Biology subjects

Wei, S.

Publications and source records attributed to Wei, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

In-cell Proteomics Enables High-Resolution Spatial and Temporal Mapping of Early Xenopus tropicalis Embryos

Early embryonic development requires tightly regulated molecular programs to coordinate cell division, fate specification, and spatial patterning. While transcriptomic profiling is widely performed, proteomic analyses of early vertebrate embryos remain limited due to technical challenges in embryonic sample preparation. Here, we propose an "in-cell proteomics" approach, which bypasses cell lysis and yolk depletion, processes individual embryos directly in functionalized filter devices, and generates liquid chromatography-mass spectrometry (LC-MS)-friendly samples in an extremely robust and streamlined manner. Combined with a single-shot data-independent acquisition (DIA) MS workflow, this approach enabled us to consistently quantify [~]6,200 proteins from a single Xenopus tropicalis embryo, representing the deepest proteomic coverage of early X. tropicalis development reported to date. Investigation of the temporal proteomes across five cleavage stages (1- to 16-cell) revealed a drastic proteomic shift between 2- and 4-cell stages, followed by more gradual transitions thereafter. Spatial analysis of dissected 8-cell blastomeres uncovered pronounced molecular asymmetry along the animal-vegetal axis, while dorsal-ventral differences were minimal. This study establishes a novel in-cell proteomics technology in conjunction with DIA-MS as a robust platform for high-resolution, low-input developmental proteomics analysis, and provides a comprehensive spatiotemporal protein atlas for early X. tropicalis embryos.

biochemistry↗

bioRxiv2025

Cervical Mucus Viscoelasticity and Sperm Velocity are Correlated and Concentration-dependent In Vitro

BackgroundMucus in the endocervix serves as fertility gatekeeper in the reproductive tract through hormonally regulated changes in biophysical properties. Cervical mucus can thicken to prevent ascension of sperm into the upper reproductive tract or thin to permit fertilization. Current reproductive studies of mucus viscoelastic properties rely on subjective visual appraisal of cervical mucus changes. Our goal was to use particle tracking microrheology (PTMR) to objectively assess cervical mucus viscoelastic properties and associate these measurements with in vitro measures of sperm velocity. MethodsUsing cervical mucus obtained from rhesus macaques (Macaca mulatta) at necropsy, we used to PTMR to measure viscoelasticity (*) under stepwise, serial dilutions. In parallel we measure sperm velocity using custom sperm tracking and analysis workflows. ResultsWe report that both mucus * and sperm velocity displayed a concentration-dependent behavior, where * increased as mucus concentration increased, and sperm velocity correspondingly decreased. Viscoelasticity and sperm velocity were strongly negatively correlated (p<0.001). ConclusionsPTMR and sperm tracking in mucus provide quantitative measure of viscoelastic mucus changes. PTMR is potentially a method for quantitatively assessing fertility potential in the cervix that could be applied to both infertility and contraceptives studies.

biophysics↗

bioRxiv2025

Beyond the Axoneme: Whole-Cell Proteomics Identifies Novel Regulators of Ciliogenesis in Xenopus Epidermal Multiciliated Cells

Motile cilia generate directional fluid flow critical for development and tissue homeostasis, and their dysfunction underlies a range of human diseases. Prior proteomic studies have focused on isolated axonemes, leaving the regulatory components of ciliogenesis located in other cellular compartments of multiciliated cells (MCCs) largely unidentified. To bridge this gap, we performed whole-cell proteomic profiling of MCCs in Xenopus using an inducible system that enables selective MCC-enrichment. Leveraging a single-vessel in-cell proteomics approach with ultra-high sample preservation, we identified over 9,000 proteins, including 832 upregulated in MCCs. These encompassed both established ciliary components and novel candidates localized to distinct ciliary structures. Functional validation confirmed the involvement of previously uncharacterized proteins in ciliogenesis. This study presents a high-resolution, whole-cell proteome of vertebrate MCCs, providing critical insights into the molecular networks that govern ciliogenesis and offering a valuable resource for understanding the mechanisms of cilia-related disorders.

