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Chen, W.

Publications and source records attributed to Chen, W..

At least 289 records · Page 16Linked to original sources

Pancreatic islet α cell function and proliferation requires the arginine transporter SLC7A2

Interrupting glucagon signaling decreases gluconeogenesis and the fractional extraction of amino acids by liver from blood resulting in lower glycemia. The resulting hyperaminoacidemia stimulates cell proliferation and glucagon secretion via a liver- cell axis. We hypothesized that cells detect and respond to circulating amino acids levels via a unique amino acid transporter repertoire. We found that Slc7a2ISLC7A2 is the most highly expressed cationic amino acid transporter in cells with its expression being three-fold greater in than {beta} cells in both mouse and human. Employing cell culture, zebrafish, and knockout mouse models, we found that the cationic amino acid arginine and SLC7A2 are required for cell proliferation in response to interrupted glucagon signaling. Ex vivo and in vivo assessment of islet function in Slc7a2-/- mice showed decreased arginine-stimulated glucagon and insulin secretion. We found that arginine activation of mTOR signaling and induction of the glutamine transporter SLC38A5 was dependent on SLC7A2, showing that boths role in cell proliferation is dependent on arginine transport and SLC7A2. Finally, we identified single nucleotide polymorphisms in SLC7A2 associated with HbA1c. Together, these data indicate a central role for SLC7A2 in amino acid-stimulated cell proliferation and islet hormone secretion.

physiology↗

The spreading of facultative H3K9me3-heterochromatin drives congenital disease

Heterochromatin marked by trimethylated histone 3 at lysine 9 (H3K9me3) plays fundamental roles in reprogramming to direct cell fate determination in higher eukaryotes. However, the upstream factors that guide the establishment and spreading of H3K9me3-heterochromatin, leading to human developmental malformations, remain elusive. In this study, we found that Cdk13, a member of RNA polymerase II (RNAPII) kinase, suppresses congenital heart syndrome by preventing global facultative H3K9me3-heterochromatin spreading. Additionally, Cdk13 directs the phosphorylation of a large set of heterochromatin proteins at specific sites, which are required for the interaction between HP1 and histone H3K9 methyltransferases. Furthermore, we identified a compound, an inhibitor of heterochromatin regulators, that can alleviate syndromic heart defects in Cdk13-mutant mice through the inhibition of H3K9me3-heterochromatin spreading. In summary, this study reveals a novel role and mechanism of Cdk13-triggered facultative H3K9me3-heterochromatin spreading in human genetic disease and paves the way for the treatment of congenital heart syndrome.

genetics↗

A molecular proximity sensor based on an engineered, dual-component guide RNA

One of the goals of synthetic biology is to enable the design of arbitrary molecular circuits with programmable inputs and outputs. Such circuits bridge the properties of electronic and natural circuits, processing information in a predictable manner within living cells. Genome editing is a potentially powerful component of synthetic molecular circuits, whether for modulating the expression of a target gene or for stably recording information to genomic DNA. However, programming molecular events such as protein-protein interactions or induced proximity as triggers for genome editing remains challenging. Here we demonstrate a strategy termed "P3 editing", which links protein-protein proximity to the formation of a functional CRISPR-Cas9 dual-component guide RNA. By engineering the crRNA:tracrRNA interaction, we demonstrate that various known protein-protein interactions, as well as the chemically-induced dimerization of protein domains, can be used to activate prime editing or base editing in human cells. Additionally, we explore how P3 editing can incorporate outputs from ADAR-based RNA sensors, potentially allowing specific RNAs to induce specific genome edits within a larger circuit. Our strategy enhances the controllability of CRISPR-based genome editing, facilitating its use in synthetic molecular circuits deployed in living cells.

synthetic biology↗

Butyrate Protects against SARS-CoV-2-induced Tissue Damage in Golden Hamsters.

