Biology subjects

Xu, Y.

Publications and source records attributed to Xu, Y..

At least 649 records · Page 36Linked to original sources

bioRxiv2022

Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLpro

The SARS-CoV-2 virus is the causal agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19). There is an urgent need for potent, specific antiviral compounds against SARS-CoV-2. The 3C-like protease (3CLpro) is an essential enzyme for the replication of SARS-CoV-2 and other coronaviruses, and thus is a target for coronavirus drug discovery. Nearly all inhibitors of coronavirus 3CLpro reported so far are covalent inhibitors. Here, we report the development of specific, non-covalent inhibitors of 3CLpro. The most potent one, WU-04, effectively blocks SARS-CoV-2 replications in human cells with EC50 values in the 10-nM range. WU-04 also inhibits the 3CLpro of SARS-CoV and MERS-CoV with high potency, indicating that it is a pan-inhibitor of coronavirus 3CLpro. WU-04 showed anti-SARS-CoV-2 activity similar to that of PF-07321332 (Nirmatrelvir) in K18-hACE2 mice when the same dose was administered orally. Thus, WU-04 is a promising drug candidate for coronavirus treatment. One-Sentence SummaryA oral non-covalent inhibitor of 3C-like protease effectively inhibits SARS-CoV-2 replication.

microbiology↗

bioRxiv2022

Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants

Multiple BA.4 and BA.5 subvariants with R346 mutations on the spike glycoprotein have been identified in various countries, such as BA.4.6/BF.7 harboring R346T, BA.4.7 harboring R346S, and BA.5.9 harboring R346I. These subvariants, especially BA.4.6, exhibit substantial growth advantages compared to BA.4/BA.5. In this study, we showed that BA.4.6, BA.4.7, and BA.5.9 displayed higher humoral immunity evasion capability than BA.4/BA.5, causing 1.5 to 1.9-fold decrease in NT50 of the plasma from BA.1 and BA.2 breakthrough-infection convalescents compared to BA.4/BA.5. Importantly, plasma from BA.5 breakthrough-infection convalescents also exhibits significant neutralization activity decrease against BA.4.6, BA.4.7, and BA.5.9 than BA.4/BA.5, showing on average 2.4 to 2.6-fold decrease in NT50. For neutralizing antibody drugs, Bebtelovimab remains potent, while Evusheld is completely escaped by these subvariants. Together, our results rationalize the prevailing advantages of the R346 mutated BA.4/BA.5 subvariants and urge the close monitoring of these mutants, which could lead to the next wave of the pandemic.

immunology↗

bioRxiv2022

Selective Androgen Receptor Modulator Microparticle Formulation Reverses Muscle Hyperalgesia in Mouse Model of Widespread Muscle Pain

Currently, there is a need for the generation of non-opioid analgesics for treating chronic pain. Preclinical and clinical studies demonstrate the analgesic effects of testosterone. However, treatment with testosterone is not feasible due to adverse effects. Selective androgen receptor modulators (SARMs) were developed to overcome these limitations by minimizing activation of androgenic side effects. First, we demonstrate SARM administration alleviates widespread muscle pain in male and female mice. We then developed a SARM-loaded PLGA microparticle formulation that reverses widespread muscle pain in two injections. In vitro and in vivo release kinetics demonstrate the microparticle formulation had sustained SARM release for 4 weeks. Antagonism of androgen receptors blocked the analgesic effects of the SARM microparticles. SARM treatment had no effect on cardiac or liver enzymes, cardiac histology, and did not produce rewarding behavior. These studies demonstrate SARM microparticles as a potential therapeutic for chronic muscle pain. One Sentence SummaryA selective androgen receptor modulator microparticle formulation alleviates widespread muscle pain in male and female mice while being non-toxic.

neuroscience↗

bioRxiv2022

A unique peptide recognition mechanism by the human relaxin family peptide receptor 4 (RXFP4)

