Biology subjects

Wang, C.

Publications and source records attributed to Wang, C..

At least 667 records · Page 37Linked to original sources

bioRxiv2022

A Host-Harbored Metabolic Susceptibility of Coronavirus Enables Broad-Spectrum Targeting

Host-based antivirals could offer broad-spectrum therapeutics and prophylactics against the constantly-mutating viruses including the currently-ravaging coronavirus, yet must target cellular vulnerabilities of viruses without grossly endangering the host. Here we show that the master lipid regulator SREBP1 couples the phospholipid scramblase TMEM41B to constitute a host "metabolism-to-manufacture" cascade that maximizes membrane supplies to support coronaviral genome replication, harboring biosynthetic enzymes including Lipin1 as druggable viral-specific-essential (VSE) host genes. Moreover, pharmacological inhibition of Lipin1, by a moonlight function of the widely-prescribed beta-blocker Propranolol, metabolically uncouples the SREBP1-TMEM41B cascade and consequently exhibits broad-spectrum antiviral effects against coronaviruses, Zika virus, and Dengue virus. The data implicate a metabolism-based antiviral strategy that is well tolerated by the host, and a potential broad-spectrum medication against current and future coronavirus diseases.

cell biology↗

bioRxiv2022

Inhibiting POLQ-mediated alternative NHEJ enhances CRISPR/Cas9 mediated precise genome editing in CHO cells

CRISPR/Cas9 mediated precise gene editing requires homology-directed repair (HDR), which occurs less frequently than non-homologous end-joining (NHEJ) including the canonical NHEJ and alternative NHEJ (Alt-EJ) in mammalian cells, especially in CHO cells that inherent resist HDR. To solve the above hurdle, here we for the first time show that knockout the DNA polymerase {theta} (POL{theta}), which is essential for Alt-EJ, significantly increases the knock-in efficiency by nearly forty-fold in CHO cells via eGFP reporter system and does not affect the normal growth and proliferation of cells. Meanwhile, even when transfecting simple circular, without negative element homologous template DNA donor and CRISPR/Cas9 plasmid to two different genomic sites, the knock-in rate of 4kb donor integration can still reach a mean of over 80% (29/36) and 2.7% (1/36) of the selected cell colonies in POLQ-/- CHO cells, however, no positive knock-in cell colonies was obtained in wild-type CHO cells which respectively selected 62 cell colonies and 36 cell colonies. Furthermore, we show that POLQ promotes random integration in CHO cells. Finally, RNA-sequence analysis reveals not significant altered DNA repair, metabolism, apoptosis, and cell cycle in POLQ-/- cells. These findings open a new target gene POLQ to overcome bottlenecks of the precision genome editing.

bioengineering↗

bioRxiv2022

A unified classification system for HIV-1 5' long terminal repeats

The HIV-1 provirus mainly consists of internal coding region flanked by the 2 same long terminal repeats (LTRs) at each terminus. The LTRs play important roles in HIV-1 reverse transcription, integration, and transcription by the association with host factors. However, despite of the significant study advances of the internal coding regions of HIV-1 by using definite reference classification, there are no systematic classifications for HIV-1 5 LTRs, which hinders our elaboration on 5 LTR and a better understanding of the viral origin, spread and therapy. Here, by analyzing all available resources of 5 LTR sequences in public databases following 4 recognized principles for the reference classification, 83 representatives and 14 consensus sequences were identified as representatives of 2 groups, 6 subtypes, 6 sub-subtypes, and 9 CRFs. To test the reliability of our established classification system, the constructed references were applied to identify the 5 LTR assignment of the 22 clinical isolates in China. The results revealed that 16 out of 22 tested strains showed a consistent subtype classification with the previous LTR-independent classification system. However, 6 strains, for which recombination events within 5 LTR were demonstrated, unexpectedly showed a different subtype classification, leading a significant change of binding sites for important transcription factors including SP1, p53, and NF-{kappa}B. The binding change of these transcriptional factors would probably affect the transcriptional activity of 5 LTR. This study established a unified classification system for HIV-1 5 LTRs, which will facilitate HIV-1 characterization and be helpful for both basic and clinical research fields. IMPORTANCEHere, a scientific, reliable, and usable classification system based on the 5 LTR sequences was established, which will allow us to effectively facilitate the precise typing of HIV-1 strains. This classification system was applied to 22 HIV-1 strains circulating in China, we found that 6 out of 22 strains analyzed, belonged to a different subtype when our results were compared to those obtained with the previous LTR-independent classification system. Thus, these data demonstrated that our classification method could greatly improve the HIV-1 subtype classification. We found that 6 5 LTR sequences showed recombination events, leading to a significant exchange of the binding sites of transcriptional factors. Thus, this work established a comprehensive HIV-1 5 LTR classification system, which will help the scientific community to precisely characterize HIV-1 variants, and better understand the origin and spread of HIV-1 strains, and it also may be helpful for pathogenicity and transmissibility evaluation studies.

microbiology↗

bioRxiv2022

Genome-wide Identification and Expression Profile Analysis of Laccase Family Genes in the Hypsizygus marmoreus

