Biology subjects

Zhu, J.

Publications and source records attributed to Zhu, J..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

AI-Driven Efficient De Novo design of GLP-1RAs with Extended Half-Life and Enhanced Efficacy

Peptide drug has revolutionized modern therapeutics, offering novel treatment avenues for various diseases. However, low efficacy, time consumption, and high cost hinder peptide drug design and discovery. We present an efficientin approach that integrates deep learning-based protein design with efficient functional screening, enabling the rapid design of biotechnologically important peptides with improved the stability and efficacy. We designed 10,000 de novo GLP-1 receptor agonists (GLP-1RAs), of which 60 met the stability, efficacy, and diversity criteria in the vitral functional screening. In vitro validation revealed a 62% success rate, while in vivo experiment demonstrated that two designed GLP-1RAs exhibited significantly extended half-lives, approximately three times longer than Semaglutide. In diabetic and obesity mouse models, the most competitive candidate showed superior therapeutic efficacy over Semaglutide. Our AI driven peptide design pipline integrats protein design, functional screening, and experiment validation, reducing the number of iterations required to find novel peptide candidates. The entire process, from design to screening, can be completed in a single cycle within two weeks.

bioengineering↗

bioRxiv2025

Deciphering the Pathogenic Landscape of Amyloid Light-Chain Cardiomyopathy

Amyloid light-chain cardiomyopathy (ALCA) is an infiltrative disorder marked by misfolded immunoglobulin light-chain deposition in the myocardium, ultimately leading to cardiac dysfunction. Despite its clinical severity, the underlying mechanisms remain poorly understood. Here, we integrated multi-omics analyses of human cardiac samples to construct a comprehensive cellular and spatial atlas of the ALCA heart. We observed a marked expansion of PTX3+ fibroblasts (FB), which undergo a distinct phenotypic transition into pro-fibrotic POSTN+ FB regulated by EGR1.Concurrently, SPP1+ macrophages (Mac) emerged as major drivers of fibrosis, interacting robustly with PTX3+ FB via APP-CD74, GAS6-MERTK, and TGF-{beta}1-TGF-{beta}1/2 pathways. Endothelial cell (EC) profiling revealed substantial vascular remodeling characterized by the emergence of specialized capillary-like immune endothelial cells expressing chemokines CXCL1, CXCL3, and CCL2, alongside depletion of functional capillary EC. Immunologically, elevated cytotoxic CD8+ T cells and reduced NK cells contributed to an imbalanced inflammatory milieu, with NF{kappa}B2 orchestrating both fibrotic and immune pathways across multiple cell types. These findings highlight the pivotal role of fibroblast-immune crosstalk, particularly the SPP1+ Mac-PTX3+ FB axis, in driving ALCA pathogenesis. Targeting these pathological cellular interactions may offer a promising therapeutic avenue to mitigate fibrosis, restore immune homeostasis, and improve cardiac function in ALCA.

bioinformatics↗

bioRxiv2025

Extracellular matrix deposition controls early differentiation patterns in human cardiac gastruloids

Amongst the various factors that affect differentiation and tissue organization, the autonomous deposition of extracellular matrix (ECM) has hardly been considered in the context of gastruloids. Using biofunctionalized colloidal particles as artificial organizing centers (aOCs), we patterned differentiation loci within 3D embryonic bodies. Our findings reveal that the spatial distribution of the aOCs induces various pattern organizations, mediated by endogenous deposition of ECM. We investigated how the interplay between meso-endoderm cell epithelial-to-mesenchymal transition, migration into germ layers, and the prolonged maintenance of local stem-cell niches orchestrates gastruloid structure and composition. These factors collectively regulate the complexity of emergent cardiac structures observed at later time points. This work uncovers a critical feedback loop between cell differentiation rates and endogenous ECM deposition patterns, which governs the differentiation paths in scaffolded cardiac gastruloids.

cell biology↗

bioRxiv2025

Widely used CaMKII regulatory segment mutations cause tight actinin binding and dendritic spine enlargement in unstimulated neurons

