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Ouyang, X.

Publications and source records attributed to Ouyang, X..

At least 19 recordsLinked to original sources
bioRxiv2026

ROCK inhibitor Ripasudil reduces Alzheimer pathological proteins and enhances cellular bioenergetics

Rho-associated kinase (ROCK) inhibitors have been explored as an Alzheimer Disease (AD) therapeutic agent. In this study, we aim to determine the efficacy of a potent ROCK inhibitor, ripasudil, in impacting AD pathological protein tau in mice. The time-course study showed that ripasudil rapidly penetrated mouse brains, reaching maximal concentration half an hour post-injection. To determine the efficacy of ripasudil, we injected AppNL-G-F knock-in mice with ripasudil at 30 mg/kg and sacrificed them after three hours. We used Tandem Mass Tag labels and compared the proteomic profiles of mouse brains exposed to ripasudil to those exposed to saline. We also treated AD-patient-derived Neural Stem Cells (NSCs) with ripasudil and performed a Seahorse Mito Stress Test to evaluate their impact on mitochondrial activity. Bioinformatics analysis of the proteomic profiles revealed differentially enriched components of chromosome. The Mito Stress Test of NSCs revealed significant increases in basal oxygen consumption, ATP-linked respiration, maximal respiration, and reserve capacity oxygen consumption compared to untreated NSCs. Importantly, we found a significant reduction of Tau and pTau 396 in brains of mice treated with ripasudil. Overall, our findings highlight the feasibility and promise of ROCK inhibitor ripasudil as an AD therapeutic agent.

neuroscience↗
bioRxiv2026

Extracellular injection system combined with peptides for intracellular Staphylococcus aureus treatment

The inaccessibility of intracellular bacteria has long rendered the treatment of Staphylococcus aureus infections an challenge. Studies have demonstrated that the extracellular injection system PVC can accurately deliver proteins into cells, which would not need small molecules, and enables effective intracellular delivery of antimicrobial peptides for treatment. Accordingly, we selected antimicrobial peptides including Cecropin, LL37 and Indolicidin that possess potent bactericidal activity, and established the Directed Antimicrobial Assault platform (DAAT) by leveraging the intracellular delivery capacity of PVC. DAAT Cecropin, DAAT LL37 and DAAT Indolicidin inhibited intracellular bacteria in a dose-dependent manner, with DAAT LL37 reaching 86.76% inhibition; after 72 h of treatment, viable-cell numbers reduse to 66--82-fold those of the control. Tail-fibre retargeting enabled direct extracellular S. aureus killing, while combined DAAT therapy promoted wound healing in mice. These findings expand the utility of PVC-derived nanosyringes and establish DAAT as a modular platform for intracellular antimicrobial peptide therapy.

synthetic biology↗
bioRxiv2026

Spatial multi-omics unveils the monoclonal origin, neuroendocrine plasticity, and microenvironment niches in combined small cell lung cancer

Combined small-cell lung cancer (cSCLC) is a rare and aggressive subtype of small-cell lung cancer (SCLC) characterized by mixed histology comprising SCLC and non-small cell lung cancer (NSCLC) or large cell neuroendocrine carcinoma (LCNEC) components. Despite its histological heterogeneity and even poorer prognosis than de novo SCLC, cSCLC is clinically managed as pure SCLC, largely due to the lack of molecular insights into its biology, lineage plasticity, and tumor microenvironment (TME). Here, we perform multi-omics profiling, including spatially-resolved whole-exome sequencing (WES), spatial transcriptomics (ST) and single-nucleus RNA sequencing (snRNA-seq), across 19 treatment-naive cSCLC tumors spanning all major histological subtypes. Our analysis reveals that SCLC and NSCLC/LCNEC components share a monoclonal origin, with histological divergence characterized by distinct mutation and copy number alteration patterns. ST and snRNA-seq uncover spatially exclusive or interspersed tumor domains, with distinct TME compositions and immune landscapes. Notably, fibroblast-rich regions enriched for an aggressive fibroblast subtype form boundaries between tumor domains, potentially influencing immune TME and treatment responses. We identify extensive lineage plasticity within cSCLC, including active LUAD-to-SCLC transdifferentiation and SCLC subtype coexistence, suggesting transitional cellular states not captured by traditional diagnostics. Leveraging these insights, we developed the cSCLC Detector, a sensitive mutation-based diagnostic assay that improves the detection of cSCLC in tissue and liquid biopsy samples. Our findings offer critical insights into cSCLC lineage plasticity, cellular evolution, and microenvironmental interactions, underscoring the need for tailored treatment strategies and diagnostic frameworks for this aggressive cancer subtype.