Butyrate, produced by gut microbe during dietary fiber fermentation, plays anti-inflammatory and antioxidant effects in chronic inflammation diseases, yet it remains to be explored whether butyrate has protective effects against viral infections. Here, we demonstrated that butyrate alleviated tissue injury in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected golden hamsters with supplementation of butyrate before and during the infection. Butyrate-treated hamsters showed augmentation of type I interferon (IFN) response and activation of endothelial cells without exaggerated inflammation. In addition, butyrate regulated redox homeostasis by enhancing the activity of superoxide dismutase (SOD) to inhibit excessive apoptotic cell death. Therefore, butyrate exhibited an effective prevention against SARS-CoV-2 by upregulating antiviral immune responses and promoting cell survival. IMPORTANCESince SARS-CoV-2 has caused severe disease characterized by acute respiratory distress syndrome (ARDS) in humans, it is essential to develop therapeutics based on relieving such severe clinical symptoms. Current therapy strategies mainly focus on individuals who have COVID-19, however, there is still a strong need for prevention and treatment of SARS-CoV-2 infection. This study showed that butyrate, a bacterial metabolite, improved the response of SARS-CoV-2-infected hamsters by reducing immunopathology caused by impaired antiviral defenses and inhibiting excessive apoptosis through reduction in oxidative stress.

microbiology↗

Microglia Regulate Sleep via Calcium-Dependent Modulation of Norepinephrine Transmission

Sleep interacts reciprocally with immune system activity, but its specific relationship with microglia - the resident immune cells in the brain - remains poorly understood. Here we show that microglia can regulate sleep through a mechanism involving Gi-coupled GPCRs, intracellular Ca2+ signaling, and suppression of norepinephrine transmission. Chemogenetic activation of microglia Gi signaling strongly promoted sleep, whereas pharmacological blockade of Gi-coupled P2Y12 receptors decreased sleep. Two-photon imaging showed that P2Y12/Gi activation elevated microglia intracellular Ca2+, and blockade of this Ca2+ elevation largely abolished the Gi-induced sleep increase. Microglia Ca2+ level also increased at natural wake-to-sleep transitions, caused partly by reduced norepinephrine. Furthermore, imaging of norepinephrine activity with its biosensor showed that microglia P2Y12/Gi activation significantly reduced norepinephrine, partly by increasing the adenosine concentration. Thus, microglia can regulate sleep through reciprocal interactions with norepinephrine transmission.

neuroscience↗

Discovery of post-translationally modified self-peptides that promote hypertension

Post translational modifications can enhance immunogenicity of self-proteins. In several conditions including hypertension, systemic lupus, and heart failure, isolevuglandins (IsoLGs) are formed by lipid peroxidation and covalently bond with protein lysine residues. Here we show that the murine class-I major histocompatibility complex (MHC-I) variant H-2Db uniquely presents isoLG modified peptides and developed a computational pipeline that identifies structural features for MHC-I accommodation of such peptides. We identified isoLG-adducted peptides from renal proteins including the sodium glucose transporter 2, Cadherin 16, Kelch Domain containing protein 7A and solute carrier family 23, that are recognized by CD8+ T cells in tissues of hypertensive mice, induce T cell proliferation in vitro, and prime hypertension after adoptive transfer. Finally, we find similar patterns of isoLG-adducted antigen restriction in class-I human leukocyte antigens as in murine analogues. Thus, we have used a combined computational and experimental approach to define likely antigenic peptides in hypertension.

immunology↗

Population suppression by release of insects carrying a dominant sterile homing gene drive targeting doublesex in Drosophila