developmental biology↗

bioRxiv2025

A global P-Process map to avoid P-value abuse

P-abuse is serious in difference identification analysis of data. How to avoid P-abuse is a huge challenge. Here, we evolve P-value (a single value) to P-Process (a global landscape of P-values under different sample size) to help researchers correctly recognize and use p-value. We observed -ln(P-Process) after rotation has very similar morphology with Wiener Process (or Brownian motion). Based on this property, for any sample size, we estimated the 95% fluctuation range of P-value and further estimated how many samples (N95()) could make sure 95% of P-values less than the given significant level . Tests proved that the estimation obtains a good performance with only a small number of samples in each group. For broader accessibility, a free web-service, P-Process Map, is available online to show the whole landscape of P-Process. At the end of the article, we explained 10 of the most typical P-abuse problems which can be easily voided by using P-Process. This "rethinking" of P-value from a higher position, which is profoundly different from the way we have seen this for the past century, would yield a new era - 2P era in which hypothesis testing is strongly required to evolve from P-value to P-Process.

bioinformatics↗

bioRxiv2025

Identification of BET Inhibitors (BETi) Against Solitary Fibrous Tumor (SFT) Through High-Throughput Screening (HTS)

Cancers, especially fusion oncoprotein (FO)-driven hematological cancers and sarcomas, often develop from a low number of key mutations. Solitary Fibrous Tumor (SFT) is a rare mesenchymal tumor driven by the NAB2-STAT6 oncofusion gene. Currently, the treatment options for SFT remain limited, with anti-angiogenic drugs providing only partial responses and an average survival of two years. To address this challenge, we constructed SFT cell models harboring specific NAB2-STAT6 fusion transcripts using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology. High-throughput drug screens demonstrated that the BET inhibitor Mivebresib can differentially reduce proliferation in SFT cell models. Subsequently, BET inhibitors Mivebresib and BMS-986158 efficiently reduced tumor growth in an SFT patient-derived xenograft (PDX) animal model. Furthermore, our data showed that NAB2-STAT6 fusions may lead to higher levels of DNA damage in SFTs. Consequently, combining BET inhibitors with PARP (Poly (ADP-ribose) polymerase) or ATR inhibitors significantly enhanced anti-proliferative effects in SFT cells. Taken together, our study established BET inhibitors Mivebresib and BMS-986158 as promising anti-SFT agents. SignificanceNew therapies are a clinical need for patients with Solitary Fibrous Tumor. We demonstrated that BET inhibitors are highly active in the preclinical setting for the treatment of this sarcoma entity.

cancer biology↗

bioRxiv2025

Development of an image-guided non-vitrectomy subretinal access approach for trans-scleral cell and gene therapy delivery

PurposeRegenerative therapies for retinal diseases include cell and gene therapy modalities that are targeted to the subretinal space. Several recent clinical trials have shown that the morbidity of surgical access is the major limitation of safe subretinal space delivery. We aimed to develop an image-guided procedure for minimally invasive subretinal access (MISA) as a platform to deliver therapeutic agents for the treatment of degenerative retinal diseases. MethodsWe engineered prototypes of a novel common-path swept source optical coherence tomography (CP-SSOCT)-enabled needle, coaxial guide (COG), and subretinal access cannula (SAC). We pilot tested the MISA procedure in ex vivo bovine eyes and in vivo porcine ocular surgery. ResultsA- and M-mode scan recordings of ex vivo and in vivo animal eye models demonstrated that CP-SSOCT imaging from the scleral side (ab externo) was capable of identifying the retinal laminae and the sub-retinal space. We show results from in vivo porcine MISA surgeries (N=4) using the novel CP-SSOCT-enabled sub-retinal injection needle, COG, and SAC through the transscleral approach. The MISA approach enabled subretinal device placement in the posterior pole, however, cases of retinal incarceration and retinal perforation were encountered. ConclusionsWe describe a novel CP-SSOCT-guided subretinal access approach that, with further optimization, may be useful in regenerative retinal surgery.

