Biology subjects

Feng, Q.

Publications and source records attributed to Feng, Q..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

MNetClass: A Control-Free Microbial Network Clustering Framework for Identifying Central Subcommunities Across Ecological Niches

Investigating microbiome subnetworks and identifying central microbes in specific ecological niches is a critical issue in human microbiome studies. Traditional methods typically require control samples, limiting the ability to study microbiomes at distinct body sites without matched controls. Moreover, some clustering methods are not well-suited for microbial data and fail to identify central subcommunities across ecological niches after clustering. In this study, we present MNetClass, a novel microbial network clustering analysis framework. It utilizes a random walk algorithm and a rank-sum ratio-entropy weight evaluation model to classify key subnetworks and identify central microbes at any body site without the need for control samples. By applying MNetClass to microbiome data from five distinct oral sites, we successfully uncovered site-specific microbial subgroups and their central microbes. Additionally, simulations and Autism Spectrum Disorder (ASD) cohort datasets demonstrated that MNetClass outperforms existing unsupervised microbial clustering methods in terms of both accuracy and predictive power. In case studies, MNetClass identified age-related microbial communities across different oral sites, highlighting its broad applicability in microbiome research. IMPORTANCEMNetClass provides a valuable tool for microbiome network analysis, enabling the identification of key microbial subcommunities across diverse ecological niches. Implemented as an R package (https://github.com/YihuaWWW/MNetClass), it offers broad accessibility for researchers. Here, we systematically benchmarked MNetClass against existing microbial clustering methods across multiple datasets using various performance metrics, demonstrating its superior efficacy. Notably, MNetClass operates without the need for control groups and effectively identifies central microbes, highlighting its potential as a robust framework for advancing microbiome research.

bioinformatics↗

bioRxiv2025

Berberrubine Inhibits Helicobacter pylori by Inducing Oxidative Stress

Helicobacter pylori is a prevalent pathogen that colonizes the pylorus and contributes to the pathogenesis of gastric cancer. The increasing antibiotic resistance in H. pylori presents a substantial challenge for effective eradication, making the development of more effective therapeutic strategies imperative. In this study, we screened 37 pure compounds (purity >95%), 3 ethanol extracts, and 6 aqueous extracts from 6 different medicinal herbs for their potential inhibitory effects against H. pylori in vitro. Among the tested compounds, 15 exhibited inhibitory activity, with berberrubine demonstrating the strongest effect, characterized by a minimum inhibitory concentration (MIC) of 0.011 mg/ml. The comparative transcriptome analysis revealed a significant upregulation of the oxidative stress response related genes, such as fumC and sodB, in H. pylori treated with berberrubine. Further in vitro assays confirmed that berberrubine exerted antibacterial activity by stimulating oxidative stress, as evidenced by increased reactive oxygen species (ROS) production and impaired cell membrane integrity. Additionally, similar inhibitory tests were applied to Escherichia coli, a common gut opportunistic pathogen. The results showed that berberrubine inhibited E. coli through the same mechanism observed for H. pylori. In conclusion, berberrubine is a potent antibacterial agent against gastrointestinal pathogens, including H. pylori and E. coli, making it a promising candidate for further development as an antimicrobial therapeutic ImportanceThis study identified berberrubine as a potent antibacterial agent against gastrointestinal pathogens, including Helicobacter pylori and Escherichia coli by inducing cellular oxidative stress. Through increased reactive oxygen species (ROS) production and disruption of bacterial cell membrane integrity, berberrubine demonstrated strong efficacy in inhibiting drug-resistant pathogens. These findings highlight its potential as a promising therapeutic candidate for eradicating drug-resistant gastrointestinal pathogens.

microbiology↗

bioRxiv2025

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200-300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X is also applicable to non-hepatic tissues such as brain and colon, and can be modified to perform spatial proteomic analysis, simultaneously profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. These findings establish Seq-Scope-X as a transformative tool for ultra-high-resolution whole-transcriptome and proteome profiling, offering unparalleled spatial precision and advancing our understanding of cellular architecture, function, and disease mechanisms.

genomics↗

bioRxiv2025

METTL3 Aggravates Intimal Hyperplasia by Facilitating the m6A-YTHDC1-dependent SGK1 Gene Transcription