Gene drive alleles, which bias their own inheritance and increase in frequency, show great promise for blocking disease transmission or directly suppressing pest populations. The most common engineered drive system is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of drive heterozygotes by homology-directed repair after CRISPR cleavage. One successful homing drive example targets a female-specific exon in doublesex in Anopheles mosquitos, suppressing the population by inducing recessive sterility in female drive homozygotes. We found that in Drosophila melanogaster, a 3-gRNA drive disrupting the doublesex female exon resulted in a masculine phenotype and dominant female sterility. Resistance alleles formed by end-joining repair were also dominant sterile. This was likely caused by expression of male-specific transcripts in females with drive and resistance alleles, disrupting sex development. Based on this construct, we proposed a new pest suppression system called "Release of Insects carrying a Dominant-sterile Drive" (RIDD). This entails continuously releasing drive heterozygous males, with drive and resistance alleles causing sterility in females. The drive remains at high frequency longer than currently used dominant female-lethal alleles (RIDL) due to drive conversion in males, and drive alleles also cause sterility based on resistance, both substantial advantages. With weekly releases of drive males into a cage population with overlapping generations, our RIDD system targeting dsx reached 100% prevalence within 27 weeks, progressively reducing egg production and eventually causing total population collapse. RIDD combines the merits of homing gene drive and RIDL. It is powerful but self-limiting, unlike unconfined standard homing drives, allowing for targeted population suppression.

genetics↗

New germline Cas9 promoters show improved performance for homing gene drive

Gene drive systems could be a viable strategy to prevent pathogen transmission or suppress vector populations by propagating drive alleles with super-Mendelian inheritance. CRISPR-based homing gene drives, perhaps the most powerful gene drive strategy, convert wild type alleles into drive alleles in heterozygotes with the help of Cas9 and gRNA. However, achieving successful outcomes with these drives often requires high performance. Specifically, it is desirable to identify Cas9 promoters that yield high drive conversion rates, minimize the formation rate of resistance alleles in both the germline and the early embryo, and limit somatic Cas9 expression. Thus far, high-performance promoters have only been discovered in Anopheles species. In Drosophila, the nanos promoter avoids leaky somatic expression, but at the cost of high embryo resistance from maternally deposited Cas9. To improve drive efficiency, we tested eleven Drosophila melanogaster germline promoters in several configurations. Some of the new promoters achieved higher drive conversion efficiency with minimal embryo resistance, but none could completely avoid somatic expression like nanos. However, such somatic expression often did not carry detectable fitness costs when the promoter-Cas9 elements supported a rescue homing drive targeting a haplolethal gene, suggesting somatic drive conversion. Based on our findings, we selected two Cas9 promoter lines for cage experiments with a 4-gRNA suppression drive. While one promoter exhibited substantial somatic effects, leading to a low drive equilibrium frequency, the other outperformed nanos, resulting in the successful suppression of the cage population. Overall, these novel Cas9 promoters hold potential advantages for homing drives in Drosophila species and may also possess valuable homologs in other organisms.

genetics↗

Structure and engineering of miniature Acidibacillus sulfuroxidans Cas12f1

The miniature CRISPR-Cas12f nucleases allow for efficient delivery via cargo-size-limited adeno-associated virus delivery vehicles, thereby showing promising potential for in vivo therapeutic applications. Acidibacillus sulfuroxidans Cas12f1 (AsCas12f1, 422 amino acids) is the most compact Cas12f nuclease identified to date, showing a moderate level of genome-editing activity in human cells compared to Cas9 and Cas12a. Understanding the mechanisms of why such a compact nuclease is active for genome editing would facilitate its rational engineering. Here, we report the cryo-EM structure of the AsCas12f1-sgRNA-dsDNA ternary complex, and reveal that AsCas12f1 functions as an asymmetric dimer for single-guide RNA (sgRNA) binding and DNA targeting. The detailed mechanisms for dimer formation, PAM recognition, and sgRNA accommodation are elucidated. Leading by the structural knowledge, we extensively engineer the AsCas12f1 nuclease and its corresponding sgRNA, resulting in an evolved AsCas12f1-sgRNA combination with drastically enhanced genome editing activity in human cells. These results provide further understanding of compact CRISPR systems and expand the mini CRISPR toolbox for therapeutic applications.

molecular biology↗

Endothelial Knockdown of the Tumor Suppressor, WWOX, Increases Inflammation in Ventilator-Induced Lung Injury