cancer biology↗
bioRxiv2025

Drosophila melanogaster model of RVCL-S demonstrates age dependent disease progression

Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCL-S) is a disease that causes deterioration of small vessels, affecting various organs: eyes, brain, liver, and others. The RVCL-S carriers have lower life expectancy. There is no cure available to date. The disease has been linked to mutations in TREX1 gene disrupting its cytoplasmic localization. To facilitate the disease mechanism investigation, we employed model organism D. melanogaster, identified human TREX1 ortholog cg3165, and confirmed its vital significance to flies. Then, we expressed human TREX1 and its mutant form TREX1 V235Gfs in flies and used optical coherence microscopy (OCM) to monitor the dynamics of flies vascular system. We detected the relapse of fly dorsal vessel, movement impairment, and reduced longevity in TREX1 V235Gfs-expressing transgenic animals. Vascular deterioration and shorter life span recapitulate the RVCL-S manifestations in humans. We have established a robust quantitative Drosophila RVCL-S phenotypic system that can potentially serve as a screening platform for drug discovery and drug targets identification.

genetics↗
bioRxiv2025

A comprehensive analysis of humanized mouse models for the study of cancer immunotherapies

Humanized immune system (HIS) mouse models, generated by engrafting tumors and hematopoietic cells of human (Hu) origin into immunodeficient host mice, effectively recapitulate key aspects of the crosstalk between human immune cells and tumors. These models represent a valuable tool for the preclinical evaluation of immunotherapies. In this study, we provide a comprehensive comparison of two widely used HIS models: the Hu-CD34+ model, which engrafts Hu-hematopoietic cells derived from Hu-CD34+ hematopoietic stem cells (HSCs), and the Hu-PBMC model, which utilizes Hu-peripheral blood mononuclear cells (PBMCs). We assess the kinetics, quality and extent of immune cell engraftment, as well as the development of graft-versus-host disease (GVHD). Additionally, we investigate the impact of different immunodeficient host mouse strains on immune cell reconstitution in the Hu-CD34+ model. Both HIS models were engrafted with human tumors derived from either cell lines or patient-derived xenografts (PDX), revealing distinct immune-tumor interactions that influenced antitumor responses. Notably, tumor responses to T-cell-directed therapies, including anti-PD1 antibodies, IL-2-anti-IL-2 antibody complexes, and T-cell engagers, varied across these models. Our findings provide novel insights into the properties and limitations of HIS models, offering a critical resource for optimizing next-generation immuno-oncology strategies and guiding the design of future therapeutic interventions.

immunology↗
bioRxiv2025

Automated SP3 Workflow Enables Robust Sample Preparation on Proteonano Ultraplex Proteomics Platform

The efficiency and reproducibility of sample preparation are critical prerequisites for obtaining reliable results in bottom-up proteomics. To conclude, we systematically evaluated three commonly used sample preparation methods: automated single-pot solid-phase-enhanced sample preparation (SP3), precipitation by organic solvents, and filter-aided sample preparation method (FASP). When processing varying input amounts of HeLa cell lysate (10, 20, 50, 100, and 150 g), the SP3 method demonstrated strong linearity (R2 = 0.95), indicating excellent quantitative consistency across a broad protein input range. A comparison between manual SP3 and manual precipitation protocols revealed comparable protein identification numbers, with a correlation coefficient of approximately 0.97. We further developed an automated version of the SP3 method based on the Proteonano Ultraplex Proteomics platform (autoSP3), which yielded highly consistent results with the manual approach, achieving a protein identification overlap of 98.5% (6,949 out of 7,056). These findings support the suitability of the autoSP3 workflow as a robust and scalable approach for high-throughput and reproducible sample preparation in proteomics sample preparation.