bioengineering↗

bioRxiv2025

A pan-gene catalogue of Asian cultivated rice

The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent japonica, indica, aus, and aromatic varietal groups. The RPRP has been consistently annotated, supported by extensive experimental data and here we report the computational assignment, characterization and dissemination of stably identified pan-genes. We identified 25,178 core pan-genes shared across all cultivars, alongside cultivar-specific and family-enriched genes. Core genes exhibit higher gene expression and proteomic evidence, higher confidence protein domains and AlphaFold structures, while cultivar-specific genes were enriched for domains under selective breeding pressure, such as for disease resistance. This resource, integrated into public databases, enables researchers to explore genetic and functional diversity via a population-aware "reference guide" across rice genomes, advancing both basic and applied research.

genomics↗

bioRxiv2025

Diverse mechanisms of DDX3Y suppression by DDX3X

The DEAD-box RNA helicase DDX3X has important roles in development and disease. Loss of DDX3X during developmental and pathological processes such as tumorigenesis can lead to compensatory upregulation of the close paralog DDX3Y in males, which may underlie the sexual dimorphism displayed by some DDX3X-associated diseases. However, how DDX3X cross-regulates DDX3Y remains largely unknown. Here, we investigated the regulation of DDX3Y by DDX3X in two male-derived human cancer cell lines, HCT116 and U87MG. Depletion of DDX3X in HCT116 cells results in moderately increased DDX3Y mRNA and protein, in part due to stabilization of DDX3Y transcripts. Conversely, reduction of DDX3X in U87MG cells markedly upregulates DDX3Y protein without affecting its mRNA, mainly by enhancing DDX3Y protein stability. We further show that DDX3X physically interacts with DDX3Y. DDX3Y is much less stable than DDX3X in U87MG cells, and substitution of two lysine residues in DDX3Y with the corresponding arginine in DDX3X stabilizes DDX3Y. Thus, the compensatory upregulation of DDX3Y following DDX3X loss can occur at either transcript or protein level, suggesting complex and cell type-specific cross-regulation between these X- and Y-linked paralogs to keep the total DDX3 dosage in check.

biochemistry↗

bioRxiv2025

IQI: Individualized Quantitative trait loci (QTL) Index

There is currently no standard efficient method to precisely detecting and characterizing the difference of quantitative trait loci (QTL) effect among groups and/or populations at individual level. The main reason is that the traditional global regression based QTL analyses can only derive an overall effect of genetic variants on the quantitative trait in a specific group. It is a big challenge to obtain the individual-level QTL effect, which is necessary for accurate testing and precise characterization. Here, we first proposed an individualized QTL index (IQI) that represents the degree of regulation between genetic variants and the trait for each individual. Based on IQI, Differential QTL (DQ) analysis framework was presented to accurately detect the case-control differences in more detail. In addition, IQI can be a new feature/biomarker applied to various accurate bioinformatics analysis, such as differential analysis, disease prediction, and survival analysis. Overall, IQI affords a new perspective on pathogenic mechanisms and will facilitate the study of genetic regulation more detailedly and precisely.

bioinformatics↗

bioRxiv2024

Evaluation of subretinally delivered Cas9 ribonucleoproteins in murine and porcine animal models highlights key considerations for therapeutic translation of genetic medicines

Genetic medicines, including CRISPR/Cas technologies, extend tremendous promise for addressing unmet medical need in inherited retinal disorders and other indications; however, there remain challenges for the development of therapeutics. Herein, we evaluate genome editing by engineered Cas9 ribonucleoproteins (eRNP) in vivo via subretinal administration using mouse and pig animal models. Subretinal administration of adenine base editor and double strand break-inducing Cas9 nuclease eRNPs mediate genome editing in both species. Editing occurs in retinal pigmented epithelium (RPE) and photoreceptor cells, with favorable tolerability in both species. Using transgenic reporter strains, we determine that editing primarily occurs close to the site of administration, within the bleb region associated with subretinal injection. Our results show that subretinal administration of eRNPs in mice mediates base editing of up to 12% of the total neural retina, with an average rate of 7% observed at the highest dose tested. In contrast, a substantially lower editing efficiency was observed in minipigs; even with direct quantification of only the treated region, a maximum base editing rate of 1.5%, with an average rate of <1%, was observed. Our data highlight the importance of species consideration in translational studies for genetic medicines targeting the eye and provide an example of a lack of translation between small and larger animal models in the context of subretinal administration of Cas9 eRNPs.