BackgroundVascular smooth muscle cell (VSMC) migration and proliferation substantially contribute to neointimal hyperplasia related to in-stent restenosis. N6-methyladenosine (m6A) catalyzed by the methyltransferase-like 3 (METTL3)-involved methyltransferase complex is the most abundant RNA epigenetic modification in eukaryotes, but the role of m6A RNA methylation in VSMC migration and proliferation as well as neointima formation remains highly controversial. MethodsPrimary human and rat VSMCs were utilized for in vitro experiments. VSMC-specific METTL3 knockout mice (Mettl3flox/floxMyh11-CreERT2) were generated to explore wire injury in carotid arteries in vivo. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) was performed to screen for target genes by METTL3-catalyzed m6A RNA methylation. Methylation site mapping, MeRIP-quantitative PCR (MeRIP-qPCR), chromatin immunoprecipitation-qPCR (ChIP-qPCR) and reporter gene assays were applied to explore how METTL3 modulates its target gene expression. ResultsMETTL3 was consistently upregulated in the neointima from mice subjected to carotid wire injury and patients undergoing carotid endarterectomy. VSMC-specific METTL3 deficiency significantly attenuated neointima formation in carotid arteries following wire injury in mice. Accordingly, METTL3 ablation markedly repressed VSMC proliferation both in vitro and in vivo. Mechanistically, METTL3 directly catalyzed m6A methylation on serum/glucocorticoid regulated kinase 1 (SGK1) mRNA and subsequently facilitated its transcription, which relies on the established association between the SGK1 transcript and SGK1 promoter DNA by recruiting the m6A reader YTHDC1. Conversely, SGK1 overexpression abolished METTL3 deficiency-mediated suppression of VSMC proliferation and postinjury neointima formation. ConclusionsMETTL3-catalyzed m6A RNA methylation promoted VSMC proliferation and aggravated postinjury neointima formation by facilitating YTHDC1-dependent SGK1 gene transcription. Targeting the METTL3-YTHDC1-SGK1 axis to modulate VSMC proliferation may be a potential strategy for in-stent restenosis therapy.

molecular biology↗

bioRxiv2024

Motor Clustering Enhances Kinesin-driven Vesicle Transport

Intracellular vesicles are typically transported by a small number of kinesin and dynein motors. However, the slow microtubule binding rate of kinesin-1 observed in in vitro biophysical studies suggests that long-range transport may require a high number of motors. To address the discrepancy in motor requirements between in vivo and in vitro studies, we reconstituted motility of 120-nm-diameter liposomes driven by multiple GFP-labeled kinesin-1 motors. Consistent with predictions based on previous binding rate measurements, we found that long-distance transport requires a high number of kinesin-1 motors. We hypothesized that this discrepancy from in vivo observations may arise from differences in motor organization and tested whether motor clustering can enhance transport efficiency using a DNA scaffold. Clustering just three motors improved liposome travel distances across a wide range of motor numbers. Our findings demonstrate that, independent of motor number, the arrangement of motors on a vesicle regulates transport distance, suggesting that differences in motor organization may explain the disparity between in vivo and in vitro motor requirements for long-range transport. Significance StatementIntracellular vesicles frequently travel long distances, despite having few kinesin and dynein motors. By reconstituting liposome motility with kinesin-1 motors, we demonstrate the need for high motor copy numbers for long-range transport when motors are randomly distributed on the liposome surface. We further show that motor clustering reduces the required motor number, emphasizing its potential role in enhancing transport efficiency. Our findings highlight the significance of motor organization in regulating intracellular transport and suggest that motor clustering, such as by scaffolding proteins or lipid domains, influences bidirectional transport outcomes.

biophysics↗

bioRxiv2024

DeepSME: De Novo Nanopore Basecalling of Motif-insensitive DNA Methylation and Alignment-free Digital Information Decryptions at Single-Molecule Level

