Biology subjects

Zhang, J.

Publications and source records attributed to Zhang, J..

At least 415 records · Page 23Linked to original sources

bioRxiv2025

ctsGRN: Inferring cell type-specific gene regulatory networks in Arabidopsis

Gene regulatory networks (GRNs) govern life processes. And exploring GRNs is of great value for understanding biological functions and developing species resources. At present, studies on plant GRNs are limited, mostly focusing on the tissue level, which hinders the discovery of cell type-specific regulatory networks and mechanisms. To address this, we have proposed a GRN research framework named ctsGRN (CellTypeSpecGRN) for conducting cell-specific GRN research at the cell type resolution. In this framework, we employed three representative algorithms from statistics (e.g., correlation analysis), traditional machine learning (e.g., random forest) and deep learning (e.g., neural networks) to construct GRNs for different cell types in Arabidopsis roots. Among these, traditional machine learning methods showed the best performance. Experimental validation through yeast one-hybrid (Y1H) assays and ChIP-seq data confirmed the high reliability and predictive power of these inferred GRNs. By analyzing these networks, we mined novel cell type-specific regulatory relationships, identified core transcription factor (TF) AT5G08790 involved in root development, discovered 249 cell-type-specific hub TFs, and 136 key functional modules were found to be enriched in biological processes. Additionally, we revealed significant heterogeneity of TF-target gene interactions across various cell types. This comprehensive analysis offers a detailed overview of TF-mediated cell type-specific transcriptional regulation in Arabidopsis roots, providing new insights into the molecular mechanisms of root development and establishing a guideline framework for GRN research at the cell-type level in plants.

bioinformatics↗

bioRxiv2025

An ultra-long acting insulin enables glucose-synchronised release

Delayed and weak glucose-responsive kinetics, coupled with short plasma exposure and complicated formulation, remain major obstacles to the clinical translation of glucose-responsive insulin formulations. Here we report a rapidly absorbable, ultra-long acting, and glucose-responsive insulin analogue via engineering recombinant human insulin with two phenylboronic acids. The insulin analogue has a long circulating half-life (t1/2{beta} [~]150 h) due to its unique, unprecedented, glucose-responsive binding to blood circulation-associated proteins. This interaction drives the formation of a unique systemic reservoir that allows synchronised dynamic response in insulin levels to glucose fluctuations. In type 1 diabetic mice and minipigs, a single subcutaneous dose can maintain normoglycaemia for over one week (47.5-fold compared to insulin glargine). After the last injection of four consecutive weekly administrations in mice, the glucose-lowering effect can last 800 hours. Administering this glucose-responsive insulin analogue with a fully automated insulin delivery system can leverage dual closed loops and achieve a glucose time in range of over 85% and a coefficient of variation of approximately 30%, better than the recommended targets for human therapy. Importantly, no toxicity was identified in the study.

bioengineering↗

bioRxiv2025

Visuospatial attention exerts opposite modulatory effects on explicit and implicit audiovisual subjective synchrony via the frontoparietal network

Synchronization and integration constitute two essential subprocesses of audiovisual binding, commonly indexed by explicit subjective synchrony (ESS) and implicit subjective synchrony (ISS), respectively. Previous studies have shown that spontaneous fluctuations in visual attention are associated with ESS, and that ESS and ISS are negatively correlated, consistent with the temporal renormalization theory. However, it remains unknown whether controlled manipulations of visuospatial attention can causally modulate ESS and ISS in opposite directions via distinct neural mechanisms. To address this question, we conducted two complementary EEG experiments. In Experiment 1, ESS was assessed using a spatially cued beep-flash synchrony judgment task and the point of subjective simultaneity (PSS). In Experiment 2, ISS was measured using fusion and fission variants of the sound- induced flash illusion, with the peak illusion rate (PIR) as the behavioral index. This dual-paradigm design enabled direct comparison between explicit and implicit synchrony under matched attentional manipulations. Behaviorally, asymmetric allocation of visuospatial attention between auditory- and visual-leading conditions induced opposite shifts in PSS and PIR, specifically in the fusion variant. At the neural level, prestimulus frontal theta oscillations were associated with variations in PSS, whereas bilateral frontotemporal and left posterior beta oscillations were associated with variations in PIR. These results demonstrate that visuospatial attention exerts opposite modulatory effects on ESS and ISS through distinct oscillatory dynamics, providing causal evidence for the temporal renormalization theory and advancing understanding of how attentional control shapes multisensory temporal binding.