molecular biology↗
bioRxiv2025

Neurons exploit stochastic growth to rapidly and economically build dense radially oriented dendritic arbors

Dendrites grow by stochastic branching, elongation, and retraction. A key question is whether such a mechanism is sufficient to form highly branched dendritic morphologies. Alternatively, are signals from other cells or is the topological hierarchy of the growing network necessary for dendrite geometry? To answer these questions, we developed a mean-field model in which branch dynamics is isotropic and homogenous (i.e., no extrinsic instruction) and depends only on the average lengths and densities of branches. Branching is modeled as density-dependent nucleation so there are no tree structures and no network topology. Despite its simplicity, the model predicted several key morphological properties of class IV Drosophila sensory dendrites, including the exponential distribution of branch lengths, the parabolic scaling between dendrite number and length densities, the tight spacing of the dendritic meshwork (which required minimal total branch length), and the radial orientation of branches. Stochastic growth also accelerated the overall expansion rate of the arbor. Therefore, stochastic dynamics is an economical and rapid space-filling mechanism for building dendritic arbors without external guidance or hierarchical branching mechanisms. Our model provides a general theoretical framework for understanding how macroscopic branching patterns emerge from microscopic dynamics.

developmental biology↗
bioRxiv2025

Super-omics and PCAS reveal rheumatoid arthritis as a tumor-like disease

Rheumatoid arthritis (RA) is a debilitating systemic autoimmune disorder that significantly impairs quality of life. To elucidate the molecular alterations in RA progression, we performed comprehensive super-omics analyses on synovial tissues from patients with joint trauma, arthritis, and RA. These analyses included transcriptomics, proteomics, metabolomics, microbiomics, and fourteen PTMs (phosphorylation, acetylation, lactylation, O-GlcNAc glycosylation, arginine monomethylation, lysine monomethylation, lysine dimethylation, lysine trimethylation, succinylation, malonylation, glutarylation, tyrosine nitration, N-glycosylation, and O-glycosylation). Additionally, we developed a protein-centered association study (PCAS) method to integrate these complex datasets. Using this approach, we identified key proteins, such as STK17B, and its interactors, which may be crucial in RA pathogenesis. Tumor-like features, including aberrant angiogenesis and epithelial-mesenchymal transition, were observed in RA, alongside the potential involvement of oncogenes and tumor suppressor genes. Finally, we constructed a molecular interaction blueprint of RA, providing a comprehensive framework for advancing RA pathogenesis, diagnosis, and therapy.

immunology↗
bioRxiv2024

A Comprehensive Engineering Strategy Improves Potency and Manufacturability of a Near Pan-neutralizing Antibody Against HIV

Anti-HIV envelope broadly neutralizing antibodies (bnAbs) are alternatives to conventional antiretrovirals with the potential to prevent and treat infection, reduce latent reservoirs, and/or mediate a functional cure. Clinical trials with "first generation" bnAbs used alone or in combination show promising antiviral effects but also highlight that additional engineering of "enhanced" antibodies will be required for optimal clinical utility, while preserving or enhancing cGMP manufacturing capability. Here we report the engineering of an anti-CD4 binding-site (CD4bs) bnAb, N49P9.3, purified from the plasma of an HIV elite-neutralizer. Through a series of rational modifications we produced a variant that demonstrates: enhanced potency; superior antiviral activity in combination with other bnAbs; low polyreactivity; and longer circulating half-life. Additional engineering for manufacturing produced a final variant, eN49P9, with properties conducive to cGMP production. Overall, these efforts demonstrate the feasibility of developing enhanced anti-CD4bs bnAbs with greatly improved antiviral properties as well as potential translational value.