Hidden messages in DNA molecules by employing chemical modifications has been suggested for private data storage and transmission at high information density. However, rapidly decoding these "molecular keys" with corresponding basecallers remains challenging. We present DeepSME, a nanopore sequencing and deep-learning based framework towards single-molecule encryption, demonstrated by using 5-hydroxymethylcytosine (5hmC) substitution for individual nucleotide recognition rather than sequential interactions. This non-natural, motif-insensitive methylation disrupts ion current, resulting in a readout failure of 67.2%-100%, concealing the privacy within the DNAs. We further develop an alignment-free DeepSME basecaller as a key to reconstitute the digital information. Our three-stage training pipeline, expands k-mer size from 46 to 49, achieving over 92% precision and recall from scratch. DeepSME deciphers fully 5hmC concealed text and image within 16x coverage depth with an F1-score of 86.4%, surpassing all the state-of-the-art basecallers. Demonstrated on edge computing devices, DeepSME holds supreme potential for DNA-based private communications and broader bioengineering and medical applications.

bioinformatics↗

bioRxiv2024

Channel width modulates the permeability of DNA origami based nuclear pore mimics

Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importin-{beta}1 substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.

biophysics↗

bioRxiv2024

NK Cell Exhaustion in Wilson's Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis

Metabolic abnormalities associated with liver disease have a significant impact on the risk and prognosis of cholecystitis. However, the underlying mechanism is complicated and remains to be elucidated. In particular, the effect of metabolic abnormalities on the progression of cholecystitis through the regulation of immune cell function is poorly understood. In this study, we investigated this issue using Wilsons disease (WD) as a model. Wilsons disease is a genetic disorder characterized by impaired mitochondrial function and abnormal copper metabolism. Our retrospective clinical study of over 600 patients with WD found that they have a significantly higher incidence of cholecystitis and a poorer prognosis. The immune cell landscape in the hepatic mesenchymal stromal microenvironment of WD patients was shown using single-cell RNA. A major change is the constitution and function of the innate immune system, including enhanced antigen presentation process, activation of the immune response, and activation of lymphocytes. The proportion of mononuclear phagocytes and natural killer (NK) cells is increased, and the primary characteristic and function of macrophage, Kupffer cell, neutrophil, and NK cell are altered. Exhaustion of NK cell is the fundamental factor, supported by an increase in the expression of the inhibitory receptors KLRC1 and TIGIT and a decrease in the expression of cytotoxic molecules. Clinical tissue and blood samples verified increased KLRC1+ and TIGIT+ NK cells and decreased IFN{gamma}+ NK cells in WD. Further bioinformatic analysis has confirmed a positive correlation between NK cell exhaustion and poor prognosis in cholecystitis and other inflammatory diseases. The study demonstrated abnormal function of liver mesenchymal immune cells triggered by specific metabolic dysfunction in WD, with a focus on the correlation between NK cell exhaustion and poor healing of cholecystitis. Our findings highlight the immune cell dysfunction due to metabolic changes in hepatocytes and provide new insights into the improvement of inflammatory diseases by assessing immune cell function.

immunology↗

bioRxiv2024

P66 is a bacterial mimic of CD47 that binds the anti-phagocytic receptor SIRPα and facilitates macrophage evasion by Borrelia burgdorferi

Summary ParagraphInnate immunity, the first line of defense against pathogens, relies on efficient elimination of invading agents by phagocytes. In the co-evolution of host and pathogen, pathogens developed mechanisms to dampen and evade phagocytic clearance. Here, we report that bacterial pathogens can evade clearance by macrophages through mimicry at the mammalian anti-phagocytic "dont eat me" signaling axis between CD47 (ligand) and SIRP (receptor). We identified a protein, P66, on the surface of Borrelia burgdorferi that, like CD47, is necessary and sufficient to bind the macrophage receptor SIRP. Expression of the gene encoding the protein is required for bacteria to bind SIRP or a high-affinity CD47 reagent. Genetic deletion of p66 increases phagocytosis by macrophages. Blockade of P66 during infection promotes clearance of the bacteria. This study demonstrates that mimicry of the mammalian anti-phagocytic protein CD47 by B. burgdorferi inhibits macrophage-mediated bacterial clearance. Such a mechanism has broad implications for understanding of host-pathogen interactions and expands the function of the established innate immune checkpoint receptor SIRP. Moreover, this report reveals P66 as a novel therapeutic target in the treatment of Lyme Disease.