animal behavior and cognition↗

bioRxiv2025

The Wnt/APC destruction complex targets SREBP2 in a β-catenin-independent pathway to control cholesterol metabolism

APC, the core scaffold of the Wnt destruction complex, targets the transcriptional co-activator {beta}-catenin for proteolysis. There is no convincing evidence that APC directs degradation of other substrates. Using a reconstituted cytosolic extract-based system and complementary in vivo and cellular assays, we show that SREBP2, the master regulator of cholesterol biosynthesis, is a direct APC-AXIN1 substrate. APC-dependent SREBP2 degradation is conserved in Xenopus embryos, mouse colon, and human colorectal cancer cells and restricts SREBP2 target-gene expression, cholesterol synthesis, and tissue cholesterol levels. Mechanistically, APC and AXIN1 promote SREBP2 degradation via a conserved phosphodegron, which marks SREBP2 for ubiquitination by the E3 enzyme, FBXW7. Like {beta}-catenin, SREBP2 is stabilized by extracellular Wnt ligands; unlike {beta}-catenin, its regulation is independent of GSK3{beta} and CK1 and requires the entire APC mutational cluster region (MCR), whereas {beta}-catenin turnover can operate with only a partial MCR. These findings define a {beta}-catenin-independent branch of Wnt signaling that couples APC to sterol metabolism, providing a mechanistic rationale to target the mevalonate/SREBP2 axis in APC-mutant colorectal cancer.

biochemistry↗

bioRxiv2025

Single-cell lineage trajectory defines CDK inhibitor-sensitive cells-of-origin in esophageal squamous cell cancer

Understanding the cells of origin is essential for overcoming therapy resistance in esophageal squamous cell carcinoma (ESCC). We utilized machine learning-based single-cell trajectory analysis on 4NQO-induced murine models and genetically engineered organoids to identify multiple distinct cell clusters that serve as cellular origins of ESCC. Gene regulatory network analysis of these populations indicated activation of stem/progenitor cell regulators, including PRRX2 and CEBP{beta}. Translating these findings, a transcriptome-based drug repurposing screen identified five chemical candidates, four of which are potent Cyclin-Dependent Kinase (CDK) inhibitors, aligning with the frequent loss-of-function mutations in TP53 and CDKN2A observed in ESCC. Notably, CDK inhibitors markedly inhibit ESCC cell proliferation. This research delineates the potential cellular origins of ESCC and their key regulons, thereby pioneering a single-cell-derived therapeutic strategy that exposes vulnerabilities in tumor-initiating cells.

cancer biology↗

bioRxiv2025

In vivo colonic epithelial cell editing attenuates intestinal inflammation in mice

Engineered epithelial cells with enhanced efferocytosis capacity promote inflammation resolution and restore tissue homeostasis. Here, we developed a therapeutic approach to generate efferocytosis boosting epithelial cells in vivo by delivering mRNA in lipid nanoparticles (LNPs). We demonstrate that LNP-mediated delivery of mRNA enables efficient in vitro and in vivo functional editing of epithelial cells. In murine models of colitis, intraperitoneal administration of mRNA-loaded nanoparticles designed to boost efferocytosis markedly attenuated intestinal inflammation and halted disease progression. This strategy provides a proof of concept that epithelial cells can be functional engineered in situ and represents a promising therapeutic avenue for mitigating inflammatory tissue damage. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/678706v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@874991org.highwire.dtl.DTLVardef@1eefbfforg.highwire.dtl.DTLVardef@e22fa6org.highwire.dtl.DTLVardef@1a6480d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