pharmacology and toxicology↗

bioRxiv2024

Genetically Labeled Premyelinating Oligodendrocytes: Bridging Oligodendrogenesis and Neuronal Activity

To myelinate axons, oligodendrocyte precursor cells (OPCs) must stop dividing and differentiate into premyelinating oligodendrocytes (preOLs). PreOLs are thought to survey and begin ensheathing nearby axons, and their maturation is often stalled at human demyelinating lesions. Lack of genetic tools to visualize and manipulate preOLs has left this critical differentiation stage woefully understudied. Here, we generated a knock-in mouse line that specifically labels preOLs across the central nervous system. Genetically labeled preOLs exhibit distinct morphology, unique transcriptomic and electrophysiological features, and do not overlap with OPCs. PreOL lineage tracing revealed that subsets of them undergo prolonged maturation and that different brain regions initiate oligodendrogenesis with the spatiotemporal specificity. Lastly, by fate mapping preOLs under sensory deprivation, we find that neuronal activity functions within a narrow time window of preOL maturation to promote their survival and successful integration. Our work provides a new tool to probe this critical cell stage during axon ensheathment, allowing for fine dissection of axon-oligodendrocyte interactions.

neuroscience↗

bioRxiv2024

Acidic Conditions Promote Clustering of Cancer Cell Derived Extracellular Vesicles and Enhance their Fusion with Synthetic Liposomes

Extracellular vesicles (EVs) are endogenous vesicles secreted by cells. Exosomes, a subset of EVs ranging from 30 to 150 nanometers in diameter, contain cytosolic proteins, gene-silencing miRNA, and gene-encoding mRNA and have roles in intercellular communication. Exosomes show promise as cancer chemotherapeutic drug delivery vehicles given their low immunogenicity and cell-specific delivery of luminal contents to the cytosol of target cells. However, loading exosomes with cancer chemotherapeutic drugs is inefficient, which limits their therapeutic application. To overcome this barrier, methods have been developed which allow fusion of EVs with synthetic liposomes preloaded with therapeutic drug. While these methods show more efficient fusion than passive incubation of EVs with liposomes, they risk either damage to the membrane proteins of the EVs or contamination of the final EV-liposome hybrid with residual depletant molecules, which can cause side effects or hinder content delivery. Here, we present a new, weakly perturbative method which uses acidic conditions (pH 5) to significantly enhance the fusion of EVs and synthetic, neutral liposomes (NLs) compared to passive incubation in pH 7.4 at 37 {degrees}C. An adapted Forster resonance energy transfer (FRET) based lipid mixing assay confirms that fusion is enhanced with this method. This significant finding implies that lipid-only synthetic liposomes are able to fuse with EVs, creating EV-liposome hybrids under relevant temperature and pH conditions, with no other non-lipidic component, such as fusogenic amphipathic peptides, added to the synthetic liposomes. Remarkably, differential interference contrast (DIC) and fluorescence microscopy show that this enhancement of fusion corresponds with the onset of clustering of mixtures of EVs and NLs, or EVs alone, in acidic but not neutral pH conditions. The findings support a hypothesis that content release from EVs in early to late endocytic environment may be a combination of protein-protein clustering interactions and a lipidic component. Further, this study provides a novel method for enhanced fusion of EVs and liposomes which is expected to preserve EV membrane proteins and functionality towards the development of therapeutic hybrid drug delivery vehicles in nanomedicine applications.

biophysics↗

bioRxiv2024

In vitro inhibition of the CFTR ion channel in the cervix thickens cervical mucus