Ca2+/calmodulin-dependent protein kinase II (CaMKII) is essential for long-term potentiation (LTP) of excitatory synapses that underlies learning. CaMKII responds to Ca2+ influx into postsynaptic spines by phosphorylating proteins and forming new protein interactions. The relative importance of these enzymatic and structural functions is debated. LTP induction triggers CaMKII docking to NMDA receptors, and recent evidence suggests that LTP can proceed without kinase activity after this event. Furthermore, CaMKII interaction with -actinin-2 is required for dendritic spine enlargement following LTP induction. CaMKII can auto-phosphorylate at T286, which enables autonomous activity after Ca2+/CaM dissociation. CaMKII also bears threonine at positions 305 and 306 in its regulatory segment. Experiments with CaMKII variants including a T305A/T306A ( AA) double substitution have led to a model whereby T305/T306 phosphorylation by autonomously active CaMKII prevents further Ca2+/CaM activation. However, this mechanism is not compatible with some existing data including CaMKII phospho-proteomics and measurements with reporters of CaMKII conformation. Furthermore, autonomous CaMKII activity is now thought to only endure for seconds after LTP induction. In this study, we show that the AA substitution has an unintended gain-of-function property - it enables tight binding to -actinin-2 in unstimulated neurons. In situ labelling shows that the AA substitution elevates CaMKII-actinin interactions in neurons to a level only normally observed after induction of LTP. The AA CaMKII variant also elevates the proportion of enlarged spines in unstimulated neurons without altering synaptic currents. Calorimetric measurements with purified protein confirm that -actinin-2 binds tightly to the AA variant of CaMKII with no requirement for kinase activation. Using x-ray crystallography, we show that the AA substitution enables -actinin-2 to adopt a different tighter binding mode. Our findings reinforce the notion that CaMKII primarily fulfils a structural role in LTP.

neuroscience↗

bioRxiv2025

Pangenome analyses of tea plant reveal structural variations driven gene expression alterations and agronomic trait diversification

Tea plants, one of the worlds most economically significant beverage crops, exhibit extensive genetic diversity and a rich array of secondary metabolites. While structural variations (SVs) are key drivers of phenotypic innovation, their regulatory roles in transcriptional networks and agronomic trait diversification remain underexplored in this perennial crop. We constructed a pangenome from 21 representative tea accessions and their wild relatives. Comparative analysis revealed that wild relatives harbor a greater abundance of gibberellin-related genes, whereas cultivated accessions exhibit an expansion of defense-related genes. We identified 522,428 non-redundant SVs, primarily insertions/deletions (73.56%), which were enriched in promoter regions. These SVs influenced the expression of genes governing flavor compounds, including those involved in flavonoid, amino acid, and terpenoid biosynthesis. Population SV analysis of 275 tea accessions uncovered three haplotypes in the ANS3 gene promoter region, with Hap1, containing a 192 bp insertion, predominantly found in wild relatives but largely lost in modern cultivars. This insertion enhanced CtANS3 expression, increasing anthocyanin accumulation. Additionally, a 159 bp insertion in the CtLRR1 promoter reduced resistance to Colletotrichum gloeosporioides in wild relatives. Our findings underscore SVs as pivotal regulators of genomic diversity, flavor differentiation, and adaptive evolution in tea plant domestication.

genomics↗

bioRxiv2025

CDKL5 modulates structural plasticity of excitatory synapses via liquid-liquid phase separation

Activity-dependent synaptic remodeling, essential for neural circuit plasticity, is orchestrated by central organizers within the postsynaptic density (PSD), including the scaffolding protein PSD95. However, the molecular mechanisms driving this process remain incompletely understood. Here, we identify CDKL5, a protein associated with a severe neurodevelopmental condition known as CDKL5 deficiency disorder (CDD), as a critical regulator of structural plasticity at excitatory synapses. We show that CDKL5 undergoes liquid-liquid phase separation (LLPS) in vitro and in cultured neurons, forming co-condensates with PSD95. This LLPS-driven process spatially organizes synaptic components, specifically enabling the synaptic recruitment of Kalirin7 to promote dendritic spine enlargement. Pathogenic mutations disrupt condensate formation by impairing the LLPS capacity of CDKL5, directly linking phase separation defects to the pathogenesis of CDD. Our findings reveal a crucial role for CDKL5 in synaptic plasticity and establish LLPS as a fundamental mechanism by which CDKL5 coordinates molecular events to reorganize PSD architecture during synaptic remodeling.

