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Cai, W.

Publications and source records attributed to Cai, W..

At least 109 records · Page 6Linked to original sources
bioRxiv2020

Tumor-stromal IL1β/ NFκB / ESE3 Signal Axis Drives Pancreatic Cancer Fibrosis, Chemoresistance, Prognosis

Pancreatic stellate cells (PSCs) play a pivotal role in pancreatic fibrosis and pancreatic ductal adenocarcinoma (PDAC) progression. The mechanisms controlling PSC activation is not completely understood. Here we investigated the role of ESE3 (Epithelium-Specific ETS factor 3) in PSC activation. We discovered that in PDAC patients ESE3 expression was increased in PSC while decreased in tumor cells. ESE3 overexpression in PSC promoted PSC activation. Condition medium from ESE3-overexprssing PSC promotes PDAC cell migration, chemoresistance, tumor growth and fibrosis. ESE3 directly induced the transcription of -SMA, Collagen 1 and IL-1{beta} by binding to ESE3 binding sites on their promoters to activate PSC. On the other hand, IL-1{beta} upregulates ESE3 in PSC through NF{kappa}B activation and ESE3 is required for PSC activation by tumor cell derived IL-1{beta}. Clinical data showed ESE3 upregulation in PSC was positively correlated with tumor size, pTNM stage, CA19-9, CEA and CA242 level in serum. ESE3 overexpression in PSC was an independent negative prognostic factor for disease-free survival and overall survival among PDAC patients. Inhibition of the IL-1{beta}/ ESE3 (PSC)/ IL-1{beta} positive feedback loop represents a promising therapeutic strategy to reduce tumor fibrosis and increase chemotherapeutic efficacy in PDAC.

cancer biology↗
bioRxiv2020

A two-stage ECG signal denoising method based on deep convolutional network

Electrocardiogram (ECG) is an effective and non-invasive indicator for the detection and prevention of arrhythmia. ECG signals are susceptible to noise contamination, which can lead to errors in ECG interpretation. Therefore, ECG pretreatment is important for accurate analysis. In this paper, a method of noise reduction based on deep learning is proposed. The method is divided into two stages, and two corresponding models are formed. In the first stage, a one-dimensional U-net model is designed for ECG signal denoising to eliminate noise as much as possible. The one-dimensional DR-net model in the second stage is used to reconstruct the ECG signal and to correct the waveform distortion caused by noise removal in the first stage. In this paper, the U-net and the DR-net are constructed by the convolution method to achieve end-to-end mapping from noisy ECG signals to clean ECG signals. The ECG data used in this paper are from CPSC2018, and the noise signal is from MIT-BIH Noise Stress Test Database (NSTDB). In the experiment, the improvement in the signal-to-noise ratio SNRimp, the root mean square error decrease RMSEde, and the correlation coefficient P, are used to evaluate the performance of the network. This two-stage method is compared with FCN and U-net alone. The experimental results show that the two-stage noise reduction method can eliminate complex noise in the ECG signal while retaining the characteristic shape of the ECG signal. According to the results, we believe that the proposed method has a good application prospect in clinical practice.

bioengineering↗
bioRxiv2020

The binding of palonosetron and other antiemetic drugs to the serotonin 5-HT3 receptor

Inaccurately perceived as niche drugs, antiemetics are key elements of cancer treatment alleviating the most dreaded side effect of chemotherapy. Serotonin 5-HT3 receptor antagonists are the most commonly prescribed class of drugs to control chemotherapy-induced nausea and vomiting (CINV). These antagonists have been clinically successful drugs since the 1980s, yet our understanding of how they operate at the molecular level has been hampered by the difficulty of obtaining structures of drug-receptor complexes. Here, we report the cryo-EM structure of the palonosetron-bound 5-HT3 receptor. We investigate the binding of palonosetron, granisetron, dolasetron, ondansetron, and cilansetron using molecular dynamics, covering the whole set of antagonists used in the clinical practice. The structural and computational results yield detailed atomic insight into the binding modes of the drugs. In light of our data, we establish a comprehensive framework underlying the inhibition mechanism by the -setron drug family.

neuroscience↗
bioRxiv2020

Correlated Gene Modules Uncovered by Single-Cell Transcriptomics with High Detectability and Accuracy