FlexRibbon: Joint Sequence and Structure Pretraining for Protein Modeling

AO_SCPLOWBSTRACTC_SCPLOWProtein foundation models have advanced rapidly, with most approaches falling into two dominant paradigms. Sequence-based language models (e.g., ESM-2) capture sequence semantics at scale, and a number of recent works incorporate structural signals into sequence encoders. MSA-based predictors (e.g., AlphaFold 2/3) achieve accurate folding by exploiting evolutionary couplings, but their reliance on homologous sequences makes them less reliable in highly mutated or alignment-sparse regimes. We present FlexRibbon{ddagger}, a pretrained protein model that jointly learns from amino acid sequences and three-dimensional structures. Our pretraining strategy combines masked language modeling with diffusion-based denoising, enabling bidirectional sequence-structure learning without requiring MSAs. Trained on both experimentally resolved structures and AlphaFold 2 predictions, FlexRibbon captures global folds as well as flexible conformations critical for biological function. Evaluated across diverse tasks spanning interface design, intermolecular interaction prediction, and protein function prediction, FlexRibbon establishes new state-of-the-art performance on 12 different tasks, with particularly strong gains in mutation-rich settings where MSA-based methods often struggle.

molecular biology↗

bioRxiv2025

Typical development of the human fetal subplate: regional heterogeneity, growth, and asymmetry assessed by in vivo T2-weighted MRI

The subplate (SP) is a transient fetal brain compartment supporting neuronal migration, axonal ingrowth, and early cortical activity, yet the dynamics of its regional development remain poorly understood in vivo. Using T2-weighted fetal MRI of 68 typically developing fetuses (22-32 weeks gestational age, GA), we developed a semi-automated pipeline to quantify regional SP morphology (thickness, surface area, and volume). SP characteristics scaled strongly with GA and residual brain volume and showed marked regional differences. After correcting for geometric confounds, regional variation of SP thickness persisted, with highest values in parietal and perisylvian regions, suggesting that SP thickness may serve as a sensitive marker of intrinsic developmental differences. Between late 2nd and early 3rd trimester, mean SP thickness increased by 39.2% with large variation across regions ({+/-}11.0 SD), whereas surface area growth was more uniform (64.3% {+/-}0.7 SD). Continuous growth trajectories clustered into distinct spatiotemporal profiles: early-developing regions (e.g., pericentral and medial occipital cortices) contrasted with later-developing regions (prefrontal, temporal, and parietal cortices). These patterns partially recapitulate primary-to-association, medial-to-lateral, and posterior-to-anterior maturational hierarchies, pointing to organized developmental program. SP development also showed region-specific hemispheric asymmetries, including leftward thickness and volume asymmetry in superior temporal and precentral gyri. Some asymmetries amplified, others attenuated or reversed with age, suggesting both transient states and potential precursors of postnatal lateralization. Together, these findings provide a framework for regional SP quantification and position SP morphology, particularly thickness, as a promising early biomarker that might link fetal SP changes to subsequent cortical development and neurodevelopmental outcomes. Significance StatementThe subplate (SP) is a transient fetal brain compartment that provides an early foundation for downstream cerebral development. Using fetal MRI, we show that SP morphology is regionally heterogeneous and that its growth follows distinct regional trajectories. Principal spatiotemporal patterns differentiate early-from later-developing regions and partially recapitulate sensory-to-association hierarchies of cortical maturation. SP also exhibits dynamic hemispheric asymmetries as early as the second trimester, with some amplifying as potential precursors of postnatal lateralization, and others reversing with age, emphasizing the importance of evaluating developmental trajectories rather than single time points. This framework positions SP morphology as an accessible early marker of fetal brain organization with potential relevance for later neurodevelopment.

neuroscience↗

bioRxiv2025

Comparative single-cell transcriptomics of orthotopic and subcutaneous gastric tumors reveal immune and stromal heterogeneity

Preclinical cancer models often use subcutaneous (SC) implantation, which fails to recapitulate the native tumor microenvironment (TME) of orthotopic (ORT) sites. To resolve these differences, we used single-cell RNA sequencing (scRNA-seq) on paired SC and ORT implants of the CKP syngeneic gastric cancer model. Histopathological differences were minimal, but scRNA-seq revealed profound TME divergence. ORT tumors displayed robust stromal activation, coordinated fibroblast and endothelial signaling, and an immune compartment marked by higher T/NK cell activation and IgA-biased B cell plasma programs, reflecting a physiological mucosal environment. In contrast, SC tumors had higher overall T cell infiltration but showed markedly increased CD8+ T cell exhaustion and an enriched oxidative tumor program. Our findings provide critical guidance: SC models are optimal for high-throughput and exhaustion-focused assays, whereas ORT models are indispensable for studying organ-specific immune and stromal biology with translational fidelity.