neuroscience↗

bioRxiv2025

WEE1 inhibitors synergise with mRNA translation defects via activation of the kinase GCN2

Inhibitors of the protein kinase WEE1 have emerged as promising agents for cancer therapy. In this study, we uncover synergistic interactions between WEE1 small- molecule inhibitors and defects in mRNA translation, mediated by activation of the integrated stress response (ISR) through the kinase GCN2. Using a pooled CRISPRi screen, we identify GSPT1 and ALKBH8 as factors whose depletion confer hypersensitivity to the WEE1 inhibitor, AZD1775. We demonstrate that this synergy depends on ISR activation, which is induced by the off-target activity of WEE1 inhibitors. Furthermore, PROTAC-based WEE1 inhibitors and molecular glues show reduced or no ISR activation, suggesting potential strategies to minimise off-target toxicity. Our findings reveal that certain WEE1 inhibitors elicit dual toxicity via ISR activation and genotoxic stress, with ISR activation being independent of WEE1 itself or cell-cycle status. This dual mechanism highlights opportunities for combination therapies, such as pairing WEE1 inhibitors with agents targeting the mRNA translation machinery. This study also underscores the need for more precise WEE1 targeting strategies to mitigate off-target effects, with implications for optimising the therapeutic potential of WEE1 inhibitors.

cancer biology↗

bioRxiv2025

HydraRNA: a hybrid architecture based full-length RNA language model

RNA, an essential component of the central dogma of molecular biology, plays versatile roles in all cellular processes. RNA large language models (LLMs) are emerging as powerful methods in RNA research to decipher its intricate network of function and regulation. However, previous RNA LLMs were based on the transformer model and pre-trained on short segment of non-coding RNAs, which limits their general usability. Here we present the first full-length RNA foundation model, HydraRNA, which is based on a hybrid architecture of bidirectional state space model and multi-head attention mechanism, and is pre-trained on a large amount of both protein-coding and non-coding RNAs. Despite being pre-trained with the fewest parameters and the least GPU resources, HydraRNA learns better RNA representations and outperforms the existing foundation models on a variety of downstream tasks, including RNA classification, prediction of RNA secondary structure, RBP binding sites, mRNA stability and translation efficiency. Furthermore, HydraRNA can accurately predict the effect of mutations and estimate the relative contributions of different mRNA regions to the RNA stability and translation. We anticipate that HydraRNA will enable dissecting the diverse properties of RNA, accelerating the research of RNA regulation and facilitating the optimal design of RNA therapeutics.

bioinformatics↗

bioRxiv2025

Analysis of Head and Neck Cancer scRNA-seq Data Identified PRDM6 Promotes Tumor Progression by Modulating Immune Gene Expression

Head and neck squamous cell carcinoma (HNSCC) is a biologically aggressive and heterogeneous group of cancers with limited treatment options for patients who do not respond to standard therapies. While HPV-related HNSCCs tend to show better therapeutic outcomes, we still had limited understanding of the immune mechanisms underlying these cancers. Immune-responsive genes (IRGs) have emerged as critical factors in regulating both tumor progression and immune response. Recent advances in single-cell RNA sequencing (scRNA-seq) and the development of cell-type specific regulon inference tools, such as IRIS3, have provided new insights into the tumor immune microenvironment. In this study, we leveraged the IRIS3 platform to analyze scRNA-seq data from HNSCC patient samples, identifying novel transcription factor (TF)-IRG networks that contribute to tumor proliferation and immune escape. Specifically, we identified PRDM6, a histone methyltransferase, possesses the previously unknown role in promoting tumor cell proliferation by inducing IRG expression. We further demonstrated that HPV viral oncoproteins (E6/E7) oncoproteins up-regulate the PRDM6 expression, which associates PRDM6 with HPV-positive HNSCC.

cancer biology↗

bioRxiv2025

Rational design of next-generation filovirus vaccines with glycoprotein stabilization, nanoparticle display, and glycan modification