bioengineering↗
bioRxiv2024

Acute increase of protein O-GlcNAcylation in mice leads to transcriptome changes in the brain opposite to what is observed in Alzheimer Disease

Enhancing protein O-GlcNAcylation by pharmacological inhibition of the enzyme O-GlcNAcase (OGA) is explored as a strategy to decrease tau and amyloid-beta phosphorylation, aggregation, and pathology in Alzheimers disease (AD). There is still more to be learned about the impact of enhancing global protein O-GlcNAcylation, which is important for understanding the mechanistic path of using OGA inhibition to treat AD. In this study, we investigated the acute effect of pharmacologically increasing O-GlcNAc levels, using OGA inhibitor Thiamet G (TG), on normal mouse brains. We hypothesized that the transcritome signature in respones to TG treatment provides a comprehensive view of the effect of OGA inhibition. We sacrificed the mice and dissected their brains after 3 hours of saline or 50 mg/kg TG treatment, and then performed mRNA sequencing using NovaSeq PE 150 (n=5 each group). We identified 1,234 significant differentially expressed genes with TG versus saline treatment. Functional enrichment analysis of the upregulated genes identified several upregulated pathways, including genes normally down in AD. Among the downregulated pathways were the cell adhesion pathway as well as genes normally up in AD and aging. When comparing acute to chronic TG treatment, protein autophosphorylation and kinase activity pathways were upregulated, whereas cell adhesion and astrocyte markers were downregulated in both datasets. Interestingly, mitochondrial genes and genes normally down in AD were up in acute treatment and down in chronic treatment. Data from this analysis will enable the evaluation of the mechanisms underlying the potential benefits of OGA inhibition in the treatment of AD. In particular, although OGA inhibitors are promising to treat AD, their downstream chronic effects related to bioenergetics may be a limiting factor. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/613769v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@178dcf6org.highwire.dtl.DTLVardef@1f2cc78org.highwire.dtl.DTLVardef@14dfe28org.highwire.dtl.DTLVardef@16918aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗
bioRxiv2024

Alpha-synuclein preformed fibril-induced aggregation and dopaminergic cell death in cathepsin D overexpression and ZKSCAN3 knockout mice

-synuclein accumulation is recognized as a prominent feature in the majority of Parkinsons disease cases and also occurs in a broad range of neurodegenerative disorders including Alzheimers disease. It has been shown that -synuclein can spread from a donor cell to neighboring cells and thus propagate cellular damage, antagonizing the effectiveness of therapies such as transplantation of fetal or iPSC derived dopaminergic cells. As we and others previously have shown, insufficient lysosomal function due to genetic mutations or targeted disruption of cathepsin D can cause -synuclein accumulation. We here investigated whether overexpression of cathepsin D or knockout (KO) of the transcriptional suppressor of lysosomal biogenesis ZKSCAN3 can attenuate propagation of -synuclein aggregation and cell death. We examined dopaminergic neurodegeneration in the substantia nigra using stereology of tyrosine hydroxylase-immunoreactive cells 4 months and 6 months after intrastriatal injection of -synuclein preformed fibrils or monomeric -synuclein control in control, central nervous system (CNS)-cathepsin D overexpressing and CNS-specific ZKSCAN3 KO mice. We also examined pS129--synuclein aggregates in the substantia nigra, cortex, amygdala and striatum. The extent of dopaminergic neurodegeneration and pS129--synuclein aggregation in the brains of CNS-specific ZKSCAN3 knockout mice and CNS-cathepsin D overexpressing mice was similar to that observed in wild-type mice. Our results indicate that neither enhancing cathepsin D expression nor disrupting ZKSCAN3 in the CNS is sufficient to attenuate pS129--synuclein aggregate accumulation or dopaminergic neurodegeneration.

