangement and post-experiment signal analysis/results interpretation in fNIRS studies. However, obtaining the exact PMDF relies on individual MR images, which are unavailable in common fNIRS studies. Previous studies alternatively adopt the PMDF derived from single head templates, i.e., template-PMDF, which ignores the anatomical difference between the template and the participants, as well as the anatomical variability across participants. Here, we propose a methodological framework using a standard channel space to construct a prior-PMDF from a structural MRI database for arbitrarily given channel locations. We demonstrate the utility of the prior-PMDF in estimating channel-wise fNIRS imaging parameters, such as subject-specific PMDF, sensitivity in intracerebral and extracerebral tissue compartments, and sensitivity to regions defined by brain atlas. The performance of the prior-PMDF tested on an independent dataset was compared with the template-PMDF. The results show that the prior-PMDF significantly surpasses the template-PMDF.

bioengineering↗

bioRxiv2025

Tumor necrosis factor receptor 2 inhibits HIV-1 infection by blocking the binding of gp120 to CD4

The HIV-1 envelope glycoprotein gp120 binds to CD4 molecule and then undergoes conformational changes to interact with the co-receptors CCR5 or CXCR4, resulting in cellular entrance. However, certain types of cells, such as macrophages and CD4+Foxp3+ regulatory T cells (Tregs), have shown to resist HIV-1 infection despite co-expressing CD4 and co-receptors. In this study, we found that TNF receptor type II (TNFR2) directly bound to gp120, with the binding site on gp120 in close proximity to that of CD4. Intriguingly, exogenous TNFR2 had the capacity to inhibit the binding of gp120 to CD4 T cells. Furthermore, the infection of CD4+CCR5+ cells by pseudoviruses containing the HIV-1 envelope was inhibited by TNFR2 protein. In contrast, TNFR1, similar in structure to TNFR2 and sharing the same ligand, failed to inhibit the infection of CD4+ T cells by HIV-1 pseudoviruses. This property of TNFR2 may be harnessed in the prevention or treatment of HIV-1 infection and thus warrant future investigation. SUMMARYThis study reveals that TNFR2 directly binds to HIV-1 gp120, inhibiting its interaction with CD4 and reducing HIV-1 infection in CD4+ T cells. The findings highlight TNFR2s potential role in protecting cells and offer insights for HIV-1 prevention or therapy.

immunology↗

bioRxiv2025

Escape from X inactivation drives sex differences and female trait variation

X chromosome inactivation (XCI) partially balances gene dosage between sexes, yet many genes are expressed from the inactive X (Xi) to a variable degree. In this study, we investigate whether variation in Xi expression among genes predicts transcriptional and phenotypic consequences of X-linked variation. We find that Xi expression levels are a strong linear predictor of female-male expression differences, suggesting that other compensatory or regulatory mechanisms play a more minor role in sex differences in X-linked gene expression. Among females, we identify traits--including BMI, estradiol, and testosterone levels--for which higher Xi expression correlates with the strength of evidence for either additive or dominance effects on the trait. We hypothesize that an underappreciated mechanism could generate dominance effects of X-linked variants on a trait--specifically when the variant influences skew in X inactivation. The work establishes Xi expression as important for understanding transcriptional sex differences and the physiological variation among females.

genomics↗

bioRxiv2025

Multifunctional Injectable GelMA Hydrogels with MSN-Mediated Spatiotemporal Icariin Release for Enhanced Osseointegration in Bone Defects

The repair of bone defects is faced with the dual challenges of limited autograft donors and single function of artificial materials. The development of new materials with mechanical adaptability, drug-controlled release and osteogenic induction has become a research hotspot in bone tissue engineering. Here, we developed an injectable photocrosslinkable hydrogel by integrating icariin (ICA)-loaded mesoporous silica nanoparticles (MSN) into gelatin methacryloyl (GelMA). The amino-functionalized MSN enhanced compressive modulus by 1.5-fold (p < 0.05) and enabled pH-responsive ICA release (91.2{+/-}4.2% cumulative release over 15 days). Our in vitro findings revealed the composite hydrogel promoted BMSC proliferation was 1.43{+/-}0.04 times that of GelMA group. And express excellent osteogenic differentiation ability (ALP activity: 3.25-fold; Mineralization: 5.01-fold). In vivo study, Micro-CT revealed significantly higher bone volume fraction (BV/TV) in rat calvarial defects at 12 weeks, with histology confirming mature trabecular bone formation. This MSN-mediated spatiotemporal delivery system synchronizes immunomodulation and osteogenesis, offering a promising strategy for non-load-bearing osseointegration.