Single cell transcriptome sequencing has become extremely useful for cell typing. However, such differential expression data has shed little light on regulatory relationships among genes. Here, by examining pairwise correlations between mRNA levels of any two genes under steady-state conditions, we uncovered correlated gene modules (CGMs), clusters of intercorrelated genes that carry out certain biological functions together. We report a novel single-cell RNA-seq method called MALBAC-DT with higher detectability and accuracy, allowing determination of the covariance matrix of the expressed mRNAs for a homogenous cell population. We observed a prevalence of positive correlations between pairs of genes, with higher correlations corresponding to higher likelihoods of protein-protein interactions. Some CGMs, such as the p53 module in a cancer cell line, are cell type specific, while others, such as the protein synthesis CGM, are shared by different cell types. CGMs distinguished direct targets of p53 and exposed different modes of regulation of these genes in different cell types. Our covariance analyses of steady-state fluctuations provides a powerful way to advance our functional understanding of gene-to-gene interactions.

genomics↗
bioRxiv2019

Single-cell transcriptomics reveals diverse and complex gene expression alterations in human trisomy 18

Trisomy 18, commonly known as Edwards syndrome, is the second most common autosomal trisomy among live born neonates. Multiple tissues including cardiac, abdominal, and nervous systems are affected by an extra chromosome 18. To delineate the complexity of anomalies of trisomy 18, we analyzed amniotic fluid cells from two normal and three trisomy 18 samples using single-cell transcriptomics. We identified six cell groups, which function in major tissue development such as kidney, vasculature, and smooth muscle, and display significant alterations in gene expression detected by single-cell RNA-sequencing. Moreover, we demonstrated significant gene expression changes in previously proposed trisomy 18 critical regions, and identified three new regions such as 18p11.32, 18q11, 18q21.32, which are likely associated with trisomy 18 phenotypes. Our results indicate complexity of trisomy 18 at the gene expression level and reveal genetic reasoning of diverse phenotypes in trisomy 18 patients.

genetics↗
bioRxiv2019

Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives

Food and drugs contain diverse small molecule additives (excipients) with unclear impacts on human physiology. Here, we evaluate their potential impact on intestinal absorption, screening 136 unique compounds for inhibition of the key transporter OATP2B1. We identified and validated 24 potent OATP2B1 transport inhibitors, characterized by higher molecular weight and hydrophobicity compared to poor or non-inhibitors. OATP2B1 inhibitors were also enriched for dyes, including 8 azo (R-N=N-R') dyes. Pharmacokinetic studies in mice confirmed that FD&C Red No. 40, a common azo dye excipient, inhibited drug absorption; however, the human gut microbiome inactivated azo dye excipients, producing metabolites that no longer inhibit OATP2B1 transport. These results support a beneficial role for the microbiome in limiting the unintended effects of food and drug additives in the intestine. One Sentence SummaryFood and drug additives inhibit intestinal drug transporters, although some are inactivated by gut bacterial metabolism.

pharmacology and toxicology↗
bioRxiv2019

Enhancer-dependence of gene expression increases with developmental age

How overall principles of gene regulation (the \"logic\") may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic and topological profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1 and Myb occupancy. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes employ distal enhancers for long-range regulation through enhancer-promoter looping, confirmed by Gata1 HiChIP. Genome editing demonstrated distal enhancers are required for gene expression in EryD but not in EryP. Applying a metric for enhancer-dependence of transcription, we observed a progressive reliance on enhancer control with increasing age of ontogeny among diverse primary cells and tissues of mouse and human origin. Our findings highlight fundamental and conserved differences in regulatory logic at distinct developmental stages, characterized by simpler promoter-centric regulation in embryonic cells and combinatorial enhancer-driven control in adult cells.\n\nHighlightsO_LIRegulation of embryonic-specific erythroid genes is promoter-centric through Gata1\nC_LIO_LIAdult-specific control is combinatorial enhancer-driven and requires Myb\nC_LIO_LIAdult specific genes have increased enhancer-promoter chromatin interactions\nC_LIO_LIEnhancer-dependence increases progressively with increasing developmental age\nC_LI

molecular biology↗
bioRxiv2019

Quantitative modeling links in vivo microstructural and macrofunctional organization of human and macaque insular cortex, and predicts cognitive control abilities