neuroscience↗
bioRxiv2024

Technical Assessment on Proteonano: A Robust Platform for Deep Plasma Proteomics Study

Complete profiling of human plasma proteome is an immerse source for disease biomarker discovery. Cutting-edge mass spectrometers, like ThermoFishers Orbitrap Astral, have promised unprecedented insights into the exploration of multiple protein biomarkers from human plasma samples. However, large-scale, deep profiling of the human plasma proteome, especially low-abundant proteins (LAPs, <10 ng.mL- 1), in a robust and fast way remains challenging. This is largely due to the lack of standardized and automated workflows including LAPs enrichment, reduction, and enzymatic digestion procedures. Until now, these complex procedures have not been incorporated into a streamlined workflow to achieve reproducibility, high-throughput, and deep proteome coverage. Here we report the Proteonano Ultraplex Proteomics (PUP) Platform for large cohort plasma proteomics studies with robustness and fast throughput by standardizing workflow by incorporating the Proteonano platform and high-resolution mass spectrometers, including Orbitrap Exploris 480, Orbitrap Astral, and timsTOF Pro. This pipeline demonstrates excellent stability and reproducibility, with tunable balance between proteome coverage and throughput. We further demonstrate the utility of this platform for potential biomarker discovery in a neurodegenerative disease cohort. This harmonized method enables robust, fast and large-cohort plasma proteomics studies to meet the need to discover new biomarkers.

biochemistry↗
bioRxiv2023

CCT3 drives Sorafenib resistance by inhibiting TFRC-mediated iron uptake in HCC

Sorafenib is commonly utilized in the management of advanced hepatocellular carcinoma (HCC). However, its efficacy in extending patients survival is hindered by the development of drug resistance. By employing protein posttranslational modification (PTM) omics, including acetylome, phosphoproteome, and ubiquitinome, in conjunction with genome-wide CRISPR/Cas9 knockout library screening, we have successfully identified chaperonin containing TCP1 subunit 3 (CCT3) as a key factor contributing to Sorafenib resistance. Furthermore, we observed a reduction in the ubiquitination of CCT3 at lysine 21 (K21) subsequent to Sorafenib treatment. This study provides evidence that CCT3 hinders the recycling of transferrin receptor protein 1 (TFRC) by interacting with alpha-actinin-4 (ACTN4), which is influenced by K6-linked ubiquitination on K21. Depleting CCT3 increased the susceptibility of cells to Sorafenib-induced ferroptosis, while reintroducing CCT3 through transfection restored resistance to ferroptosis. Additionally, impairing ACTN4 or TFRC depletion compromised CCT3s ability to inhibit Sorafenib-induced ferroptosis. In summary, targeting CCT3 presents a potential strategy for overcoming Sorafenib resistance in HCC.

cancer biology↗
bioRxiv2023

Proteonano: a novel deep proteomics platform with 1000-plex profiling capacity and picogram sensitivity and its application in diabetic kidney disease

The development of blood-based multi-biomarker panels for screening diabetic patients, and as an easy-to-access tool for identifying individuals at greatest risk of developing diabetic kidney disease (DKD) and its progression, is essential. However, conventional blood biomarker-based methodologies (e.g. clinical tests and ELISA) are unable to predict DKD progression with high sensitivity and specificity. To overcome these challenges, we developed a deep, untargeted plasma proteome profiling technology (Proteonano platform) to identify potential multiple protein biomarkers involved in DKD progression. The Proteonano technology is an affinity selective mass spectrometric platform that comprises nanoparticle-based affinity binders (nanobinders) for low abundant protein enrichment, automated workflow for parallel sample preparation, and machine learning empowered bioinformatic software for data analysis. Using the Proteonano platform, we performed untargeted proteomics on 75 subjects (DKD progressors, n = 30; DKD non-progressors, n = 45) and identified an average of 953 {+/-} 80 (AVG {+/-} SD) protein groups, with a wide dynamic range of 8 orders of magnitude (with the lowest concentration down to 3.00 pg/mL). Among these, 38 proteins were differentially expressed between DKD progressors relative to non-progressors, and the predictive power for these proteins were assessed. Further, we performed random forest and LASSO analyses for additional variable selection. Variables selected by these approaches were assessed by Akaike information criterion method followed by ROC analysis, which identified a combination of multiple proteins (including VWF, PTGDS, B2M, BT3A2, and LCAT) that showed excellent predictive power over current methods, with an area under the curve value up to 0.97. Some of these plasma proteins are not previously recognized in the context of DKD progression, suggesting they are novel biomarkers. Our studies pave the way to develop multi-biomarker panels for DKD progression management. This study suggests that the Proteonano technology platform reported here can be employed as an established workflow enabling untargeted deep proteomic analysis to identify highly discriminative biomarkers for precise medicine.