Members of the insulin superfamily regulate a variety of biological processes through two types of target-specific but structurally conserved peptides, insulin/insulin-like growth factors and relaxin/insulin-like peptides. The latter bind to the human relaxin family peptide receptors (RXFPs), which are class A G protein-coupled receptors (GPCRs), to exert pleiotropic actions. Here, we report three cryo-electron microscopy structures of RXFP4-Gi protein complexes in the presence of the endogenous ligand insulin-like peptide 5 (INSL5) or one of the two small molecule agonists, compound 4 and DC591053, both were discovered through medicinal chemistry efforts. The B chain of INSL5 adopts a single -helix that penetrates into the orthostatic pocket, while the A chain sits above the orthosteric pocket to interact with the extracellular surface of RXFP4, revealing a unique peptide-binding mode previously unknown. Together with mutagenesis and functional analyses, the key determinants responsible for the peptidomimetic agonism and subtype selectivity were identified. DC591053 selectively mimicked the action of INSL5 at RXFP4 whereas compound 4 activated both RXFP3 and RXFP4. Comparison of peptide binding modes within the insulin superfamily displayed diverse interaction mechanisms distinct to each type of the peptides. Our findings not only provide valuable insights into ligand recognition and subtype selectivity among class A GPCRs, but also expand the knowledge of signaling mechanisms in the insulin superfamily.

molecular biology↗

bioRxiv2022

The response mechanism of oreorchis patens (Lindl.) Lindl. to cold stress

Cold stress, a major environmental factor, has an important impact on the production of landscape plants and crop yield, and its stress and resistance mechanisms have always been hot research issues. Oreorchis patens (Lindl.) Lindl., an important germplasm resource, has strong frost resistance and can resist low temperatures of -40 {degrees}C. However, the mechanism by which O. patens responds to cold stress remains poorly understood. Here, we examined the adaptation to the low-temperature environment of O. patens by changing the leaf tissue structure, while the synergistic effect of osmotic regulation, reactive oxygen scavenging and protein improved the resistance to cold stress. In addition, analysis of the photosynthetic system showed that cold stress changes the photosynthetic capacity of O. patens leaves to affect cold resistance. Analysis by nonparametric transcriptome sequencing revealed 2402 genes that were differentially expressed, most of which were related to resistance. Simultaneously, quantitative real-time polymerase chain reaction (qRT-PCR) analysis obtained results consistent with the transcriptome. These results indicated that O. patens could alter leaf structure and physiological and biochemical metabolic processes by initiating resistance-related molecular regulatory networks to improve the ability to resist cold stress. This study was the first to discuss the physiological, biochemical and molecular regulatory mechanisms of O. patens resistance to cold stress, which laid a foundation for revealing the biological and molecular mechanisms of overwintering of O. patens and breeding cold-resistant horticultural crops in northern China.

plant biology↗

bioRxiv2022

Biological condensates form percolated networks with molecular motion properties distinctly different from dilute solutions

Formation of membraneless organelles or biological condensates via phase separation hugely expands cellular organelle repertoire. Biological condensates are dense and viscoelastic soft matters instead of canonical dilute solutions. Unlike discoveries of numerous different biological condensates to date, mechanistic understanding of biological condensates remains scarce. In this study, we developed an adaptive single molecule imaging method that allows simultaneous tracking of individual molecules and their motion trajectories in both condensed and dilute phases of various biological condensates. The method enables quantitative measurements of phase boundary, motion behavior and speed of molecules in both condensed and dilute phases as well as the scale and speed of molecular exchanges between the two phases. Surprisingly, molecules in the condensed phase do not undergo uniform Brownian motion, but instead constantly switch between a confined state and a random motion state. The confinement is consistent with formation of large molecular networks (i.e., percolation) specifically in the condensed phase. Thus, molecules in biological condensates behave distinctly different from those in dilute solutions. This finding is of fundamental importance for understanding molecular mechanisms and cellular functions of biological condensates in general.

cell biology↗

bioRxiv2022

Structure-Preserving and Batch-Correcting Visualization Using Deep Manifold Transformation for Single-cell RNA-Seq Profiles