Cervical mucus changes throughout the menstrual cycle in response to hormonal fluctuations, regulating access of sperm and pathogens to the reproductive tract. CFTR is an anion channel that plays a critical role in mediating epithelial mucus secretions. Primary endocervical cells obtained from rhesus macaques Macaca mulatta were cultured using conditional reprogramming and treated with vehicle controls or CFTR inhibitors. In order to measure changes in hydration and viscosity of secreted mucus, we adapted two airway mucus assays, airway surface liquid and particle-tracking microrheology, for our endocervical culture system. Endocervical cells treated with CFTR inhibitors demonstrated dehydrated, thicker mucus secretions compared to controls in both assay outputs. Our studies suggest that CFTR may be an important mediator of fertility changes and provide experimental evidence for the infertility phenotype seen in women with cystic fibrosis. Additionally, assays developed in these studies provide new endpoints for assessing cervical mucus changes in vitro. Summary SentenceInhibition of CFTR, a key epithelial ion channel in primary endocervical cells leads to dehydrated, thickened mucus production in vitro

cell biology↗

bioRxiv2024

An integrative proteotranscriptomics approach reveals new ADAM9 substrates and downstream pathways

The disintegrin metalloprotease ADAM9 is a cell-surface protease that can shed the ectodomain of membrane protein substrates. Dysregulated ADAM9 activity has been implicated in several diseases such as solid tumors, autoimmunity, inflammatory diseases, and COVID-19. Despite its importance, the substrates and targets of ADAM9 in normal and pathological processes are poorly understood. Here, we developed an integrative proteotranscriptomics approach to systematically identify the transcriptional and post-transcriptional targets of ADAM9 in HCT116 cells, which have a stable diploid karyotype suitable for omics analyses. Using this approach, we uncovered major signaling pathways downstream of ADAM9, including the oncogenic mTOR pathway and the tumor suppressor FOXO pathway. We also identified several direct and indirect substrates for ADAM9, which may mediate the pathophysiological roles of this protease. This study provides new mechanistic insights into the function of ADAM9 as well as a method that can be applied to other membrane proteases.

biochemistry↗

bioRxiv2024

Identification and characterization of ugpE required for the full virulence of Streptococcus suis

Streptococcus suis (S. suis) is an emerging zoonotic pathogen that threatens both animal and human health worldwide. UgpE is a protein subunit of the Ugp (uptake of glycerol phosphate) transporter system that is involved in glycerophospholipid synthesis in bacterial membranes. In this study, an ugpE deletion mutant was constructed and the effects of ugpE deletion on cell morphology, biofilm formation, and virulence were investigated. Deletion of ugpE did not affect bacterial growth but impaired cell chain formation and capsular synthesis by downregulating the mRNA levels of the capsular regulon genes cps-2B, cps-2C, and cps-2S. Deletion of ugpE also led to decreased tolerance to heat, oxidative, and acid-base stress. Crystal violet staining and scanning electron microscopy demonstrated ugpE negatively regulated biofilm formation in liquid culture and the rdar biofilm morphotype on agar plates. Moreover, ugpE deletion not only reduced hemolysin activity, survival in whole human blood, and anti-phagocytosis ability against porcine alveolar macrophages (PAM) but also enhanced bacterial adhesion and invasion of human cerebral microvascular endothelial cells (hCMEC/D3) by upregulating the expression of multiple genes associated with cell adhesion. In a mouse infection model, ugpE deletion significantly attenuated virulence and lowered the number of viable bacteria in the blood and major organs, as well as distribution of macrophages. In conclusion, this study identified UgpE as a novel virulence factor that plays a pivotal role in the regulation of virulence and biofilm formation of S. suis.

microbiology↗

bioRxiv2024

Age-related decline of PKA-RIIβ level in SNc dopaminergic neurons underlies PD pathogenesis