cancer biology↗

bioRxiv2025

Quantifying the effects of cell death and agar density on yeast colony biofilms using an extensional flow mathematical model

We use a combination of experiments, mathematical modelling, and parameter estimation to better understand how agar density affects colony biofilm growth of the yeast species Saccharomyces cerevisiae. We obtained 15 total experimental replicates on rectangular plates filled with 0.6%, 0.8%, 1.2%, and 2.0% agar. In the experiments, we measured the horizontal expansion over time, the number of living cells, and the colony-biofilm aspect ratio. These measurements quantify the colony-biofilm size, composition, and shape, respectively. We modelled colony-biofilm expansion using a thin-film extensional-flow mathematical model. By fitting five unknown model parameters to mean experimental data, we show that nutrient uptake decreases and biofilm-substratum adhesion strength increases with an increase in agar density. Sensitivity analysis, fitting to individual replicates, and synthetic-data analysis confirmed that increased biofilm-substratum adhesion is the most consistent effect of increased agar density. This finding aligns with similar results reported for bacteria, and suggests that substratum properties are important for yeast-colony-biofilm growth.

biophysics↗

bioRxiv2025

An Empirical Study on Quantifying Physical Energy Expenditure during High-intensity Exercise

In the process of high-intensity exercise (HIE), the accurate evaluation of Physical Energy Expenditure (PEE) is of great significance to many occupational fields. However, due to the limitation of current technology, the quantitative ability of existing PEE evaluation methods in HIE situations is still insufficient. Based on the existing physiological coupling mechanism between cardiovascular parameters and energy metabolism, this study analyzed the dynamic changes of high-frequency blood pressure (BP) and heart rate (HR) during incremental load exercise and high-intensity interval training. The results show that although HR has a nonlinear response to the increase of exercise intensity, its time pattern-when analyzed synergistically with BP fluctuation-can provide reliable metabolic indicators. We used Doubly Labeled Water (DLW) as the gold standard for PEE determination and measured the total energy expenditure (TEE) in three consecutive days. During the monitoring period, high frequency invasive BP and HR monitoring was performed simultaneously, and the time integral value of SBP x HR and its ratio to TEE (i.e. Quotient value) were calculated. By dividing the corresponding SBP x HR integral value during HIE by the above quotient value, the PEE of this exercise can be estimated. Specifically, TEE can be accurately estimated by time integration of the product of SBP and HR. The short-term PEE rate can be solved by the differential equation constructed by the systolic blood pressure(SBP) trend function in this period, and can also be obtained by dividing the PEE in this period by the duration of this period. In this study, based on the results of invasive measurements, a new method for real-time monitoring of HIE using non-invasive cardiovascular parameters during PEE was proposed, providing new ideas and methodological support for applications in related fields.

physiology↗

bioRxiv2025

ETV2 mediated differentiation of human pluripotent stem cells results in functional endothelial cells for engineering advanced vascularized microphysiological models

Patient-specific microphysiological models, exemplified by organs-on-a-chip and organoids, have become a valuable tool for broad applications, revolutionizing biomedical research. However, limitations persist, with functional vasculature being a significant challenge. Generating functional human induced pluripotent stem cell (h-iPSC) derived endothelial cells (h-iECs) represent an urgent need. With the discovery of ETV2s determinant role in specifying EC lineages during differentiation, researchers have adopted techniques involving ETV2 overexpression to produce h-iECs more efficiently and consistently. However, the capacity of these cells to form functional vasculatures has not yet been thoroughly investigated. Here, we generated multiple h-iPSC lines with inducible ETV2 expression, and subsequently differentiated them into h-iECs, which were validated functionally and by key endothelial markers and RNA-seq analysis. These cells are capable of self-organizing into stable microvascular networks (MVNs) in a microfluidic chip reproducibly, forming lumenized and functional vessels that mimic the in vivo capillary bed in both morphology and function - a result not achieved using h-iECs differentiated with conventional two-step methods using the same h-iPSC lines. Furthermore, complex microphysiological models featuring perfusable vasculature were also successfully developed using ETV2 activated h-iECs, demonstrated with vascularized tumor and blood-brain barrier (BBB) models. Additionally, by pooling genetically engineered h-iPSCs with inducible ETV2, we effectively employed an orthogonally induced differentiation approach to enhance vascularization of an organoid model. Our methodology opens avenues in precision medicine, leading to personalized microphysiological models with perfusable vasculature for various applications.