Dimensionality reduction and visualization play an important role in biological data analysis, such as data interpretation of single-cell RNA sequence (scRNA-seq). It is desired to have a visualization method that can not only be applicable to various application scenarios, including cell clustering and trajectory inference, but also satisfy a variety of technical requirements, especially the ability to preserve inherent structure of data and handle with batch effects. However, no existing methods can accommodate these requirements in a unified framework. In this paper, we propose a general visualization method, deep visualization (DV), that possesses the ability to preserve inherent structure of data and handle batch effects and is applicable to a variety of datasets from different application domains and dataset scales. The method embeds a given dataset into a 2- or 3-dimensional visualization space, with either a Euclidean or hyperbolic metric depending on a specified task type with type static (at a time point) or dynamic (at a sequence of time points) scRNA-seq data, respectively. Specifically, DV learns a structure graph to describe the relationships between data samples, transforms the data into visualization space while preserving the geometric structure of the data and correcting batch effects in an end-to-end manner. The experimental results on nine datasets in complex tissue from human patients or animal development demonstrate the competitiveness of DV in discovering complex cellular relations, uncovering temporal trajectories, and addressing complex batch factors. We also provide a preliminary attempt to pre-train a DV model for visualization of new incoming data.

bioinformatics↗

bioRxiv2022

FOXP2 confers oncogenic effects in prostate cancer through activating MET signalling

Identification oncogenes is fundamental to revealing the molecular basis of cancer. Here, we found that FOXP2 is overexpressed in human prostate cancer cells and prostate tumors, but its expression is absent in normal prostate epithelial cells and low in benign prostatic hyperplasia. To date, little is known regarding the link of FOXP2 to prostate cancer. We observed that high FOXP2 expression and frequent amplification are significantly associated with high Gleason score. Ectopic expression of FOXP2 induces malignant transformation of mouse NIH3T3 fibroblasts and human prostate epithelial cell RWPE-1. Conversely, FOXP2 knockdown suppresses the proliferation of prostate cancer cells. Transgenic overexpression of FOXP2 in the mouse prostate causes prostatic intraepithelial neoplasia. Overexpression of FOXP2 aberrantly activates oncogenic MET signalling and inhibitors targeting MET signalling effectively reverts the FOXP2-induced oncogenic phenotype. Additionally, the novel recurrent FOXP2-CPED1 fusion identified in prostate tumors results in high expression of truncated FOXP2, which exhibit a similar capacity for malignant transformation. Together, our data demonstrate for the first time that FOXP2 is an oncogene involved in tumorigenicity of prostate.

cancer biology↗

bioRxiv2022

Accurate background reduction in adaptive optical 3D-STED nanoscopy by dynamic phase switching

Stimulated emission depletion (STED) fluorescence nanoscopy allows the three-dimensional (3D) visualization of nanoscale subcellular structures, providing unique insights into their spatial organization. However, 3D-STED imaging and quantification of dense features are obstructed by the low signal-to-background ratio (SBR), resulting from optical aberrations and out-of-focus background. Here, combining with adaptive optics, we present an easy-to-implement and flexible method to improve SBR by dynamic phase switching. By switching to a counterclockwise vortex phase mask and a top-hat one with an incorrect inner radius, the depletion pattern features a nonzero-intensity center, enabling accurate background recordings. When the recorded background is subtracted from the aberration-corrected 3D-STED image, the SBR in dense sample areas can be improved by a factor of 3-6 times. We demonstrate our method on various dense subcellular structures, showing more advantages than the software-based background subtraction algorithms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/497623v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@7aacd6org.highwire.dtl.DTLVardef@1e91f14org.highwire.dtl.DTLVardef@1f774acorg.highwire.dtl.DTLVardef@10ccf5d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Characterization of a KDM5 Small Molecule Inhibitor with Antiviral Activity against Hepatitis B Virus