bioinformatics↗
bioRxiv2021

Harzianic Acid has multi-target antimicrobial activity against Gram-Positive Bacteria

The thermophilic fungus Oidiodendron flavum is a saprobe that is commonly isolated from soil. Here, we identified a Gram-positive bacteria-selective antimicrobial secondary metabolite from this fungal species, harzianic acid (HA). Using Bacillus subtilis strain 168 combined with several assays, we found that HA targeted the cell membrane, though only at high concentrations. To further study the antimicrobial activity of HA, we isolated an HA-resistant strain, Bacillus subtilis strain M9015, and discovered that the mutant has more translucent colonies, has cross resistance to rifampin, and harbors five mutations in the coding region of four distinct genes. Further analysis of these genes indicated that the mutation in atpE might be responsible for the translucency of the colony, and mutation in yusO for resistance to both HA and rifampin. We conclude that HA is a multi-target antimicrobial agent against Gram-positive bacteria.

microbiology↗
bioRxiv2021

Classification of antimicrobial mechanism of action using bacterial time-lapse imaging

Antimicrobial resistance is a major threat to human health. Basic knowledge of antimicrobial mechanism of action (MoA) is imperative for patient care and for identification of novel antimicrobials. However, the process of antimicrobial MoA identification is relatively laborious. Here, we developed a simple, quantitative time-lapse fluorescence imaging method, Dynamic Bacterial Morphology Imaging (DBMI), to facilitate this process. It uses a membrane dye and a nucleoid dye to track the morphological changes of single Bacillus subtilis cells in response to antimicrobials for up to 60 min. DBMI of bacterial cells facilitated assignment of the MoAs of 14 distinct, known antimicrobial compounds to the five main classes. Using this method, we found that the poorly studied antimicrobial, harzianic acid, a secondary metabolite that we purified from the fungal culture of Oidiodendron flavum, targets the cell envelope. We conclude that DBMI is a simple method, which facilitates rapid classification of the MoA of antimicrobials in functionally distinct classes.

microbiology↗
bioRxiv2020

In-House Forecasting of Crop Latitude Adaptation through a Daylength-sensing-based Environment Adaptation Simulator (DEAS)

Global climate change necessitates the accelerated breeding of new crop varieties that can sustain yields in new environments. As a proxy for environmental adaptation, the selection of crops that can adapt to different latitudes is an appealing strategy. However, such selection currently involves a lengthy procedure that severely restricts the rapid breeding of varieties. Here, we aimed to combine molecular technologies with an in-house streamlined screening method to facilitate rapid selection for latitude adaptation. We established the Daylength-sensing-based Environment Adaptation Simulator (DEAS) to measure crop latitude adaptation via the transcriptional dynamics of florigen genes at different latitudes. We used different statistical approaches to demonstrate that DEAS predicts the florigen expression profiles in rice with high accuracy. Furthermore, we demonstrated the potential for application of DEAS in different crops. Incorporating DEAS into the breeding programs of conventional and underutilized crops could help meet the future needs for crop adaptation and promote sustainable agriculture.

plant biology↗