Biology subjects

Xu, Y.

Publications and source records attributed to Xu, Y..

At least 883 records · Page 49Linked to original sources

bioRxiv2020

The Pathogenicity of 2019 Novel Coronavirus in hACE2 Transgenic Mice

Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the Corona Virus Disease 2019 (COVID-19) cases in China has become a public health emergency of international concern (PHEIC). Based on angiotensin converting enzyme 2 (ACE2) as cell entry receptor of SARS-CoV, we used the hACE2 transgenic mice infected with SARS-CoV-2 to study the pathogenicity of the virus. Weight loss and virus replication in lung were observed in hACE2 mice infected with SARS-CoV-2. The typical histopathology was interstitial pneumonia with infiltration of significant lymphocytes and monocytes in alveolar interstitium, and accumulation of macrophages in alveolar cavities. Viral antigens were observed in the bronchial epithelial cells, alveolar macrophages and alveolar epithelia. The phenomenon was not found in wild type mice with SARS-CoV-2 infection. The pathogenicity of SARS-CoV-2 in hACE2 mice was clarified and the Kochs postulates were fulfilled as well, and the mouse model may facilitate the development of therapeutics and vaccines against SARS-CoV-2.

microbiology↗

bioRxiv2020

Melon ethylene-mediated transcriptome and methylome dynamics provide insights to volatile production

During climacteric ripening large-scale transcriptional modifications are governed by ethylene. While ripening-related chromatin modifications are also known to occur, a direct connection between these factors has not been demonstrated. We characterized ethylene-mediated transcriptome modification, genome methylation dynamics, and their relation to organoleptic modifications during fruit ripening in the climacteric melon and an ethylene repressed line where the fruit-specific ACC oxidase 1 (ACO1) gene was targeted by antisense. The ACO1 antisense line exhibited mainly reduced transcriptional repression of ripening-related genes associated with DNA CHH hypomethylation at the onset of ripening. Additionally, transcription of a small set of ethylene-induced genes, including known ripening-associated genes, was inhibited by ACO1 repression and this inhibition was associated with CG hypermethylation. In the ACO1 antisense line, the accumulation of aromatic compounds, which are mainly derived from the catabolism of amino acids, is known to be inhibited. One of the ethylene-mediated transcriptionally up-regulated genes, CmTHA1, encoding a threonine aldolase, exhibited differential cytosine methylation. Threonine aldolase catalyzes the conversion of L-threonine/L-allo threonine to glycine and acetaldehyde and thus is likely involved in threonine-dependent ethyl ester biosynthesis. Yeast mutant complementation and incubation of melon discs with labeled threonine verified CmTHA1 threonine aldolase activity, revealing an additional ethylene-dependent amino acid catabolism branch involved in climacteric melon ripening.

plant biology↗

bioRxiv2020

Single-cell RNA-seq Imputation using Generative Adversarial Networks

Single-cell RNA-sequencing (scRNA-seq) enables the characterization of transcriptomic profiles at the single-cell resolution with increasingly high throughput. However, it suffers from many sources of technical noises, including insufficient mRNA molecules that lead to excess false zero values, termed dropouts. Computational approaches have been proposed to recover the biologically meaningful expression by borrowing information from similar cells in the observed dataset. However, these methods suffer from oversmoothing and removal of natural cell-to-cell stochasticity in gene expression. Here, we propose the generative adversarial networks (GANs) for scRNA-seq imputation (scIGANs), which uses generated cells rather than observed cells to avoid these limitations and balances the performance between major and rare cell populations. Evaluations based on a variety of simulated and real scRNA-seq datasets show that scIGANs is effective for dropout imputation and enhances various downstream analysis. ScIGANs is robust to small datasets that have very few genes with low expression and/or cell-to-cell variance. ScIGANs works equally well on datasets from different scRNA-seq protocols and is scalable to datasets with over 100,000 cells. We demonstrated in many ways with compelling evidence that scIGANs is not only an application of GANs in omics data but also represents a competing imputation method for the scRNA-seq data.

bioinformatics↗

bioRxiv2020

Neutralizing PD-L1 and PD-L2 Enhances the Efficacy of Immune Checkpoint Inhibitors in Ovarian Cancer.