bioengineering↗

bioRxiv2025

Biomechanical Phenotyping Reveals Unique Mechanobiological Signatures of Early-Onset Colorectal Cancer

While both incidence and mortality of sporadic average-onset colorectal cancer (AO CRC, above 50 years of age) are in constant decline, sporadic early-onset colorectal cancer (EO CRC, under 50 years of age) is rising rapidly. Yet, the causes behind this rise remain poorly understood. Epidemiological studies indicate that lifestyle and environmental exposures may result in chronic inflammation, which is known to trigger tissue fibrosis. This study tests the hypothesis that fibrotic remodeling and biomechanical stiffening of colorectal tissues represent measurable hallmarks and potential drivers of EO CRC. Using primary human tissues, this work shows that EO CRC is associated with changes in collagen microstructure, increased stiffness and elevated viscosity of primary tumors. Spatial transcriptional profiling and immunostaining reveal pro-fibrotic signatures in stromal cells, alongside enhanced Yes-associated protein (YAP) mechanotransduction and proliferation in epithelial cells of EO CRC tissues. Mechanistically, increasing matrix stiffness in vitro promotes proliferation of epithelial cells in 2D and 3D colorectal cancer models. Together, these findings establish EO CRC as a disease marked by early and widespread biomechanical remodeling, suggesting that a fibrotic and stiffened tissue microenvironment may orchestrate EO CRC tumor initiation.

bioengineering↗

bioRxiv2025

Inhibition of De Novo Autoantibody Production Attenuates Chronic Antibody-Mediated Rejection of Kidney Allografts Despite Maintenance of High Donor-Specific Antibody Titers

Acute and chronic antibody mediated rejection (ABMR) continues to decrease clinical kidney graft function and survival. Dysregulated donor-specific antibody (DSA) responses are induced in B6.CCR5-/- recipients of complete MHC-mismatched A/J kidney allografts with NK cells playing a critical role in the acute ABMR. We tested the role of neutrophils in ABMR by transplanting A/J kidneys to CCR5-/- mice with a deletion in the neutrophil serine protease cathepsin G. Whereas B6.CCR5-/- recipients rejected all kidney allografts between days 18-25, 70% of allografts survived beyond day 60 in B6.CCR5-/-cG-/- recipients. At days 15-17 post-transplant DSA titers in B6.CCR5-/-cG-/- recipients were 24.3-fold higher than those in wild-type C57BL/6 allograft recipients. Allografts from B6.CCR5-/-cG-/- recipients on days 45 and 60 had typical characteristics of chronic graft injury including interstitial collagen deposition and peri-glomerular fibrosis that was accompanied by a fibrogenic transcript signature and late post-transplant production of autoantibodies to many targets, including structural proteins including collagen IV and fibronectin. Depletion of B cells at the time DSA peak titers were achieved on day 14 post-transplant decreased serum autoantibodies levels, the kidney allograft fibrogenic transcript signature, and the chronic kidney allograft injury, despite maintenance of the high DSA titers. These results indicate a critical role for neutrophil cathepsin G during acute ABMR of kidney allografts and in its absence, DSA induced late appearance of autoantibodies mediating development of chronic kidney allograft injury.

immunology↗

bioRxiv2025

DCPS modulates TDP-43 mediated neurodegeneration through P-body regulation

The proteinopathy of the RNA-binding protein TDP-43, characterized by nuclear clearance and cytoplasmic inclusion, is a hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimers disease (AD). Through CRISPR interference (CRISPRi) screening in human neurons, we identified the decapping enzyme scavenger (DCPS) as a novel genetic modifier of TDP-43 loss-of-function (LOF)-mediated neurotoxicity. Our findings reveal that TDP-43 LOF leads to aberrant mRNA degradation, via disrupting the properties and function of processing bodies (P-bodies). TDP-43 interacts with P-body component proteins, potentially influencing their dynamic equilibrium and assembly into ribonucleoprotein (RNP) granules. Reducing DCPS restores P-body integrity and RNA turnover, ultimately improving neuronal survival. Overall, this study highlights a novel role of TDP-43 in RNA processing through P-body regulation and identifies DCPS as a potential therapeutic target for TDP-43 proteinopathy-related neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Coherent Structures in Active Flows on Dynamic Surfaces