BackgroundChronic cigarette smoke exposure downregulates lung expression of WWOX, an ARDS relevant tumor suppressor. Prior work has revealed a barrier protective function of WWOX during infectious models of ARDS. Proteomic analysis of WWOX-silenced lung endothelial cells suggest involvement of WWOX in protection against mechanical stretch-induced inflammation. MethodsProtein lysates from WWOX-silenced endothelial cells (ECs) were analyzed using tandem mass tag mass spectrometry (TMT-MS) to determine the differential expression status of the proteome compared to wild type ECs. WWOX-silenced ECs as well as those isolated from endothelial Wwox knockout (EC Wwox KO) mice were subjected to cyclic stretch (18% elongation, 0.5 Hz, 4 hours). Cellular lysates and media supernatant were harvested for assays of cellular signaling, protein expression, and cytokine release. Dual silencing of WWOX and zyxin was achieved to determine the role of zyxin upregulation in IL-8 production following mechanical stretch and during WWOX knockdown. Control and EC Wwox KO mice were subjected to high tidal volume ventilation (VILI, 40ml/kg, 65 breath/min, 4hours). Bronchoalveolar lavage fluid and mouse lung tissue were harvested for cellular signaling, cytokine secretion, and histologic assays. ResultsTMT-MS revealed upregulation of zyxin expression during WWOX knockdown which predicted a heightened inflammatory response to mechanical stretch. WWOX-silenced ECs and ECs isolated from EC Wwox mice displayed significantly increased cyclic stretch-mediated secretion of various cytokines (IL-6, KC/IL-8, IL-1{beta}, and MCP-1) relative to controls. This was associated with increased ERK and JNK phosphorylation but decreased p38 MAPK phosphorylation. EC Wwox KO mice subjected to VILI sustained a greater degree of injury than corresponding controls. Silencing of zyxin during WWOX knockdown abrogated stretch-induced increases in IL-8 secretion. ConclusionLoss of WWOX function in ECs is associated with a heightened inflammatory response during mechanical stretch that is associated with increased MAPK phosphorylation and appears to be dependent on upregulation of zyxin.

molecular biology↗

Evolution of Shewanella oneidensis MR-1 in competition with Citrobacter freundii

Interspecific competition is one of the most important metabolic interactions within microbial communities, and exoelectrogenic bacteria that can conduct extracellular electron transfer act essential roles in nature and engineering systems for pollutants removal. In the present study we investigated the long-term impact of substrate competition from non-exoelectrogenic Citrobacter freundii An1 on exoelectrogenic Shewanella oneidensis MR-1. Without additional electron acceptor or with electron acceptor of oxygen, C. freundii An1 typically suppressed the growth of S. oneidensis MR-1. In contrast, S. oneidensis MR-1 grown better with electron acceptor of ferrihydrite by taking advantage of extracellular electron transfer. However, the presence of ferrihydrite did not enhance the ferrihydrite reduction of S. oneidensis MR-1 after the 160 d-acclimation. The whole genome resequencing showed a complex evolution of S. oneidensis MR-1 when the strain faced the competition from C. freundii An1 for substrate.

microbiology↗

Building a genetic and epigenetic predictive model of breast cancer intrinsic subtypes using large-scale data and hierarchical structure learning

Breast cancer subtyping is a difficult clinical and scientific challenge. The prevalent Prediction Analysis of Microarray of 50 genes (PAM50) system and its Immunohistochemistry (IHC) surrogate showed significant inconsistencies. This is because of the limited training samples, highly variable molecular features and in-efficient strategies used in these classifiers. The rapid development of early screening technologies, especially in the field of circulating tumor DNA, has also challenged the subtyping of breast cancer at the DNA level. By integrating large-scale DNA-level data and using a hierarchical structure learning algorithm, we developed Unified Genetic and Epigenetic Subtyping (UGES), a new intrinsic subtype classifier. The benchmarks showed that the use of all classes of DNA alterations worked much better than single classes, and that the multi-step hierarchical learning is crucial, which improves the overall AUC score by 0.074 compared to the one-step multi-classification method. Based on these insights, the ultimate UGES was trained as a three-step classifier on 50831 DNA features of 2065 samples, including mutations, copy number aberrations, and methylations. UGES achieved overall AUC score 0.963, and greatly improved the clinical stratification of patients, as each stratas survival difference became statistically more significant p-value=9.7e-55 (UGES) vs 2.2e-47 (PAM50). Finally, UGES identified 52 subtype-level DNA biomarkers that can be targeted in early screening technology to significantly expand the time window for precision care. The analysis code is freely available at https://github.com/labxscut/UGES.