Immune checkpoint inhibitors targeting the PD-1/PD-L1 pathway have improved for a number of solid tumors. Unfortunately, ovarian cancer represents a major clinical hurdle for immune checkpoint blockade (ICB) with reported low patient response rates. Using IHC staining, we find that PD-L2 is highly expressed in ovarian cancers and other malignancies with sub-optimal response to ICB, and is expressed at low levels in cancers responsive to ICB. Based on this observation, we hypothesized that the elevated expression of PD-L2 produced by both tumor and surrounding stromal cells contributes to immune-suppression. Since PD-L2 has been reported to have a 6- to10-fold higher native binding affinity to PD-1 compared with PD-L1, we hypothesized that high levels of PD-L2 can lead to insufficient blockade of the PD-1 signaling pathway. To overcome the immune repressive activity of PD-L2, we engineered a soluble PD-1 decoy molecule (sPD-1 mutant) that binds and neutralizes both PD-L1 and PD-L2 with a 10,000- and 200- fold improvement in binding affinity, respectively, when compared to wild-type binding to these same molecules. Such enhancement in binding affinity is facilitated by amino acid mutations both within and outside of the binding interface. Furthermore, this high affinity sPD-1 mutant molecule demonstrates superior in vivo efficacy in multiple cancer models including ovarian cancer where PD-L2 is highly expressed on the cell surface. One Sentence SummaryDual Inhibition of PD-L1 and PD-L2 using an affinity enhanced sPD-1 decoy molecule delivers superior antitumor activity when compared with PD-1 and PD-L1 antibodies in ovarian cancer.

cancer biology↗

bioRxiv2020

The origin of domestication genes in goats

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here we analyze the genomes of worldwide domestic goats, wild caprid species and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7,200 and 8,100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanism of animal domestication. One Sentence SummaryGoat domestication mainly focused on immune and neural genes, with adaptive leaps driven by introgression and selection.

genomics↗

bioRxiv2020

The relationship between the waiting time of postoperative radiotherapy and the prognosis of high grade glioma:a systemic review and meta-analysis.

Objective: The relationship between the waiting time of postoperative radiotherapy and the prognosis of patients with high-grade glioma is still inconclusive, and we addressed this issue through a systematic review and meta-analysis. Methods: Twenty studies published between 1975 and 2019 about waiting times (WT) of radiotherapy with high-grade glioma were retrieved for meta-analysis.The meta-analysis was performed by converting the effect sizes of different WT into regression coefficients ({beta}) and standard error (SE) to indicate the daily impact of delay on OS. Results: A total of 8462 high-grade glioma patients were included in the 20 studies, and no correlation between WT delay and OS was found in the unadjusted model through meta-analysis (HR=1, 95%CI=0.99-1.01, p=0.962). Meta-regression was used to adjust for other prognostic factors and no clear evidence of the relationship between WT delay and OS was found. Conclusion: This meta-analysis suggests that there is no clear evidence for the effect of delayed radiotherapy on OS with high-grade glioma patients.

cancer biology↗

bioRxiv2020

Role of DNA Methylation in Persister Formation in Uropathogenic E. coli

Uropathogenic Escherichia coli (UPEC) persister bacteria play crucial roles in clinical treatment failure and relapse. DNA methylation is known to regulate gene expression in bacteria, but its role in persister formation has not been investigated. Here, we created adenine methylation deletion mutant ({Delta}dam) and cytosine methylation mutant ({Delta}dcm) from UPEC strain UTI89 and found that the{Delta} dam mutant but not{Delta} dcm mutant had significant defect in persister formation during exposure to various antibiotics (gentamicin, fluroquinolones and cephalosporin) and stresses (acid pH and hyperosmosis), and that complementation of the dam mutant restored its persister defect phenotype. PacBio sequencing of epigenetic genomewide methylation signature and RNA sequencing of the{Delta} dam mutant were performed to define, for the first time, the role of adenine methylation in persister formation. Methylome data analysis showed that 99.73% of m6A modifications on GATC were demethylated in the{Delta} dam mutant, and demethylation nucleotide site related genes suggested an overwhelming effect on transcription and metabolic processes. Transcriptome analysis of the{Delta} dam mutant in comparison to wild type showed that flagella biosynthesis, galactitol transport/utilization, and signaling related genes were upregulated while pilus, fimbriae, virulence, glycerol, nitrogen metabolism pathways and transcriptional regulators were downregulated. The comparative COG analysis of methylome and transcriptome enriched pathways identified translation, ribosomal structure and biogenesis, and cell motility were upregulated, whereas DNA repair, secondary metabolite biosynthesis and diverse transport systems, some of which are known to be involved in persister formation, were downregulated in the{Delta} dam mutant. These findings provide new insights about the molecular basis of how DNA adenine methylation may be involved in persister formation and offer novel therapeutic targets for combating persister bacteria.