bioengineering↗

bioRxiv2025

Pervasive splicing in a plant DNA virus

RNA splicing is considered an oddity in plant viruses; here, unexpectedly, we find it to be prevalent in the geminivirus tomato yellow leaf curl virus. Transcriptome analysis revealed eight splicing events generating novel protein isoforms, six of which were validated and two shown to depend on the plant spliceosome. Splicing impairment reduced viral accumulation and symptom severity, demonstrating that splicing contributes to infectivity, potentially by expanding the viral proteome, and suggesting that plant virus transcriptomes need to be reassessed.

plant biology↗

bioRxiv2025

Increased sensitivity to myopia and altered retinal ON/OFF balance in a mouse model lacking Dusp4

Myopia, influenced by environmental and genetic factors, occurs when the emmetropization process fails to stop, causing excessive eyeball growth. Highly myopic animal models lacking a functional ON-pathway identified Dusp4 as a potential gene implicated in myopia. Here, we used a mouse model lacking DUSP4 to gain a better understanding of its retinal role and the mechanisms implicated in myopia development. Dusp4-/- mice have a reduced basal level of retinal dopamine and a higher susceptibility to lens-induced myopia. Dusp4 is expressed in ON-bipolar cells and a subset of OFF-bipolar cells in a light dependent manner. The absence of DUSP4 causes a hyperactivation of the MAPK/ERK pathway. Dusp4-/- mice showed reduced optomotor responses, increased ON-bipolar cell depolarization, reduced oscillatory potentials together with altered OFF and ON-OFF RGC responses to light flashes. These data provide insights into retina-driven mechanisms of myopization, nuancing the impact of ON and OFF pathways upon emmetropization.

neuroscience↗

bioRxiv2025

Overcoming rapaprotin resistance through inhibition of P-glycoprotein

The 26S proteasome is an essential regulator of protein homeostasis and a clinically validated therapeutic target in multiple myeloma (MM). Rapaprotin, a novel macrocycle identified from a rapamycin-inspired rapafucin library, disrupts 26S proteasome function by inducing disassembly of the 19S regulatory particle in the 26S proteasome, leading to apoptosis in MM cells. Its bioactivation requires prolyl endopeptidase (PREP)-mediated cleavage to generate Rapaprotin-L, a negatively charged, linear metabolite with potent proteasome-disassembly activity. Using the PRISM cancer cell line profiling platform, we identified high P-glycoprotein (P-gp/ABCB1) expression as a major determinant of Rapaprotin resistance in solid tumor cell lines. Efflux assays confirmed Rapaprotin-L, but not its parent Rapaprotin, as a high-affinity P-gp substrate. Co-treatment with the third-generation P-gp inhibitor tariquidar restored the intracellular accumulation of Rapaprotin-L, reinstating proteasome inhibition and consequent apoptosis of Rapaprotin-resistant colorectal cancer cell lines. Strong synergy between Rapaprotin and tariquidar was observed in a 3D spheroid model. These results establish P-gp as a key mediator of resistance to Rapaprotin and identify a rare example of a negatively charged Rapaprotin-L as a P-gp substrate. Together, these findings expand the potential therapeutic scope of Rapaprotin beyond hematologic malignancies to a broader range of solid tumors.

pharmacology and toxicology↗

bioRxiv2025

A comprehensive functional landscape of α-tubulin TUBA1A variants illuminates microtubule biology and refines clinical classification