Chronic hepatitis B (CHB) is a global health care challenge and a major cause of liver disease. To find new therapeutic avenues with a potential to functionally cure chronic Hepatitis B virus (HBV) infection, we performed a focused screen of epigenetic modifiers to identify replication inhibitors. From this work we identified isonicotinic acid inhibitors of the histone lysine demethylase 5 (KDM5) with potent anti-HBV activity. To enhance the cellular permeability and liver accumulation of the most potent KDM5 inhibitor identified (GS-080) an ester prodrug was developed (GS-5801) that resulted in improved bioavailability and liver exposure as well as an increased H3K4me3:H3 ratio on chromatin. GS-5801 treatment of HBV-infected primary human hepatocytes inhibited HBV replication and antigen levels. Evaluation of GS-5801 antiviral activity in a humanized mouse model of HBV infection, however, did not result in antiviral efficacy, despite achieving pharmacodynamic levels of H3K4me3:H3 predicted to be efficacious from the in vitro model. Here we discuss potential reasons for the disconnect between in vitro and in vivo efficacy, which highlight the translational difficulties of epigenetic targets for viral diseases.

pharmacology and toxicology↗

bioRxiv2022

Neutrophils reprograms the bone marrow to impair T-cell immunity during tuberculosis

Mycobacterium tuberculosis (Mtb) infection induces persistent influx of neutrophils that associates with poor bacterial control and clinical outcome from tuberculosis (TB). Although implicated in TB pathology, the mechanism by which these cells contribute to pathogenesis is poorly understood. Using Cell-DIVE multiplexed immunofluorescence imaging and spatial analysis of inflammatory TB lesions, we demonstrated that persistent neutrophil infiltration affects the spatiotemporal organization of T-lymphocytes and impairs their function. Instead of directly suppressing T-cells, neutrophils produce granulocyte colony stimulating factor (CSF3/G-CSF) that collaborates with type I interferon (IFN-I) to promote a granulocyte-skewed hematopoiesis impacting T-lymphocyte production. Importantly, neutrophil-intrinsic IFN-I receptor 1 (IFNAR1) is both necessary and sufficient to promote pathologic granulopoiesis. Finally, inhibition of IFNAR1-signaling alone mitigates immunopathogenesis by restoring hematopoietic equilibrium. Collectively, our work uncovers a potential immunevasion strategy by which virulent Mtb strains induce IFN-I to generate pathogen-permissive neutrophils that produce G-CSF and sustain pathogenic hematopoiesis to impair T-cell immunity during TB.

immunology↗

bioRxiv2022

PRPF31 interacts with PRPH2 confirmed by co-immunoprecipitation and co-localization

PurposeTo investigate the potential interaction between PRPF31 and PRPH2. MethodsHEK293T and human retinal pigment epithelial cells 19 (APRE-19) were used for our experiments. eGFP and mCherry reporter expression vectors were constructed for PRPF31 and PRPH2, respectively. Immunoblotting and co-immunoprecipitation (Co-IP) were used for gene expression validation and protein interaction. Immunofluorescence staining assay was used to test the co-localization analysis of PRPF31 and PRPH2. ResultsPRPF31-eGFP and PRPH2-mcherry were highly expressed in HEK293T and APRE-19 cells on fluorescence microscopy and western blot. Co-IP experiments showed that PRPF31 could be pulled down with an anti-PRPH2 antibody. There was co-localization between PRPF31 and PRPH2 in HEK293T, APRE-19 and mouse retina. ConclusionCo-IP and co-localization experiments suggest that PRPF31 interacted with PRPH2.

genetics↗

bioRxiv2022

Arabidopsis AAR2, a conserved splicing factor in eukaryotes, acts in microRNA biogenesis

MicroRNAs (miRNAs) play an essential role in plant growth and development, and as such, their biogenesis is fine-tuned via regulation of the core microprocessor components. Here, we report that Arabidopsis AAR2, a homolog of a U5 snRNP assembly factor in yeast and humans, not only acts in splicing but also promotes miRNA biogenesis. AAR2 interacts with the microprocessor component HYPONASTIC LEAVES1 (HYL1) in the cytoplasm, nucleus and dicing bodies. In aar2 mutants, abundance of nonphosphorylated HYL1, the active form of HYL1, and the number of HYL1-labeled dicing bodies are reduced. Primary miRNA (pri-miRNA) accumulation is compromised despite normal promoter activities of MIR genes in aar2 mutants. RNA decay assays show that the aar2-1 mutation leads to faster degradation of pri-miRNAs in a HYL1-dependent manner, which reveals a previously unknown and negative role of HYL1 in miRNA biogenesis. Taken together, our findings reveal a dual role of AAR2 in miRNA biogenesis and pre-mRNA splicing. SignificanceIn yeast and humans, AAR2 is involved in pre-mRNA splicing through regulating U5 snRNP assembly. This study shows that Arabidopsis AAR2 promotes microRNA (miRNA) accumulation in addition to its conserved role in pre-mRNA splicing. AAR2 is associated with the microprocessor component HYL1 and promotes its dephosphorylation to produce the active form in miRNA biogenesis. The study also reveals a previously unknown role of HYL1 in causing the degradation of the primary precursors to miRNAs (pri-miRNAs) and a role of AAR2 in protecting pri-miRNAs from HYL1-depedent degradation. Taken together, our findings provide new insights into the role of a conserved splicing factor in miRNA biogenesis in plants.