Filoviruses pose a significant threat to human health due to frequent outbreaks and high mortality. Although two vector-based vaccines are available for Ebola virus, a broadly protective filovirus vaccine remains elusive. Here, we evaluate a general strategy for stabilizing glycoprotein (GP) structures from Ebola, Sudan, and Bundibugyo orthoebolaviruses and Ravn orthomarburgvirus. A 3.2 [A] crystal structure provides atomic-level details of the redesigned Ebola virus GP, while cryo-electron microscopy reveals how a pan-orthoebolavirus neutralizing antibody targets a conserved site on the stabilized Sudan virus GP (3.13 [A] resolution), along with a low-resolution model of antibody-bound Ravn virus GP. A self-assembling protein nanoparticle (SApNP), I3-01v9, is redesigned at the N terminus to enable optimal surface display of filovirus GP trimers. Following detailed in vitro characterization, we examine the lymph node dynamics of Sudan virus GP and GP-presenting SApNPs in mice. Compared with the soluble trimer, SApNPs exhibit [~]112-fold longer retention in lymph node follicles, up to 28-fold greater presentation on follicular dendritic cell dendrites, and up to 3-fold stronger germinal center reactions. Functional antibody responses induced by filovirus GP trimers and SApNPs bearing wild-type and modified glycans are assessed in mice. This study provides a foundation for next-generation filovirus vaccine development. ONE-SENTENCE SUMMARYFilovirus glycoproteins and nanoparticles were rationally designed and characterized in vitro and in vivo to aid filovirus vaccine development.

microbiology↗

bioRxiv2025

PRRSV evades innate immune cGAS-STING antiviral function via its Nsp5 to deter STING translocation and activation

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is an important pathogen that seriously endangers pig breeding, causing significant economic losses to the global swine industry. Our previous study found that the DNA sensing innate cGAS-STING signaling pathway plays an important role in inducing interferon (IFN) upon PRRSV infection and inhibition of PRRSV replication. However, the immune evasion and its mechanism by PRRSV is still unclear. In current study, we found that PRRSV Non-structural protein 5 (Nsp5) strongly inhibits the cGAS-STING-IFN antiviral response. Further, we found that Nsp5 interacts with STING, blocking STING transport from ER to Golgi apparatus and interfering with STING recruitment of TBK1/IKK{varepsilon}/IRF3. Finally, we demonstrated that the Nsp5 36-47 and 58-67 amino acid regions are critical regions for inhibiting STING activity and PRRSV replication. The study describes a novel mechanism by PRRSV for suppression of the host innate antiviral response and have implications for our understanding of PRRSV pathogenesis. Author summaryThe innate immune system is the first line of host defense against infections. PRRSV is an immunosuppressive pathogen that has developed different strategies to evade the host innate immune responses. Here, we demonstrate for the first time that PRRSV utilizes its non-structural protein Nsp5 to inhibit the innate immune cGAS-STING-IFN signaling pathway, promoting the viral replication. Nsp5 can inhibit the cGAS-STING pathway by interacting with STING, blocking STING transport from ER to Golgi apparatus and interfering with STING recruitment of TBK1/IKK{varepsilon}/IRF3. In particular, the 36-47 and 58-67 amino acid regions of the Nsp5 is indispensable. This information will help us understand PRRSV-host interactions and provides new insights into the prevention and control of PRRSV.

immunology↗

bioRxiv2025

Mechanistic target of rapamycin/blood-testes barrier mechanism mediates acceleration of sperm epigenetic aging by environmental factors

Our previous research suggested that mechanistic target of rapamycin (mTOR)/blood-testis barrier (BTB) mechanism is involved in the regulation of the rates of epigenetic aging of sperm, where increased activity of mTORC1 opens BTB and accelerates epigenetic aging and increased activity of mTORC2 produces opposite results - increases BTB integrity and rejuvenates sperm epigenome. In the present study, we use our newly developed epigenetic clock model to investigate whether the mTOR/BTB mechanism is involved in the epigenetic reprogramming of sperm in mice exposed to heat stress (HS) and cadmium (Cd). Our findings show that both mTOR-dependent BTB disruption caused by HS and mTOR-independent BTB disruption due to Cd exposure accelerate sperm epigenetic aging, resulting in similar changes to sperm DNA methylation patterns. These results suggest that the mTOR/BTB mechanism is a novel molecular pathway through which environmental stressors influence sperm epigenetic aging, and this pathway may be relevant to a broad range of factors, including environmental, lifestyle, dietary, and health influences.