Missense variant interpretation in highly conserved, paralog-rich gene families remains a critical bottleneck for precision medicine. Here, we developed an integrated experimental-computational platform to systematically assess the functional impact of all possible missense mutations in the -tubulin TUBA1A. Combining high-throughput comprehensive mutagenesis, high-content imaging, convolutional neural network- driven phenotyping, and machine learning-guided prediction, we quantified microtubule assembly phenotypes for every coding variant. This approach outperforms conservation-based predictors and enables functional reinterpretation of disease-associated variants. Structural mapping of the TUBA1A mutational landscape reveals distinct domains critical for GTP binding, chaperone-assisted folding or protofilament interaction, illuminating diverse mechanisms of tubulin-related diseases. Integration with ACMG-AMP guidelines demonstrates this mutational landscape improves clinical variant classification in redundant gene families. This framework is broadly applicable to other structurally conserved proteins, linking variant effect prediction to mechanistic insight and clinical translation.

genetics↗

bioRxiv2025

NLRP3 is a thermosensor that is negatively regulated by high temperature

Inflammation is an essential response to infection and injury, but unregulated inflammation is damaging and must be limited by negative feedback signalling. Inflammasome signalling drives local inflammation and systemic responses like fever. However, our understanding of how inflammasome signalling is negatively regulated is limited. NLRP3 is activated by a vast number of stimuli and senses perturbations of cytoplasmic homeostasis. As temperature is a fundamental environmental stressor, we hypothesised that NLRP3 inflammasome signalling would be sensitive to increased temperatures and so we investigated the effects of high temperatures on NLRP3 in macrophages. Short-term incubation at high fever range temperatures significantly inhibits NLRP3 activation, while secretion of the inflammasome-independent cytokines TNF and IL-6 are much less affected. High temperature blocks NLRP3 inflammasome formation in a transcription-independent manner, and NLRP3 is highly sensitive to temperature-mediated inhibition relative to the NLRC4, AIM2, and NLRP1 inflammasomes. Using cellular assays and molecular simulations we show that the effect of high temperature on NLRP3 is protein intrinsic. NLRP3 activation is associated with a decrease in the thermal stability of the protein and multiscale molecular dynamics simulations identified a peptide in the C-terminal of the FISNA domain (COFI) that is highly flexible and undergoes a significant conformational shift at high temperature. Cellular assays demonstrate that the COFI regulates NLRP3 stability and is required for activation. Furthermore, mice exposed to high temperature display attenuated inflammatory cytokine production upon in vivo LPS challenge. Our studies thus reveal that high temperatures associated with fever limit NLRP3 activity and identify a novel role for NLRP3 as a protein thermosensor.

immunology↗

bioRxiv2025

The regulatory effect of Ca2+/calmodulin dependent protein kinase II mediated by receptor interacting protein kinase 3 on necroptosis of hypertrophic cardiomyocytes

Receptor interacting protein kinase 3 (RIPK3) plays a crucial role in the signaling pathway of necroptosis and calcium/calmodulin dependent protein kinase II (CaMKII) is a novel substrate for RIPK3 induced necroptosis. The aim of this study is to investigate the regulation and mechanism of RIPK3 on AngII induced cardiomyocyte hypertrophy.AngII was used to stimulate myocardial cells for 72 hours, inducingcardiomyocytehypertrophy; Use RIPK3 inhibitor GSK872 to reduce RIPK3 expression.Detect indicators related to myocardial hypertrophy, cell damage, necroptosis,CaMKII activation and gene expression, oxidative stress, mitochondrial membrane potential, etc. After AngII stimulation of cardiomyocytes, the expression of hypertrophy markers ANP and BNP increased, LDH release increased, ATP levels decreased, splicing factors ASF and SC35 expression increased, CaMKII oxidation and phosphorylation levels increased, and CaMKII{delta} alternative splicing was disrupted. However, treatment with GSK872 can alleviate myocardial dysfunction, inhibit CaMKII activation, correct CaMKII{delta} variant splicing disorder and ultimately alleviating myocardial hypertrophy. In addition, pretreatment with RIPK3 can reduce the accumulation of reactive oxygen species (ROS) induced by AngII, decrease the activity of ASF and SC35, and restore mitochondrial membrane potential. RIPK3 inhibitor GSK872 can inhibit the activation of CaMKII, alleviate necroptosis and oxidative stress to alleviate myocardial hypertrophy. It has a protective effect on myocardial hypertrophy and is expected to become a new targeted drug for clinical treatment of dilated cardiomyopathy and heart failure.

cell biology↗