Coherent structures--flow features that organize material transport and deformation--are central to analyzing complex flows in fluids, plasmas, and active matter. Yet, identifying such structures on dynamic surfaces remains an open challenge, limiting their application to many living and synthetic systems. Here, we introduce a geometric framework to extract Lagrangian and Eulerian coherent structures from velocity data on arbitrarily shaped, time-evolving surfaces. Our method operates directly on triangulated meshes, avoiding global parametrizations while preserving objectivity and robustness to noise. Applying this framework to active nematic vesicles, collectively migrating epithelial spheroids, and beating zebrafish hearts, we uncover hidden transport barriers and Lagrangian deformation patterns--such as dynamic attractors, repellers, isotropic and anisotropic strain--missed by conventional Eulerian analyses. This approach offers a new perspective on soft and living matter, revealing how geometry and activity can be harnessed to program synthetic materials, and how Lagrangian strain and principal deformation directions can help uncover mechanosensitive processes and directional cues in morphogenesis.

biophysics↗

bioRxiv2025

Adrenergic Hypersensitivity Drives Ventricular Arrhythmias Following Loss of Plexin-Mediated Cardiac Innervation

BackgroundVentricular arrhythmias (VAs) are a leading cause of death and arise from a combination of cardiac muscle injury and dysfunction of the intramyocardial sympathetic nerves that control cardiac electrophysiology. The adrenergic mechanisms by which intramyocardial nerves contribute to arrhythmogenesis are poorly understood. Semaphorin-plexin signaling pathways are responsible for developmental guidance of sympathetic nerves onto the heart and have previously been associated with VAs in humans. ObjectiveTo investigate adrenergic control of arrhythmogenesis, we probed the cardiac electrophysiology of a Plexin-A3/-A4 double knockout mouse with loss of cardiac adrenergic nerves. MethodsWe studied cardiac structure and function using tissue clearing, immunohistochemistry, and echocardiography. We utilized ECG and optical mapping of action potentials to evaluate electrophysiologic responses to pharmacologic beta ({beta})-adrenergic stimulation and blockade. We measured circulating catecholamines and quantified {beta}-adrenergic receptor ({beta}AR) density in cardiac membranes. Finally, we performed a phenome-wide association study utilizing data from the UK Biobank to search for associations between PLXNA4 and human arrhythmias. ResultsMice with loss of plexin-dependent cardiac innervation had structurally normal hearts but displayed spontaneous VAs driven by adrenergic hypersensitivity, as well as increased cardiac {beta}AR density. Several human PLXNA4 variants were associated with arrhythmia phenotypes. ConclusionThese data establish a model of VAs driven by enhanced adrenergic receptor signaling, in the absence of structural heart disease, which can be used to investigate adrenergic mechanisms of arrhythmogenesis and to identify novel antiarrhythmic targets.

physiology↗

bioRxiv2025

AlphaFold3 for Non-canonical Cyclic Peptide Modeling: Hierarchical Benchmarking Reveals Accuracy and Practical Guidelines

Despite the revolutionary impact of AlphaFold3 on structural biology, this models capability in predicting non-canonical cyclic peptides remains unexplored. Given the clinical significance of cyclic peptides containing unnatural residues as a therapeutic modality, we present the first systematic evaluation of AlphaFold3 for this class of molecules. To facilitate benchmarking, we developed an automated input pipeline to streamline AlphaFold3 predictions for cyclic peptides. Our study aims to: (1) quantify the hierarchical accuracy (all-atoms, C atoms, and atoms of unnatural residue levels) of AlphaFold3 in predicting both non-canonical cyclic peptide monomers and complexes; (2) assess the reliability of AlphaFold3s confidence metrics; (3) evaluate the influence of multiple sequence alignment (MSA) and structural templates; and (4) identify systematic biases in AlphaFold3s predictions. Based on these analyses, we provide practical guidelines for applying AlphaFold3 in cyclic peptide structure prediction for facilitating the related research of bioactive cyclic peptides.