microbiology↗

bioRxiv2020

Single cell atlas of trisomy 21 cerebral cortex

Down syndrome (DS) is one of the most common human birth defects caused by trisomy 21 (T21), leading to a variety of cognitive impairments. The cellular composition of human brain has been explored using single cell RNA sequencing in both physiological and pathological conditions. However, the cellular heterogeneity of human brain with chromosome aneuploidy is largely unknown. Here, we profiled the transcriptome of 36046 cells in cerebral cortex of T21 human fetus, covering frontal lobe, parietal lobe, occipital lobe and temporal lobe. Intriguingly, we detected several genes positively associated with neurons maturation was dysregulated in T21 frontal cortex (HIC2, POU2F2, ZGLP1 and FOXK1). To share, explore and utilized the data resources of T21 cerebral cortex, we developed a comprehensive platform named T21atlas, composing of two functional modules (T21cluster and T21talk). Overall, our study provides, as far as we know, the first single cell atlas for T21 cerebral cortex, which could promote our understanding of the molecular mechanism of DS at an unprecedented resolution and could potentially facilitate the development of novel clinical therapeutics against T21.

neuroscience↗

bioRxiv2019

Kinetic improvement of an algal diacylglycerol acyltransferase 1 via fusion with an acyl-CoA binding protein

Microalgal oils in the form of triacylglycerols (TAGs) are broadly used as nutritional supplements and biofuels. Diacylglycerol acyltransferase (DGAT) catalyzes the final step of acyl-CoA-dependent biosynthesis of TAG and is considered a key target for manipulating oil production. Although a growing number of DGAT1s have been identified and over-expressed in some algal species, the detailed structure-function relationship, as well as the improvement of DGAT1 performance via protein engineering, remain largely untapped. Here, we explored the structure-function features of the hydrophilic N-terminal domain of DGAT1 from the green microalga Chromochloris zofingiensis (CzDGAT1). The results indicated that the N-terminal domain of CzDGAT1 was less disordered than those of the higher eukaryotic enzymes and its partial truncation or complete removal could substantially decrease enzyme activity, suggesting its possible role in maintaining enzyme performance. Although the N-terminal domains of animal and plant DGAT1s were previously found to bind acyl-CoAs, replacement of CzDGAT1 N-terminus by an acyl-CoA binding protein (ACBP) could not restore enzyme activity. Interestingly, the fusion of ACBP to the N-terminus of the full-length CzDGAT1 could enhance the enzyme affinity for acyl-CoAs and augment protein accumulation levels, which ultimately drove oil accumulation in yeast cells and tobacco leaves to higher levels than the full-length CzDGAT1. Overall, our findings unravel the distinct features of the N-terminus of algal DGAT1 and provide a strategy to engineer enhanced performance in DGAT1 via protein fusion, which may open a vista in generating improved membrane-bound acyl-CoA-dependent enzymes and boosting oil biosynthesis in plants and oleaginous microorganisms. SIGNIFICANCE STATEMENTHere, we explored the N-terminus of a microalgal DGAT1, a membrane-bound enzyme determining oil biosynthesis, using in silico analysis, truncation mutagenesis, protein fusion and in vitro and in vivo characterization, and demonstrated its distinct structure-function features from the higher eukaryotic enzymes. We further engineered enhanced performance in DGAT1 via N-terminal fusion of ACBP, and obtained a kinetically improved enzyme with augmented protein production levels, which could boost oil accumulation in yeast and plant vegetative tissues.

plant biology↗

bioRxiv2019

A novel G protein-biased and subtype selective agonist for a G protein-coupled receptor discovered from screening herbal extracts

Subtype selectivity and functional bias are vital in current drug discovery for G protein-coupled receptors (GPCRs) as selective and biased ligands are expected to yield drug leads with optimal on-target benefits and minimal side-effects. However, structure-based design and medicinal chemistry exploration remain challenging in part because of highly conserved binding pockets within subfamilies. Herein, we present an affinity mass spectrometry approach for screening herbal extracts to identify active ligands of a GPCR, the 5-HT2C receptor. Using this method, we discovered a naturally occurring aporphine 1857 that displayed strong selectivity for activating 5-HT2C without activating the 5-HT2A or 5-HT2B receptors. Remarkably, this novel ligand exhibited exclusive bias towards G protein signaling for which key residues were identified, and it showed comparable in vivo efficacy for food intake suppression and weight loss as the anti-obesity drug, lorcaserin. Our study establishes an efficient approach to discovering novel GPCR ligands by exploring the largely untapped chemical space of natural products.

biochemistry↗

bioRxiv2019

STAT3 localizes in mitochondria-associated ER membranes instead of in mitochondria