The human insular cortex is a heterogenous brain structure which plays an integrative role in guiding behavior. The cytoarchitectonic organization of the human insula has been investigated over the last century using postmortem brains but there has been little progress in noninvasive in vivo mapping of its microstructure and large-scale functional circuitry. Quantitative modeling of multi-shell diffusion MRI (dMRI) data from 440 HCP participants revealed that human insula microstructure differs significantly across its functionally defined dorsal anterior, ventral anterior, and posterior insula subdivisions that serve distinct cognitive and affective functions. The microstructural organization of the insula was mirrored in its functionally interconnected circuits with the anterior cingulate cortex that anchor the salience network, a system important for adaptive switching of cognitive control systems. Novel validation of the human insula findings came from quantitative dMRI modeling in macaques which revealed microstructural features consistent with known primate insula cytoarchitecture. Theoretical analysis and computer simulations, using realistic 3-dimensional models of neuronal morphology from postmortem tissue, demonstrated that dMRI signals reflect the cellular organization of cortical gray matter, and that these signals are sensitive to cell size and the presence of large neurons such as the von Economo neurons. Crucially, insular microstructural features were linked to behavior and predicted individual differences in cognitive control ability. Our findings open new possibilities for probing psychiatric and neurological disorders impacted by insular cortex dysfunction, including autism, schizophrenia, and fronto-temporal dementia.\n\nStatement of SignificanceThe human insular cortex is a heterogenous brain structure which plays an integrative role in identifying salient sensory, affective, and cognitive cues for guiding attention and behavior. It is also is one of the most widely activated brain regions in all of human neuroimaging research. Here we use novel quantitative tools with in vivo diffusion MRI in large group (N=440) of individuals to uncover several unique microstructural features of the human insula and its macrofunctional circuits. Crucially, microstructural properties of the insular cortex predicted human cognitive control abilities, in agreement with its crucial role in adaptive human behaviors. Our findings open new possibilities for probing psychiatric and neurological disorders impacted by insular dysfunction, including autism, schizophrenia, and fronto-temporal dementia.

neuroscience↗
bioRxiv2019

Adaptation of Mycobacterium tuberculosis to biofilm growth is genetically linked to drug tolerance

Mycobacterium tuberculosis (Mtb) spontaneously grows at the air-medium interface forming pellicle biofilms, which harbor more drug tolerant persisters than planktonic cultures. The underlying basis for increased persisters in Mtb biofilms is unknown. Using a Tn-seq approach, we show here that multiple genes that are necessary for fitness of Mtb cells within biofilms, but not in planktonic cultures, are also important for their tolerance to a diverse set of stressors and antibiotics. Thus, development of Mtb biofilms appears to be associated with population enrichment, in which endogenous stresses presumably generated by challenging growth conditions within biofilm architecture select for cells that maintain tolerance to exogenous stresses including antibiotic exposure. We further observed that the intrinsic drug tolerance of constituent cells of biofilms determines the frequency of persisters: morphologically indistinguishable monoculture biofilms of a {Delta}pstC2A1 mutant hypersensitive to rifampicin harbor [~]20-fold fewer persisters than wild-type. These findings together allow us to propose that the selection of elite cells during biofilm development significantly contributes to the persister frequency. Furthermore, probing the possibility that the population enrichment is an outcome of unique environment within biofilms, we demonstrate biofilm-specific induction in the synthesis of isonitrile lipopeptides (INLP). Mutation analysis indicates that INLP is necessary for the architecture development of Mtb biofilms. In summary, the study offers an insight into persistence of Mtb biofilms under antibiotic exposure, while identifying INLP as a biomarker for further investigation of this phenomenon.\n\nSIGNIFICANCEThe tuberculosis (TB) pathogen Mycobacterium tuberculosis (Mtb) is one of the deadliest bacterial pathogens known to mankind, and TB treatment is inefficient. A lengthy chemotherapy for TB is attributed to a small subpopulation of Mtb bacilli exhibiting phenotypic tolerance to antibiotics. Drugs targeting these persisters are expected to shorten TB chemotherapy, but their development is dependent on in vitro growth models that reproducibly generate high frequency of persisters. Biofilms of Mtb are a suitable model for understanding the origin of persisters. Here, we provide an explanation for the elevated persister frequency in Mtb biofilms. We also identify isonitrile lipopetides as a biomarker of Mtb biofilms. These findings will facilitate further advancements of our efforts to identify and target Mtb persisters.