immunology↗

bioRxiv2024

Effect of Electroacupuncture Pretreatment on Cognitive Impairment and Mitophagy in Aging Model Rats and its mechanism

ObjectiveInvestigate the effects of "Shuanggu Yitong" EA pretreatment on cognitive impairment, mitochondrial function, and mitophagy in aging model rats, and to analyze the related mechanisms. MethodsForty 3-month-old male SD rats were randomly divided into a blank group, a model group, an EA group, and a sham EA group, with 10 rats in each group. And the Morris water maze test was performed after the intervention. HE staining, to observe the morphological changes of the hippocampus of the model rats. Nissl staining was used to observe the changes in the number of hippocampal neurons in rats, Western Blotting (WB) was used to observe the expression of endogenous PTEN-induced hypothetical kinase 1 (PINK1) and human Parkinsons protein 2 (Parkin) in the hippocampus, spectrophotometry was employed to detect the activity of respiratory chain complex I in the hippocampus of the model rats, and flow cytometry was utilized to detect hippocampal mitochondrial membrane potential (MMP) and hippocampal mitochondrial permeability transition pore (MPTP) opening. Results"Shuanggu Yitong" EA pretreatment relieved the cognitive impairment induced by D-galactose in subacute aging model rats. The mechanism of "Shuanggu Yitong" EA pretreatment in the improvement of cognitive impairment of subacute aging model rats may be related to the enhancement of Pink1/Parkin mediated mitophagy and the timely removal of accumulated abnormal mitochondria, thus improving mitochondrial function. Conclusion"Shuanggu Yitong" EA pretreatment can significantly improve the cognitive impairment induced by D-galactose in subacute aging model rats.

cell biology↗

bioRxiv2024

Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data

Single-cell RNA sequencing (scRNA-seq) technologies have been widely used to characterize cellular landscapes in complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked in the initial clustering step, making them difficult to distinguish. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate rare cell types and achieve accurate identification. We benchmark scCAD on 25 real-world scRNA-seq datasets, demonstrating its superior performance compared to 10 state-of-the-art methods. In-depth case studies across diverse datasets, including mouse airway, brain, intestine, human pancreas, immunology data, and clear cell renal cell carcinoma, showcase scCADs efficiency in identifying rare cell types in complex biological scenarios. Furthermore, scCAD can correct the annotation of rare cell types and identify immune cell subtypes associated with disease, providing new insights into disease progression.

bioinformatics↗

bioRxiv2024

Large-scale multi-omics analyses identified root-microbiome associations underlying plant nitrogen nutrition

The microbiome determines the performance and fitness of the host plant. Nevertheless, the causal interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here we generated 1,341 paired root transcriptome, rhizosphere microbiome and root ionome samples and performed a multi-omics analyses of the host-microbe association at the root-soil interface using 175 rapeseeds (Brassica napus L.) resequenced ecotypes at two field environments. We observed the highest statistically explained variance for root nitrogen uptake among natural ionomic variation by overall transcriptome-wide gene expression and microbial abundance variation. Moreover, we identified significant genome-wide associations for 203 highly heritable amplicon sequence variants (ASVs) at multiple genetic loci regulated by eQTL hotspots associated with nitrogen metabolism components. These associations involved a central bacterial genus (Sphingopyxis), which plays a dominant role on gene regulatory effect on its variation regulated by eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected Sphingopyxis to whole genome sequencing. Finally, targeted metabolite profiling and confocal imaging assays demonstrated a host-microbiome regulatory effect on Sphingopyxis established by lateral root development and plant nitrogen nutrition. In summary, our integrative approach reveals the genetic basis of host-microbiome trait associations in the transcriptional, nutritional and environmental domains and suggests that the microbiome might have causal effects on root development with implications towards the breeding of nutrient-efficient crops.