Signal Transducer and Activator of Transcription 3 (STAT3) is a transcription factor (TF) that regulates a variety of biological processes, including a key role in mediating mitochondrial metabolism. It has been shown that STAT3 performs this function by translocating in minute amounts into mitochondria and interacting with mitochondrial proteins and genome. However, whether STAT3 localizes in mitochondria is still up for debate. To decipher the role of mitochondrial STAT3 requires a detailed understanding of its cellular localization. Using Percoll density gradient centrifugation, we surprisingly found that STAT3 is not located in the mitochondrial fraction, but instead, in the mitochondria-associated endoplasmic reticulum membrane (MAM) fraction. This was confirmed by sub-diffraction image analysis of labeled mitochondria in embryonic astrocytes. Also, we find that other TFs that have been previously found to localize in mitochondria are also found instead in the MAM fraction. Our results suggest that STAT3 and other transcriptional factors are, contrary to prior studies, consolidated specifically at MAMs, and further efforts to understand mitochondrial STAT3 function must take into consideration this localization, as the associated functional consequences offer a different interpretation to the questions of STAT3 trafficking and signaling in the mitochondria.

cell biology↗

bioRxiv2019

Structural brain architectures match intrinsic functional networks and vary across domains: A study from 15000+ individuals

Brain structural networks have been shown to consistently organize in functionally meaningful architectures covering the entire brain. However, to what extent brain structural architectures match the intrinsic functional networks in different functional domains remains under explored. In this study, based on independent component analysis, we revealed 45 pairs of structural-functional (S-F) component maps, distributing across 9 functional domains, in both a discovery cohort (n=6005) and a replication cohort (UK Biobank, n=9214), providing a well-match multimodal spatial map template for public use. Further network module analysis suggested that unimodal cortical areas (e.g. somatomotor and visual networks) indicate higher S-F coherence, while heteromodal association cortices, especially the frontoparietal network (FPN), exhibit more S-F divergence. Collectively, these results suggest that the expanding and maturing brain association cortex demonstrates a higher degree of changes compared to unimodal cortex, which may lead to higher inter-individual variability and lower S-F coherence.

neuroscience↗

bioRxiv2019

ZBED2 is an antagonist of Interferon Regulatory Factor 1 and modulates cell identity in pancreatic cancer

Lineage plasticity is a prominent feature of pancreatic ductal adenocarcinoma (PDA) cells, which can occur via deregulation of lineage-specifying transcription factors. Here, we show that the zinc finger protein ZBED2 is aberrantly expressed in PDA and alters tumor cell identity in this disease. Unexpectedly, our epigenomic experiments reveal that ZBED2 is a sequence-specific transcriptional repressor of interferon-stimulated genes, which occurs through antagonism of Interferon Regulatory Factor 1 (IRF1)-mediated transcriptional activation at co-occupied promoter elements. Consequently, ZBED2 attenuates the transcriptional output and growth arrest phenotypes downstream of interferon signaling in multiple PDA cell line models. We also found that ZBED2 is preferentially expressed in the squamous molecular subtype of human PDA, in association with inferior patient survival outcomes. Consistent with this observation, we show that ZBED2 can repress the pancreatic progenitor transcriptional program, enhance motility, and promote invasion in PDA cells. Collectively, our findings suggest that high ZBED2 expression is acquired during PDA progression to suppress the interferon response pathway and to promote lineage plasticity in this disease. SIGNIFICANCE STATEMENTPancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies, attributed in part to lineage infidelity downstream of deregulated lineage-specifying transcription factors (TFs). Here we define the biological effects of a poorly understood TF ZBED2 in the most aggressive subtype of PDA, defined by the expression of squamous lineage markers. Our study reveals two molecular functions of ZBED2 in PDA cells: an inhibitor of interferon response genes and a modifier of epithelial lineage programs. Both functions can be explained by the ability of ZBED2 to antagonize the functional output of Interferon Regulatory Factor-1 (IRF1). Our study reinforces the concept of aberrant lineage identity in cancer and highlights an unexpected connection between interferon response pathways and squamous-subtype PDA.

cancer biology↗

bioRxiv2019

Deep learning enables structured illumination microscopy with low light levels and enhanced speed

Using deep learning to augment structured illumination microscopy (SIM), we obtained a fivefold reduction in the number of raw images required for super-resolution SIM, and generated images under extreme low light conditions (100X fewer photons). We validated the performance of deep neural networks on different cellular structures and achieved multi-color, live-cell super-resolution imaging with greatly reduced photobleaching.

biophysics↗

bioRxiv2019

A Novel LysR-Type Global Regulator RpvA Controls Persister Formation and Virulence in Staphylococcus aureus