bioinformatics↗

bioRxiv2025

Targeting USP2 induces degradation of PML-RARα with or without drug-resistant mutations in acute promyelocytic leukemia

Despite the high efficacy of all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) in treating acute promyelocytic leukemia (APL), approximately 10-20% of patients develop drug resistance due to mutations in PML-RAR and other factors. Here, it is demonstrated that inhibiting USP2 with ML364 or silencing USP2 reduces PML-RAR protein levels in both ATRA-sensitive and -resistant APL cells, an effect reversed by proteasome inhibition. Conversely, USP2 overexpression enhances PML-RAR stability. Mechanistically, USP2 interacts with and deubiquitinates PML-RAR, including drug-resistant mutants. Consistent with PML-RAR degradation, ML364 treatment significantly induces apoptosis in APL cell lines and primary leukemia cells. In conclusion, this study identifies USP2 as a novel deubiquitinating enzyme for PML-RAR and highlights USP2 inhibition as a potential therapeutic strategy for APL with PML-RAR mutations.

cell biology↗

bioRxiv2025

13C tracing in synaptosomes reveals that SGLT2 inhibition with dapagliflozin prevents metabolic deficits in the 5X-FAD model of Alzheimer's Disease

Metabolic dysfunction is linked to several forms of age-related neurodegeneration including Alzheimers Disease (AD), and targeting brain energy metabolism is an increasingly attractive mode of therapeutic intervention. However, commonly used in vitro methods to identify specific metabolic pathways of interest in preclinical models of neurodegenerative disease have considerable limitations. They are prone to subselection of sample material, unable to identify cell type-specific effects, or cannot identify metabolic defects upstream of mitochondria. Here we address these challenges by validating a method for stable isotope tracing with isolated synaptic nerve terminals, or synaptosomes. We further applied this approach to study glucose metabolism in synaptosomes isolated from the 5X-FAD mouse model of AD treated with the antidiabetic sodium-glucose linked transporter-2 (SGLT-2) inhibitor Dapagliflozin. Treatment with Dapagliflozin preserved steady-state levels of synaptosomal metabolites and enrichment from labeled glucose into citrate that was reduced in the 5X-FAD model. These changes correlated with trends towards improved spatial working memory but not amyloid burden. The results highlight the utility of stable isotope tracing in synaptosomes to identify precise sites of metabolic dysfunction and mechanisms of action for metabolic drug candidates in preclinical models of neurodegeneration.

biochemistry↗

bioRxiv2025

The H3K27me3 reader UAD-2 recruits a TAF-12-containing transcription condensates to initiate piRNA expression within heterochromatic clusters

Metazoans utilize the small RNA pathway to regulate gene expression and maintain genome integrity. This pathway directs histone H3 lysine 9 tri-methylation (H3K9me3) or histone H3 lysine 27 tri-methylation (H3K27me3) at target loci to induce transcriptional gene silencing. Interestingly, some small RNAs are generated from genomic loci enriched in H3K9me3 or H3K27me3. However, the transcription mechanism of small RNA precursors from these heterochromatic regions remains unclear. In C. elegans, piRNAs originate from two genomic clusters enriched with H3K27me3 marks, which recruit the H3K27me3 reader UAD-2 and the upstream sequence transcription complex (USTC). Here, we demonstrate that piRNA transcription in C. elegans relies on TAF-12, a subunit of the basal transcription factor IID (TFIID). Depletion of TAF-12 reduces the production of both piRNA precursors and mature piRNAs. TAF-12 interacts with UAD-2 and facilitates piRNA focus formation in germ cell nuclei. We further show that TAF-12 triggers piRNA transcription by recruiting the RNA polymerase II subunit RPB-5, the Mediator complex subunit MDT-8, and the general transcription factors GTF-2F2 and GTF-2H2C. Thus, piRNA transcription within heterochromatic regions depends on the collaboration between histone modification readers, piRNA-specific transcription factors, and core transcription machinery.

genetics↗