microbiology↗
bioRxiv2019

JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila

In flies, the chromosomal kinase JIL-1 is responsible for most interphase histone H3S10 phosphorylation and has been proposed to protect active chromatin from acquiring heterochromatic marks, like dimethylated histone H3K9 (H3K9me2) and HP1. Here, we show that JIL-1s targeting to chromatin depends on a new PWWP domain-containing protein JASPer (JIL-1 Anchoring and Stabilizing Protein). The JASPer-JIL-1 (JJ)-complex is the major form of the kinase in vivo and is targeted to active genes and telomeric transposons via binding of the PWWP domain of JASPer to H3K36me3 nucleosomes. Put in place, the complex modulates the transcriptional output. JIL-1 and JJ-complex depletion in cycling cells lead to small changes in H3K9me2 distribution at active genes and telomeric transposons. Finally, we identified many new interactors of the endogenous JJ-complex and propose that JIL-1 not only prevents heterochromatin formation, but also coordinates chromatin-based regulation in the transcribed part of the genome.

molecular biology↗
bioRxiv2019

Live-cell Imaging Analysis of Antimycin-Type Depsipeptides via Bioorthogonal Stimulated Raman Scattering Microscopy

Small-molecule natural products have been an essential source of pharmaceuticals to treat human diseases, but very little is known about their behavior inside dynamic, living human cells. Here, we demonstrate the first structure-activity-distribution study of complex natural products, the anti-cancer antimycin-type depsipeptides, using the emerging bioorthogonal Stimulated Raman Scattering (SRS) Microscopy. Our results show that the intracellular enrichment and distribution of these compounds are driven by their potency and specific protein targets, as well as the lipophilic nature of compounds.

bioengineering↗
bioRxiv2019

Remodeling gut microbiota by Streptococcus thermophilus 19 attenuates inflammation in septic mice

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection and is the leading cause of death in burn patients. Streptococcus thermophilus 19 is a highly effective probiotic, with well-studied health benefits, but its role in protecting viscera against injury caused by sepsis and the underlying mechanism is poorly understood. The goal of this study was to evaluate protection potency of S. thermophilus against inflammation in mice and evaluate the influence of sepsis and S. thermophilus on microbial community. We tested the utility of S. thermophilus 19 in attenuating inflammation in vitro and vivo of LPS-induced sepsis mouse model. We also evaluated the influence of sepsis and S. thermophilus on microbial community. In vitro, S. thermophilus 19 decrease the expression of inflammatory factors. Additionally, in a lipopolysaccharide-induced septic mouse model, mice administered the probiotic 19 was highly resistant to Lps and exhibited decreased expression of inflammatory factors compared to Lps-treated control mice. A MiSeq-based sequence analysis revealed that gut microbiota alterations in mice intraperitoneally injected with 1 mg/ml LPS were mitigated by the administration of oral probiotics 19. Together these findings indicate that S. thermophilus 19 may be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases. In an analysis of the gut microbiota of the all group mice, we found that sepsis is associated with gut microbiota and probiotics attenuate the inflammation through remodeling gut microbiota. ImportanceSepsis is life-threatening organ dysfunction which is the leading cause of death in burn patients. Although our understanding of sepsis has increased substantially in recent years, its still reported to be the leading cause of death in seriously ill patients. Evidences showed that gut microbiota play an important role in sepsis. Moreover, probiotics have been used to prevent numbers of gut health disorders and alleviate inflammation associated with some human diseases by promoting changes in the gut microbiota composition. Hence, to investigate the mechanism of probiotics in the treatment of sepsis has emerged. The significance of our research is in identifying the role of gut microbiota in sepsis and found an effective probiotic that reduces inflammation, S. thermophilus 19, and investigating the therapeutic effect and mechanism of S. thermophilus 19 on sepsis, which might be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases.

microbiology↗
bioRxiv2019

Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage

Colibactin is an as-yet-uncharacterized human gut bacterial genotoxin, whose biosynthesis is linked to clb genomic island that distributes widespread in pathogenic and commensal human enterobacteria. Colibactin-producing gut microbes promote colon tumor formation and enhance progression of colorectal cancer (CRC) via DNA double-strand breaks (DSBs)-induced cellular senescence and death; however, the chemical basis contributing to the pathogenesis at the molecular level remains elusive. Here we report the discovery and the mechanism of action of colibactin-645 as the highly sought final colibactin metabolite with a novel molecular scaffold. Colibactin-645 recapitulates its previously assumed genotoxicity and cytotoxicity, exhibiting a strong DNA DSBs activity in vitro and in human cell cultures via a unique copper-mediated oxidative mechanism. We also present a complete model for colibactin biosynthesis, revealing an unprecedented dual function of the aminomalonate-utilizing polyketide synthases. This work thus provides the first molecular basis for colibactins genotoxic activity and facilitates further mechanistic study of colibactin-related CRC incidence and prevention.