plant biology↗

bioRxiv2023

A paradoxical population structure of var DBLα types in Africa

The var multigene family encodes the P. falciparum erythrocyte membrane protein 1 (PfEMP1), which is important in host-parasite interaction as a virulence factor and major surface antigen of the blood stages of the parasite, responsible for maintaining chronic infection. Whilst important in the biology of P. falciparum, these genes (50 to 60 genes per parasite genome) are routinely excluded from whole genome analyses due to their hyper-diversity, achieved primarily through recombination. The PfEMP1 head structure almost always consists of a DBL-CIDR tandem. Categorised into different groups (upsA, upsB, upsC), different head structures have been associated with different ligand-binding affinities and disease severities. We study how conserved individual DBL types are at the country, regional, and local scales in Sub-Saharan Africa. Using publicly-available sequence datasets and a novel ups classification algorithm, cUps, we performed an in silico exploration of DBL conservation through time and space in Africa. In all three ups groups, the population structure of DBL types in Africa consists of variants occurring at rare, low, moderate, and high frequencies. Non-rare variants were found to be temporally stable in a local area in endemic Ghana. When inspected across different geographical scales, we report different levels of conservation; while some DBL types were consistently found in high frequencies in multiple African countries, others were conserved only locally, signifying local preservation of specific types. Underlying this population pattern is the composition of DBL types within each isolate DBL repertoire, revealed to also consist of a mix of types found at rare, low, moderate, and high frequencies in the population. We further discuss the adaptive forces and balancing selection, including host genetic factors, potentially shaping the evolution and diversity of DBL types in Africa.

genetics↗

bioRxiv2023

Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain

Multivalent antigen display on nanoparticles can enhance the immunogenicity of nanovaccines targeting viral moieties, such as the receptor binding domain (RBD) of SARS-CoV-2. However, particle morphology and size of current nanovaccines are significantly different from those of SARS-CoV-2. Additionally, surface antigen patterns are not controllable to enable the optimization of B cell activation. Herein, we employed an icosahedral DNA origami (ICO) as a display particle for SARS-CoV-2 RBD nanovaccines. The morphology and diameter of the particles were close to those of the virus (91 {+/-} 11 nm). The surface addressability of the DNA origami permitted facile modification of the ICO surface with numerous RBD antigen clusters (ICO-RBD) to form various antigen patterns. Using an in vitro screening system, we demonstrate that the antigen spacing, antigen copies within clusters and cluster number parameters of the surface antigen pattern all impact the ability of the nanovaccines to activate B cells. Importantly, the optimized ICO-RBD nanovaccines evoked stronger and more enduring humoral and T cell immune responses in mouse models compared to soluble RBD antigens. Our vaccines activated similar humoral immunity and slightly stronger cellular immunity compared to mRNA vaccines. These results provide reference principles for the rational design of nanovaccines and exemplify the utility of DNA origami as a display platform for vaccines against infectious disease.

bioengineering↗

bioRxiv2023

Proteome-Wide Association Studies for Blood Lipids and Comparison with Transcriptome-Wide Association Studies

Blood lipid traits are treatable and heritable risk factors for heart disease, a leading cause of mortality worldwide. Although genome-wide association studies (GWAS) have discovered hundreds of variants associated with lipids in humans, most of the causal mechanisms of lipids remain unknown. To better understand the biological processes underlying lipid metabolism, we investigated the associations of plasma protein levels with total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL), and low-density lipoprotein cholesterol (LDL) in blood. We trained protein prediction models based on samples in the Multi-Ethnic Study of Atherosclerosis (MESA) and applied them to conduct proteome-wide association studies (PWAS) for lipids using the Global Lipids Genetics Consortium (GLGC) data. Of the 749 proteins tested, 42 were significantly associated with at least one lipid trait. Furthermore, we performed transcriptome-wide association studies (TWAS) for lipids using 9,714 gene expression prediction models trained on samples from peripheral blood mononuclear cells (PBMCs) in MESA and 49 tissues in the Genotype-Tissue Expression (GTEx) project. We found that although PWAS and TWAS can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p-values across all the genes, which suggests a high-level consistency between proteome-lipid associations and transcriptome-lipid associations.

genomics↗

bioRxiv2023

SMB controls decompartmentalization in Arabidopsis root cap cells to execute programmed cell death