Staphylococcus aureus is the leading cause of wound and nosocomial infections. Persister formation and virulence factors play crucial roles during S. aureus infection. However, the mechanisms of persister formation and its relationship to virulence in S. aureus are poorly understood. In this study, we screened a transposon mutant library and identified a LysR-type global transcriptional regulator NWMN_0037, which we called RpvA, for regulator of persistence and virulence, whose mutation leads to higher susceptibility to antibiotics ampicillin and norfloxacin and various stresses including oxidative stress, heat, and starvation in late exponential and early stationary phase. Interestingly, the rpvA mutant was highly attenuated for virulence compared with the parent S. aureus Newman strain as shown by a much higher lethal dose, reduced ability to survive in macrophages and to form abscess in the mouse model. Transcriptional profiling and metabolomic analysis revealed that RpvA could repress multiple genes including gapR, gapA, tpi, pgm, eno, glpD, and acs expression and enhance production of numerous intermediate metabolites including dihydroxyacetone phosphate, 2-phosphoglycerate, acetyl-CoA, glycerol 3-phosphate, L-glutamate in the cells. The differentially expressed genes and altered production of metabolites are distributed in global metabolism including carbohydrate metabolism, amino acid metabolism, energy metabolism and metabolism of cofactors and vitamins. These metabolic adjustments could cause the cell to go into dormancy, thus promoting S. aureus to convert to persisters. In addition, RpvA could upregulate the expression of virulence genes including hla, hlgA, hlgB, hlgC, lukF, lukS, lukD, sea and coa, and carotenoid biosynthesis genes (crtI, crtM, crtN). Gel shift assay confirmed that RpvA could bind to the promoters of candidate target genes hla, hlgB and crtM, thus promoting S. aureus virulence. Because of the important functions of the RpvA, it may serve as an attractive target for developing new drugs and vaccines to more effectively control S. aureus infections.

microbiology↗

bioRxiv2019

The rice PPR756 coordinates with MORFs for multiple RNA editing in mitochondria

In land plants, the pentatricopeptide repeat (PPR) proteins form a large family involved in post-transcriptional processing of RNA in mitochondria and chloroplasts, which is critical for plant development and evolutionary adaption. Although studies showed a number of PPR proteins generally influence the editing of organellar genes, few of them were characterized in detail in rice. Here, we report a PLS-E subclass PPR protein in rice, PPR756, loss of function of which led to the abolishment of RNA editing events among three mitochondrial genes including atp6, ccmC, and nad7. Their defective C-to-U transformation then resulted in improper amino acid retention which could cause abortive pollen development. Furthermore, PPR756 could bind to the three target genes directly and interact with three OsMORFs (multiple organellar RNA editing factors): OsMORF1, OsMORF8-1, and OsMORF8-2. The knock-out plants of PPR756 exhibited retarded growth and greener leaves during the early vegetative stages, along with sterile pollen and lower seed setting at the reproductive stage. These results established a role for PPR756 in rice development, participating in RNA editing of three various transcripts and cooperating with OsMORFs via an editosome manner in rice.

developmental biology↗

bioRxiv2019

Prediction of liquid-liquid phase separation proteins using machine learning

The liquid-liquid phase separation (LLPS) of bio-molecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cellular functions. The dysregulation of LLPS might be implicated in a number of diseases. Although the LLPS of biomolecules has been investigated intensively in recent years, the knowledge of the prevalence and distribution of phase separation proteins (PSPs) is still lag behind. Development of computational methods to predict PSPs is therefore of great importance for comprehensive understanding of the biological function of LLPS. Here, a sequence-based prediction tool using machine learning for LLPS proteins (PSPredictor) was developed. Our model can achieve a maximum 10-CV accuracy of 96.03%, and performs much better in identifying new PSPs than reported PSP prediction tools. As far as we know, this is the first attempt to make a direct and more general prediction on LLPS proteins only based on sequence information.

bioinformatics↗

bioRxiv2019

IRIS: Big data-informed discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing

Aberrant alternative splicing (AS) is widespread in cancer, leading to an extensive but largely unexploited repertoire of potential immunotherapy targets. Here we describe IRIS, a computational platform leveraging large-scale cancer and normal transcriptomics data to discover AS-derived tumor antigens for T-cell receptor (TCR) and chimeric antigen receptor T-cell (CAR-T) therapies. Applying IRIS to RNA-Seq data from 22 glioblastomas resected from patients, we identified candidate epitopes and validated their recognition by patient T cells, demonstrating IRISs utility for expanding targeted cancer immunotherapy.

bioinformatics↗