The cyclic-AMP dependent protein kinase A (Protein kinase A, PKA) regulates dopaminergic function in the substantia nigra pars compacta (SNc). However, whether PKA is involved in the pathogenesis of Parkinsons disease (PD) is unknown. Here, by collecting and analyzing the current worldwide SNc transcriptomic datasets of PD patients, we found a decline of PKA-RII{beta} subunit level in the SNc of PD patients. The decreased PKA-RII{beta} subunit level was positively correlated with decreased dopamine synthesis and increased oxidative stress in the SNc of PD patients. PKA-RII{beta} subunit is expressed in the striatum and the SNc. PKA-RII{beta} gene knockout mice (RII{beta}-KO) showed a age-related parkinsonism at 12 months of age. Using Cre-LoxP system, we observed that RII{beta} re-expression in the SNc dopaminergic neurons rescued parkinsonism of RII{beta}-KO mice. RII{beta} re-expression in striatal neurons did not affect parkinsonism of RII{beta}-KO mice. The spontaneous parkinsonism could be developed in 12-month-old SNc dopaminergic neuron-specific RII{beta}-deficient mice. Single-nucleus RNA sequencing revealed decreased PKA activity, reduced dopamine synthesis and raised oxidative stress in the SNc dopaminergic neurons of RII{beta}-KO mice. Adeno-associated virus (AAV)-mediated gene therapy targeting PKA-RII{beta} in the SNc dopaminergic neurons rescued parkinsonism in PD mouse model. Taken together, these findings indicate that PKA-RII{beta} may be a key factor of human genetic etiologies of PD. The therapy targeting PKA-RII{beta} in the SNc dopaminergic neurons may be promising for PD treatment.

neuroscience↗

bioRxiv2024

Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings

Cellular electrophysiology is the foundation of many fields, from basic science in neurology, cardiology, oncology to safety critical applications for drug safety testing, clinical phenotyping, etc. Patch-clamp voltage clamp is the gold standard technique for studying cellular electrophysiology. Yet, the quality of these experiments is not always transparent, which may lead to erroneous conclusions for studies and applications. Here, we have developed a new computational approach that allows us to explain and predict the experimental artefacts in voltage-clamp experiments. The computational model captures the experimental procedure and its inadequacies, including: voltage offset, series resistance, membrane capacitance and (imperfect) amplifier compensations, such as series resistance compensation and supercharging. The computational model was validated through a series of electrical model cell experiments. Using this computational approach, the artefacts in voltage-clamp experiments of cardiac fast sodium current, one of the most challenging currents to voltage clamp, were able to be resolved and explained through coupling the observed current and the simulated membrane voltage, including some typically observed shifts and delays in the recorded currents. We further demonstrated that the typical way of averaging data for current-voltage relationships would lead to biases in the peak current and shifts in the peak voltage, and such biases can be in the same order of magnitude as those differences reported for disease-causing mutations. Therefore, the presented new computational pipeline will provide a new standard of assessing the voltage-clamp experiments and interpreting the experimental data, which may be able to rectify and provide a better understanding of ion channel mutations and other related applications.

systems biology↗

bioRxiv2024

dsRNAEngineer: a web-based tool of comprehensive dsRNA design for pest control

RNA interference (RNAi) is a form of gene silencing triggered by double-stranded RNA (dsRNA) that operates in all eukaryotic organisms, including insects, mites, nematodes and fungi. In the last two decades, many dsRNAs have been synthesized to silence the target genes for exploration of the underlying function in these pests. Some of them are lethal to pests or inhibit the growth of the pest population, leading to a new concept of pesticides. The generation of these environment-friendly pesticides requires precise in silico design of dsRNA molecules that are specific to target pests but do not target non-pest organisms. Current efforts for dsRNA design are mostly focused on gene sequence level, lacking comprehensive analysis of RNAi-based mode-of-action at the whole transcriptome level of given species, causing low efficiency and imprecise dsRNA target exploration. To address these limitations, we have created dsRNAEngineer, a publicly available online tool that allows a comprehensive and rational dsRNA design, incorporating hundreds of pests and non-pests transcriptomes. Developed functionalities include screen-target (screen conserved genes for co-targets of various pest species), on-target, off-target, and multi-target to generate optimal dsRNA for precise pest control. dsRNAEngineer is available at https://dsrna-engineer.cn/. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/604585v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@9ee7fdorg.highwire.dtl.DTLVardef@90b015org.highwire.dtl.DTLVardef@11857eborg.highwire.dtl.DTLVardef@1340f18_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