Programmed cell death (PCD) is a fundamental cellular process crucial to development, homeostasis, and immunity in multicellular eukaryotes. In contrast to our knowledge on the regulation of diverse animal cell death subroutines, information on execution of PCD in plants remains fragmentary. Here we make use of the accessibility of the Arabidopsis thaliana root cap to visualize the execution process of developmentally controlled PCD. We identify a succession of selective decompartmentalization events and ion fluxes that are controlled by a gene regulatory network downstream of the NAC transcription factor SOMBRERO (SMB). Surprisingly, breakdown of the large central vacuole is a relatively late and variable event, preceded by an increase of intracellular calcium levels and acidification, release of mitochondrial matrix proteins, leakage of nuclear and endoplasmic reticulum lumina, and release of fluorescent membrane reporters into the cytosol. Elevated intracellular calcium levels and acidification are sufficient to trigger cell death execution specifically in cells that are rendered competent to undergo PCD by SMB activity, suggesting that these ion fluxes act as PCD-triggering signals.

plant biology↗

bioRxiv2023

DCBLD1 modulates angiogenesis by regulating of the VEGFR-2 endocytosis in endothelial cells

ObjectiveUnwanted angiogenesis is involved in the progression of various malignant tumors and cardiovascular diseases, and the factors that regulate angiogenesis are potential therapeutic targets. We tested the hypothesis that DCBLD1 (Discoidin, CUB, and LCCL domain-containing protein 1) is a co-receptor of VEGFR-2 and modulates angiogenesis in endothelial cells(ECs). Approach and ResultsA carotid artery ligation model and retinal angiogenesis assay were used to study angiogenesis using globe knockout or EC-specific conditional DCBLD1 knockout mice in vivo. Immunoblotting, immunofluorescence staining, plasma-membrane subfraction isolation, Co-immunoprecipitation and mass-spectrum assay were performed to clarify the molecular mechanisms.Loss of DCBLD1 impaired VEGF response and inhibited VEGF-induced EC proliferation and migration. DCBLD1 deletion interfered with adult and developmental angiogenesis. Mechanistically, DCBLD1 bound to VEGFR-2 and regulated the formation of VEGFR-2 complex with negative regulators: protein tyrosine phosphatases, E3 ubiquitin ligases(Nedd4 and c-Cbl), and also DCBLD1 knockdown promoted lysosome-mediated VEGFR-2 degradation in ECs. ConclusionsThese findings demonstrated the essential role of endothelial DCBLD1 in regulating VEGF signaling and provided evidence that DCBLD1 promotes VEGF-induced angiogenesis by limiting the dephosphorylation, ubiquitination, and lysosome degradation after VEGFR-2 endocytosis. We proposed that endothelial DCBLD1 is a potential therapeutic target for ischemic cardiovascular diseases by the modulation of angiogenesis through regulating of the VEGFR-2 endocytosis.

molecular biology↗

bioRxiv2023

U1 AMO (antisense morpholino oligos) disrupts U1 snRNP structure to promote intronic PCPA (premature cleavage and polyadenylation)

Functional depletion of U1 snRNP with a 25 nt U1 AMO (antisense morpholino oligonucleotides) may lead to intronic premature cleavage and polyadenylation (PCPA) of thousands of genes, a phenomenon known as U1 snRNP telescripting; however, the underlying mechanism remains elusive. In this study, we demonstrated that U1 AMO could disrupt U1 snRNP structure both in vitro and in vivo, thereby affecting U1 snRNP/RNAP polymerase II (RNAPII) interaction. We further showed that U1 AMO treatment might promote RNAPII disassociation with pre-mRNA in an RNA pull-down assay. By performing ChIP-seq for phosphorylation of Ser2 (Ser2P) and Ser5 (Ser5P) of the C-terminal domain (CTD) of RNA polymerase II (RNAPII), we showed that transcription elongation was disturbed upon U1 AMO treatment, with a particular high Ser2P signal at intronic cryptic polyadenylation sites (PASs). In addition, we showed that core 3 processing factors CPSF/CstF are involved in the processing of intronic cryptic PAS. Their recruitment accumulated toward cryptic PASs upon U1 AMO treatment, as indicated by ChIP-seq and iCLIP-seq analysis. Furthermore, we showed that most of these PCPAed transcripts could be exported to cytoplasm and have the potential to be translated. Conclusively, our data provide more insight into U1 snRNP telescripting, and suggest a common theme that modulation of transcription elongation may be an important mode for the regulation of mRNA polyadenylation.

molecular biology↗