bioinformatics↗

Macrophages modulate fibrosis during newt lens regeneration

Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. Next, we used clodronate liposomes to deplete macrophages, which inhibited lens regeneration in both newt species. Macrophage depletion induced the formation of scar-like tissue, an increased and sustained inflammatory response, an early decrease in iris pigment epithelial cell (iPEC) proliferation and a late increase in apoptosis. Some of these phenotypes persisted for at least 100 days and could be rescued by exogenous FGF2. Re-injury alleviated the effects of macrophage depletion and re-started the regeneration process. Together, our findings highlight the importance of macrophages in facilitating a pro-regenerative environment in the newt eye, helping to resolve fibrosis, modulating the overall inflammatory landscape and maintaining the proper balance of early proliferation and late apoptosis.

developmental biology↗

Exploring Urban Street Green Perception from the Perspective of Combining GVI and NDVI: A Case Study of Zhongshan City, Guangdong Province

Urban street greening has a positive impact on the health of citizens and the urban environment. This study takes the representative streets in the main urban area of Zhongshan City, Guangdong Province as an example to explore urban street greening perception from the perspective of combining Green visual index (GVI) and Normalized difference vegetation index (NDVI). This study uses a deep learning based image semantic segmentation method to analyze Baidu Street View to calculate the GVI of the street, and uses GF-1 satellite data to calculate NDVI to compare and analyze the characteristics and correlation of GVI and NDVI of urban streets. The results show that: 1. The GVI of streets in the central urban area of Zhongshan varies from 8.06% to 36.00%, with Xingzhong Road in Shiqi District Street having the highest GVI; 2. The mean value of NDVI of each street shows different changes with the increase of buffer scale, and the mean value of NDVI has a strong scale sensitivity; 3. The highest Pearson correlation coefficient between GVI and 25m DNVI mean value was 0.862; 4. The GVI prediction model based on NDVI is: y=0.8249x+0.0181, R2=0.7433. On this basis, the shortcomings of street landscape are analyzed and optimization suggestions are given, providing reference for urban street landscape evaluation, spatial optimization, and landscape improvement.

ecology↗

Long-read sequencing reveals extensive DNA methylations in human gut phagenome contributed by prevalently phage-encoded methyltransferases

DNA methylation is essential for the survival of bacteriophages (phages), yet, we know little about the methylation of their genomes. Here, we analyze the DNA methylation patterns of 8,848 metagenome-assembled high-quality phages across 104 fecal samples using single-molecule real-time (SMRT) sequencing. We show that 97.60% of gut phages could be methylated, and reveal factors that correlate with methylation densities. Phages having higher methylation densities are more prevent, suggesting putative viability advantages of the DNA methylation. Strikingly, more than a third of the phages encode their own DNA methyltransferases (MTases). More MTase copies are associated with increased genome methylation densities, methylation motifs, and higher prevalence of certain phage groups. Most MTases are closely homologous to gut bacterium-encoded ones, likely exchanged during phage-bacterium interactions, and could be used to accurately predict phage-host relationships. Taken together, our results suggest that the gut DNA phages universally use DNA methylation to escape from host defense systems with significant contribution from phage-encoded MTases.

bioinformatics↗

Combining Bacteriophage and Vancomycin is Efficacious Against MRSA biofilm-like Aggregates Formed in Synovial Fluid