plant biology↗

bioRxiv2022

scFLUX: a web server for metabolic flux and variation prediction using transcriptomics data

Quantitative assessment of single cell fluxome is critical for understanding the metabolic heterogeneity in diseases. Unfortunately, single cell fluxomics using laboratory approaches is currently infeasible, and none of the current flux estimation tools could achieve single cell resolution. In light of the natural associations between transcriptomic and metabolomic profiles, it remains both a feasible and urgent task to use the available single cell transcriptomics data for prediction of single cell fluxome. We present scFLUX here, which provides an online platform for prediction of metabolic fluxome and variations using transcriptomics data, on individual cell or sample level. This is in contrast to other flux estimation methods that are only able to model the fluxes for cells of pre-defined groups. The scFLUX webserver implements our in-house single cell flux estimation model, namely scFEA, which integrates a novel graph neural network architecture with a factor graph derived from the complex human metabolic network. To the best of our knowledge, scFLUX is the first and only web-based tool dedicated to predicting individual sample-/cell-metabolic fluxome and variations of metabolites using transcriptomics data. scFLUX is available at http://scflux.org/. The stand-alone tools for using scFLUX locally are available at https://github.com/changwn/scFEA.

bioinformatics↗

bioRxiv2022

The domain-separation low-dimensional language network dynamics in the resting-state support the flexible functional segregation and integration during language and speech processing

Modern linguistic theories and network science propose that the language and speech processing is organized into hierarchical, segregated large-scale subnetworks, with a core of dorsal (phonological) stream and ventral (semantic) stream. The two streams are asymmetrically recruited in receptive and expressive language or speech tasks, which showed flexible functional segregation and integration. We hypothesized that the functional segregation of the two streams was supported by the underlying network segregation. A dynamic conditional correlation approach was employed to construct frame-wise time-varying language networks and investigate the temporal reoccurring patterns. We found that the time-varying language networks in the resting-state robustly clustered into four low-dimensional states, which dynamically reconfigured following a domain-separation manner. Spatially, the hub distributions of the first three states highly resembled the neurobiology of primary auditory processing and lexical-phonological processing, motor and speech production processing, and semantic processing, respectively. The fourth state was characterized by the weakest functional connectivity and subserved as a baseline state. Temporally, the first three states appeared exclusively in limited time bins ([~]15%), and most of the time (> 55%), the language network kept inactive in state 4. Machine learning-based dFC-linguistics prediction analyses showed that dFCs of the four states significantly predicted individual linguistic performance. These findings suggest a domain-separation manner of language network dynamics in the resting-state, which forms a dynamic "meta-networking" (network of networks) framework. HighlightsO_LIThe time-varying language network in the resting-state is robustly clustered into four low-dimensional states. C_LIO_LISpatially, the first three dFC states are cognitively meaningful, which highly resemble the neurobiology of primary auditory processing and lexical-phonological representation, speech production processing, and semantic processing, respectively. C_LIO_LITemporally, the first three states appeared exclusively in limited time bins ([~]15%), and most of the time (> 55%), the language network kept inactive in state 4. C_LIO_LIA dynamic "meta-networking" framework of language network in the resting-state is proposed. C_LI