molecular biology↗

bioRxiv2025

Excavating Podocyte-Protective Targets of phloroglucinol-terpene hybrids Utilizing AI Models and Omics Analysis

Lupus nephritis (LN) is a multifactorial autoimmune inflammatory disorder, with podocyte dysfunction or structural abnormalities playing a pivotal role in its pathogenesis. Eucalyptus leaves, traditionally employed in folk medicine, have demonstrated notable efficacy in managing non-infectious inflammations. Eucarbwenstols D (R14) is a novel phloroglucinol-terpene that has been isolated from Eucalyptus robusta. To further refine potential targets, we utilized an AI scoring system and successfully identified the epidermal growth factor receptor (EGFR) as the novel target of R14. This discovery was built upon the foundation of transcriptome and connectivity mapping (CMap) analysis. Molecular docking and molecular dynamics simulations were employed to analyze the interaction between R14 and EGFR, surface plasmon resonance (SPR) and homogeneous time-resolved fluorescence (HTRF) assays were utilized to accurately quantify the binding affinity between R14 and EGFR. Western blot (WB) and immunofluorescence assays were then conducted to explore the downstream signaling pathways initiated by EGFR, specifically the PI3K/AKT/mTOR pathway. These assays demonstrated that R14 modulates the expression of apoptotic proteins Bax and Bcl-2 through this pathway, thereby exerting a protective effect on podocytes from undergoing apoptosis. The modulation of key podocyte proteins, nephrin and podocin, further substantiates this protective effect. Overall, we have applied a novel AI algorithm model that transcends bioinformatics analysis to precise identification of the novel podocyte target of R14. In this study, R14 was identified for the first time as a novel scaffold compound for EGFR inhibition. Moreover, R14 has demonstrated its capacity to inhibit podocyte apoptosis, thereby protecting these critical cells. This discovery establishes a robust theoretical foundation for the use of phloroglucinol-terpene hybrids (PTHs) in the treatment of LN.

cell biology↗

bioRxiv2025

D-LMBmapX: Generalized Deep-Learning Pipeline for Automated Whole-brain Neural Circuitry Profiling Across Any Developmental Stages

Understanding whole-brain circuitry development is essential for uncovering the origins of disorders linked to abnormal neural wiring, yet progress has been limited by the lack of tools for accurate, comprehensive analysis. Brain development is highly dynamic and region-specific, with pronounced inter-individual variability during early stages, and no existing method achieves whole-brain profiling at arbitrary stages. The rapidly changing morphology of developing axons further complicates segmentation. Here, we present D-LMBmapX, a deep learning pipeline for automated whole-brain circuitry profiling across postnatal development. D-LMBmapX constructs sample-inferred atlases from flanking anchor stages, enabling accurate registration at any time point. By developing a foundation model for generalised axon and soma segmentation, it supports quantitative mesoscale developmental connectomics, demonstrated through spatial-temporal profiling of catecholaminergic projections. D-LMBmapX also enables robust cross-modality and cross-dimensional registration, including precise alignment of single 2D slices to 3D references, and offers generalizable strategies for 5D analysis of diverse biomedical spatial datasets.

neuroscience↗

bioRxiv2025

A multiomic network approach uncovers disease modifying mechanisms of inborn errors of metabolism

For many inborn errors of metabolism (IEM) the understanding of disease mechanisms remains limited in part explaining their unmet medical needs. We hypothesize that the expressivity of IEM disease phenotypes is affected by the activity of specific modifier pathways, which is controlled by rare and common polygenic variation. To identify these modulating pathways, we used RNA sequencing to generate molecular signatures of IEM in disease relevant tissues. We then integrated these disease signatures with multiomic data and gene regulatory networks generated from animal and human populations without overt IEM. We identified and subsequently validated glucocorticoid signaling as a candidate modifier of mitochondrial fatty acid oxidation disorders, and we re-capitulated complement signaling as a modifier of inflammation in Gaucher disease. Our work describes a novel approach that can overcome the rare disease-rare data dilemma, and reveal new IEM pathophysiology and potential drug targets using multiomics data in seemingly healthy populations. Take-home message: Multiomic data and gene regulatory networks derived from animal and human populations without overt IEM can be used to study disease mechanisms in inborn errors of metabolism.