BackgroundBiofilm formation is a major clinical challenge contributing to treatment failure of periprosthetic joint infection (PJI). Lytic bacteriophages (phages) can target biofilm associated bacteria at localized sites of infection. The aim of this study is to investigate whether combination therapy of phage and vancomycin is capable of clearing Staphylococcus aureus biofilm-like aggregates formed in human synovial fluid. MethodsIn this study, S. aureus BP043, a PJI clinical isolate was utilized. This strain is a methicillin-resistant S. aureus (MRSA) biofilm-former. Phage Remus, known to infect S. aureus, was selected for the treatment protocol. BP043 was grown as aggregates in human synovial fluid. The characterization of S. aureus aggregates was assessed for structure and size using scanning electron microscopy (SEM) and flow cytometry, respectively. Moreover, the formed aggregates were subsequently treated in vitro with: a) phage Remus ([~]108 plaque-forming units (PFU)/mL), b) vancomycin (500 {micro}g/mL), or c) phage Remus ([~]108 PFU/mL) followed by vancomycin (500 {micro}g/mL), for 48 hours. Bacterial survival was quantified by enumeration (colony-forming units (CFU)/ mL). The efficacy of phage and vancomycin against BP043 aggregates was assessed in vivo as individual treatments and in combination. The in vivo model utilized Galleria mellonella larvae which were infected with BP043 aggregates pre-formed in synovial fluid. ResultsSEM images and flow cytometry data demonstrated the ability of human synovial fluid to promote formation of S. aureus aggregates. Treatment with Remus resulted in significant reduction in viable S. aureus residing within the synovial fluid aggregates compared to the aggregates that did not receive Remus (p < 0.0001). Remus was more efficient in eliminating viable bacteria within the aggregates compared to vancomycin (p < 0.0001). Combination treatment of Remus followed by vancomycin was more efficacious in reducing bacterial load compared to using either Remus or vancomycin alone (p = 0.0023, p < 0.0001, respectively). When tested in vivo, this combination treatment also resulted in the highest survival rate (37%) 96 hours post-treatment, compared to untreated larvae (3%; p < 0.0001). ConclusionWe demonstrate that combining phage Remus and vancomycin led to synergistic interaction against MRSA biofilm-like aggregates in vitro and in vivo.

microbiology↗

Hybrid vesicle and reaction-diffusion modeling with STEPS

Vesicles carry out many essential functions within cells through the processes of endocytosis, exocytosis, and passive and active transport. This includes transporting and delivering molecules between different parts of the cell, and storing and releasing neurotransmitters in neurons. To date, computational simulation of these key biological players has been rather limited and has not advanced at the same pace as other aspects of cell modeling. As computational power advances and researchers want to add new realism to their models an important advance in the field of computational biology is to simulate vesicles in a realistic yet efficient manner. We describe a general vesicle modeling tool that has been designed for wide application to a variety of cell models, implemented within our voxel-based approach to modeling reaction-diffusion processes in realistic mesh reconstructions of cell tissue in our software STEPS. The implementation is validated in an extensive test suite, parallel performance demonstrated in a realistic synaptic bouton model, and example models are visualized in a Blender extension module.

systems biology↗

Aging-associated Decline in Vascular Smooth Muscle Cell Mechanosensation is Mediated by Piezo1 Channel

Aging of the vasculature is associated with detrimental changes in vascular smooth muscle cell (VSMC) mechanosensitivity to extrinsic forces in their surrounding microenvironment. However, how chronological aging alters VSMCs ability to sense and adapt to mechanical perturbations remains unexplored. Here, we show defective VSMC mechanosensation in aging measured with ultrasound tweezers-based micromechanical system, force instantaneous frequency spectrum and transcriptome analyses. The mechanobiological study reveals that aged VSMCs adapt a relatively inert solid-like state with altered actin cytoskeletal integrity, resulting in an impairment in their mechanosensitivity and dynamic mechanoresponse to mechanical perturbations. The aging-associated decline in mechanosensation behaviors is mediated by hyperactivity of Piezo1-dependent calcium signaling. Inhibition of Piezo1 alleviates vascular aging and partially restores the loss in dynamic contractile properties in aged cells. Altogether, our study reveals the novel signaling pathway underlying aging-associated aberrant mechanosensation in VSMC and identifies Piezo1 as a potential therapeutic mechanobiological target to alleviate vascular aging.

bioengineering↗