neuroscience↗

bioRxiv2022

Regulation of protein translation by TRIM21

AbstractRegulation of translation initiation is essential for maintenance of protein homeostasis and typically involves the phosphorylation of translation initiation factor eIF2 in eukaryotes. In response to stressors, cells employ eIF2-dependent signaling to control translation initiation, which regulates multiple biological and physiological processes. However, the precise regulatory mechanism remains unclear. In this study, we focus on the role of TRIM21 in the regulation of protein translation mediated by protein kinase R (PKR), one of the classic kinases that phosphorylates eIF2. TRIM21 deficiency enhances the activation of PKR under different types of stress. TRIM21 interacts with PKR, and the E3 ligase activity of TRIM21 is crucial for stress-triggered PKR inactivation. TRIM21 interacts with the PKR phosphatase PP1 and promotes K6-linked polyubiquitination of PP1 under stresses. Ubiquitination of PP1 augments its interaction with PKR, causing PKR inactivation and subsequent dephosphorylation of eIF2, initiating protein synthesis. Moreover, TRIM21 constitutively restricts viral infection by reversing PKR-mediated inhibition of the protein synthesis of intrinsic antiviral genes. The TRIM21-PP1 axis acts as a newly discovered program that regulates PKR-associated protein synthesis and broadens our knowledge of antiviral genes. Moreover, TRIM21-mediated regulation of PKR activation provides evidence that TRIM21 may anticipate the interferon-dependent immunotherapy. Our study highlights the essential role of TRIM21 in regulating protein translation and may provide a novel target for the treatment of translation-associated diseases.

immunology↗

bioRxiv2022

Application of metallo-supramolecular branched polymer improves particle distribution and orientation in single-particle cryo-EM

Recent technological breakthroughs in single-particle cryo-electron microscopy (cryo-EM) enabled rapid atomic structure determination of biological macromolecules. A major bottleneck in the current single particle cryo-EM pipeline is the preparation of good quality frozen cryo-EM grids, which is mostly a trial-and-error process. Among many issues, preferred particle orientation and sample damage by air-water interface (AWI) are common practical problems. Here we reported a method of applying metallo-supramolecular branched polymer (MSBP) in the cryo-sample preparation for high-resolution single-particle cryo-EM. Our data shows that MSBP keeps a majority of particles away from air-water interface and mitigates preferred orientation as verified by the analyses of apoferritin, hemagglutinin (HA) trimer and various sample proteins. The use of MSBP is a simple method to improve particle distribution for high-resolution structure determination in single-particle cryo-EM.

biophysics↗

bioRxiv2022

Development and application of an uncapped mRNA platform

A novel uncapped mRNA platform was developed. Five lipid nanoparticle (LNP)-encapsulated mRNA constructs were made to evaluate several aspects of our platform, including transfection efficiency and durability in vitro and in vivo and the activation of humoral and cellular immunity in several animal models. The constructs were eGFP-mRNA-LNP (for enhanced green fluorescence mRNA), Fluc-mRNA-LNP (for firefly luciferase mRNA), S{delta}T-mRNA-LNP (for Delta strain SARS-CoV-2 spike protein trimer mRNA), gDED-mRNA-LNP (for truncated glycoprotein D mRNA coding ectodomain from herpes simplex virus type 2 (HSV2)) and gDFR-mRNA-LNP (for truncated HSV2 glycoprotein D mRNA coding amino acids 1[~]400). Quantifiable target protein expression was achieved in vitro and in vivo with eGFP-and Fluc-mRNA-LNP. S{delta}T-mRNA-LNP, gDED-mRNA-LNP and gDFR-mRNA-LNP induced both humoral and cellular immune responses comparable to those obtained by previously reported capped mRNA-LNP constructs. Notably, S{delta}T-mRNA-LNP elicited neutralizing antibodies in hamsters against the Omicron and Delta strains. Additionally, gDED-mRNA-LNP and gDFR-mRNA-LNP induced potent neutralizing antibodies in rabbits and mice. The mRNA constructs with uridine triphosphate (UTP) outperformed those with N1-methylpseudouridine triphosphate (N1m{psi}TP) in the induction of antibodies via S{delta}T-mRNA-LNP. Our uncapped, process-simplified, and economical mRNA platform may have broad utility in vaccines and protein replacement drugs.

bioengineering↗