genetics↗

bioRxiv2025

PROBind: A Web Server for Prediction, Analysis and Visualization of Protein-Protein and Protein-Nucleic Acid Binding Residues

Protein-protein and protein-nucleic acids interactions are fundamental to numerous cellular functions, yet only a small fraction have been experimentally characterized. Although modern computational methods have been developed for predicting interacting residues in proteins, they are challenging to use due to individual installation and execution requirements, lack of a standardized input or output format, and absence of support for result analysis. Moreover, methods trained using structures of complexes or intrinsically disordered regions, may not perform well on other types. To overcome these challenges, we develop PROBind, a web server for predicting, analyzing, and interactively visualizing protein, DNA and RNA binding residues from both protein sequences and structures. PROBind integrates 12 predictors trained on structural or disordered proteins, and supports the upload of results from external predictors. By normalizing and averaging predictions from multiple predictors targeting the same ligand type, PROBind generates meta-predictions that balance discrepancies among different methods. Furthermore, it provides interactive graphical tools for result analysis and contextualization. Overall, PROBind accommodates diverse ligand types and supports predictions and analysis based on both structure and sequence data, overcoming the limitations of existing tools. PROBind is freely accessible at https://www.csuligroup.com/PROBind.

bioinformatics↗

bioRxiv2025

Spatial transcriptomics reveals heterogeneous cell-cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions

The cuprizone (CPZ) model is widely used for modeling demyelination in multiple sclerosis (MS) and for testing potential remyelination therapies. We integrated single-cell and spatial transcriptomics (ST) to fine map the spatial cellular and molecular responses during de and remyelination. ST revealed global demyelination and neuroinflammation in the brain beyond the corpus callosum, with region-specific differences. We identified oligodendroglia and microglia as two major cell types with significant transcriptomic changes in the model. Ligand receptor pairing analyses predicted growth factor and phagocytic pathway enrichment during demyelination, which is consistent with changes in MS lesions. During remyelination, while mature oligodendrocytes nearly reversed their phenotype back to the control state, microglia remained associated with the demyelination phenotype. Finally, astrocytes in the CPZ model had the greatest preservation of disease-associated modules to MS lesions, while the MOL, OPC, and microglia showed moderate to low preservation, which overall suggested that the CPZ model had moderate translatability to chronically active MS lesions.

neuroscience↗

bioRxiv2025

Unifying Genetic and Chemical Perturbagen Representation through a Hybrid Deep Learning Framework

Artificial Intelligence virtual cell (AIVC) holds transformative potential for biomedical research. Central to this vision is the systematic modeling of genetic and chemical perturbation phenotypes to accurately predict cellular dynamic states from diverse interventions. However, disparities in screening agents, library scales, experimental technologies, and data production efficiency hinder the integration, modeling, and analysis of the cross-data. Here we present UniPert-G2CP, a two-phase deep learning approach comprising i) UniPert, a multimodal molecular representation model that bridges genetic and chemical domains, and ii) G2CP (Genetic-to-Chemical Perturbation transfer learning), which systematically transforms CRISPR screen-based genetic insights into chemical perturbation modeling for cost-effective in silico drug screening. UniPert not only encodes multimodal perturbagens into a unified functionally interpretable sematic embedding space, but also improves phenotypic effect prediction for previously unseen gene perturbations and drug treatments. Building upon UniPert, G2CP successfully modeled large-scale cellular post-perturbation states spanning 4,994 gene and 7,821 compound perturbagens, while reducing modeling data costs by over 60%. We demonstrate that UniPert-G2CP enables efficient, generalizable simulations of multicellular, multi-domain perturbation cause-effect spaces, revealing differential cellular biological causality and informing mechanism-driven therapy. UniPert-G2CP opens new avenues for biological causal foundation model building, AIVC creation, and AI-powered precision medicine.

bioinformatics↗