microbiology↗
bioRxiv2018

Identifying the Biosynthetic Gene Cluster for Triacsins with an N-hydroxytriazene Moiety

Triacsins are a family of natural products containing an N-hydroxytriazene moiety not found in any other known secondary metabolites. Though many studies have examined the biological activity of triacsins in lipid metabolism, the biosynthesis of triacsins has remained unknown. Here, we report the identification of the triacsin biosynthetic gene cluster in Streptomyces aureofaciens ATCC 31442. Bioinformatic analysis of the gene cluster led to the discovery of the tacrolimus producer Streptomyces tsukubaensis NRRL 18488 as a new triacsin producer. In addition to targeted gene disruption to identify necessary genes for triacsin production, stable isotope feeding was performed in vivo to advance the understanding of N-hydroxytriazene biosynthesis.

biochemistry↗
bioRxiv2018

Proteomic Profile of TGF-β1 treated Lung Fibroblasts identifies Novel Markers of Activated Fibroblasts in the Silica Exposed Rat Lung

We performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) on control and TGF-{beta}1-exposed rat lung fibroblasts to identify proteins differentially expressed between cell populations. A total of 1648 proteins were found to be differentially expressed in response to TGF-{beta}1 treatment and 196 proteins were expressed at [≥] 1.2 fold relative to control. Guided by these results, we next determined whether similar changes in protein expression were detectable in the rat lung after chronic exposure to silica dust. Of the five proteins selected for further analysis, we found that levels of all proteins were markedly increased in the silica-exposed rat lung, including the proteins for the very low density lipoprotein receptor (VLDLR) and the transmembrane (type I) heparin sulfate proteoglycan called syndecan 2 (SDC2). Because VLDLR and SDC2 have not, to our knowledge, been previously linked to the pathobiology of silicosis, we next examined whether knockdown of either gene altered responses to TGF-{beta}1 in MRC-5 lung fibroblasts. Interestingly, we found knockdown of either VLDLR or SDC2 dramatically reduced collagen production to TGF-{beta}1, suggesting that both proteins might play a novel role in myofibroblast biology and pathogenesis of silica-induced pulmonary fibrosis. In summary, our findings suggest that performing LC-MS/MS on TGF-{beta}1 stimulated lung fibroblasts can uncover novel molecular targets of activated myofibroblasts in silica-exposed lung.\n\nHighlightsWe identified 196 proteins differentially expressed between control and TGF-{beta}1 treated fibroblastsby LC-MS/MS.\n\nSeveral proteins identified by LC-MS/MS were also found to be differentially expressed in whole lung tissues and isolated fibroblasts after chronic exposure to silica dust, including the very low density lipoprotein receptor (VLDLR) and the transmembrane type I heparan sulfate proteoglycan called syndecan 2\n\nKnockdown of SDC2 or VLDLR markedly inhibited collagen production in MRC-5 fibroblasts, suggesting a novel pathogenic role for these proteins in myofibroblast biology.

pharmacology and toxicology↗
bioRxiv2018

Superresolved and reference-free microparticle traction force microscopy (MP-TFM) reveals the complexity of the mechanical interaction in phagocytosis

Force exertion is an integral part of cellular behavior. Traction force microscopy (TFM) has been instrumental for studying such forces, providing both spatial and directional force measurements at subcellular resolution. However, the applications of classical TFM are restricted by the typical planar geometry. Here, we develop a particle-based force sensing strategy, specifically designed for studying ligand-dependent cellular interactions. We establish an accessible batch approach for synthesizing highly uniform, deformable and tunable hydrogel particles. In addition, they can be easily derivatized to trigger specific cellular behavior. The 3D shape of such particles can be resolved with superresolution (< 50 nm) accuracy using conventional confocal microscopy. We introduce a computational method that allows us to infer surface traction forces with high sensitivity (~ 10 Pa), directly from the particle shape without embedding tracers in the particle. We illustrate the potential and flexibility of this approach by measuring forces throughout phagocytic engulfment. This strategy can readily be adapted for studying cellular forces in a wide range of applications.

biophysics↗
bioRxiv2018

Isonitrile Formation by a Non-heme Iron(II)-dependent Oxidase/Decarboxylase

The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We here provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, members of which are critical for the virulence of pathogenic mycobacteria.

biochemistry↗