Laccase exists widely in plants and fungi. It is a copper-containing polyphenol oxidase that can degrade lignin, oxidate, and phenolic substances, inhibit heterophytes, promote fruiting body formation, and improve the quality of mushrooms. In this study, 18 laccase genes were identified from the whole genome of a white strain (HM62) of Hypsizygus marmoreus, and the mapping, structure, and evolution of laccase genes were analyzed at the whole genome level, while the spatiotemporal expression was evaluated at different developmental stages. The laccase genes mainly distributed on chromosomes 1, 2, 3, 4, 6, 9, and 10, and 9 genes were clustered linearly on chromosome 6, indicating gene doubling. Phylogenetic tree analysis showed that the laccase gene family was divided into three subfamilies. The spatiotemporal expression analysis of the laccase gene family showed that HmLac09 and HmLac10 were highly expressed in different periods and might be involved in lignin degradation and fruit body formation, respectively. The expression levels of HmLac02, HmLac05, HmLac08, and HmLac17 genes in gray or gray and white heterozygous strains were higher than those in white strains, which might be related to the difference in lignin decomposition in gray strains, and one of the factors leading to different growth rates. The present study investigated the characterization of the H. marmoreus laccase gene family, extending our understanding of laccase mediated fruiting body development and growth rate mechanisms in this fungi.

microbiology↗

bioRxiv2022

scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data

In droplet-based single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) assays, systematic contamination of ambient RNA molecules biases the estimation of genuine transcriptional levels. To correct the contamination, several computational methods have been developed. However, these methods do not distinguish the contamination-causing genes and thus either under- or over-corrected the contamination in our in-house snRNA-seq data of virgin and lactating mammary glands. Hence, we developed scCDC as the first method that specifically detects the contamination-causing genes and only corrects the expression counts of these genes. Benchmarked against existing methods on synthetic and real scRNA-seq and snRNA-seq datasets, scCDC achieved the best contamination correction accuracy with minimal data alteration. Moreover, scCDC applies to processed scRNA-seq and snRNA-seq data with empty droplets removed. In conclusion, scCDC is a flexible, accurate decontamination method that detects the contamination-causing genes, corrects the contamination, and avoids the over-correction of other genes.

bioinformatics↗

bioRxiv2022

scFormer: A Universal Representation Learning Approach for Single-Cell Data Using Transformers

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell sequencing has emerged as a promising technique to decode cellular heterogeneity and analyze gene functions. With the high throughput of modern techniques and resulting large-scale sequencing data, deep learning has been used extensively to learn representations of individual cells for downstream tasks. However, most existing methods rely on fully connected networks and are unable to model complex relationships between both cell and gene representations. We hereby propose scFormer, a novel transformer-based deep learning framework to jointly optimize cell and gene embeddings for single-cell biology in an unsupervised manner. By drawing parallels between natural language processing and genomics, scFormer applies self-attention to learn salient gene and cell embeddings through masked gene modelling. scFormer provides a unified framework to readily address a variety of downstream tasks such as data integration, analysis of gene function, and perturbation response prediction. Extensive experiments using scFormer show state-of-the-art performance on seven datasets across the relevant tasks. The scFormer model implementation is available at https://github.com/bowang-lab/scFormer.

bioinformatics↗

bioRxiv2022

Extracting Mitochondrial Cristae Characteristics from 3D Focused Ion Beam Scanning Electron Microscopy Data

1Mitochondria are the main suppliers of energy for cells and their bioenergetic function is regulated by mitochondrial dynamics: the constant changes in mitochondria size, shape, and cristae morphology to secure cell homeostasis. Although mitochondrial dysfunction is implicated in a wide range of diseases, our understanding of mitochondrial function remains limited by the complexity of inferring these spatial features from 2D electron microscopical (EM) images of intact tissue. Here, we present a semi-automatic method for segmentation and 3D reconstruction of mitochondria, cristae, and intracristal spaces based on 2D EM images of the murine hippocampus. We show that our method provides a more accurate characterization of mitochondrial ultrastructure in 3D than common 2D approaches and propose an operational index of mitochondrias internal organization. We speculate that this tool may help increase our understanding of mitochondrial dynamics in health and disease.

neuroscience↗

bioRxiv2022

Peyers Patch B cells undergo cell death via neutrophil-released toxic DNA following sterile tissue injury

Lymphocyte contraction (LC) in central immune organs is a concomitant of sterile tissue injury, for example after stroke. Intestinal Peyers patches (PP) harbor large numbers of B cells, but how sterile tissue injury leads to LC in PP has not been explored. We observed rapid and macroscopically evident shrinkage of PP after stroke and myocardial infarction. Light-sheet fluorescence microscopy and flow cytometry revealed a strong reduction in the number of PP-resident B cells. Mechanistically, tissue injury triggered the activation of neutrophils that released B cell-toxic neutrophil extracellular traps (NETs) decorated with citrullinated histone-H3. Antibody-mediated or genetically induced neutrophil-loss, NETs-degradation or blockade of their generation completely reversed B cell loss and preserved the tissue architecture of PP. We also found NET-like elements in human post-stroke plasma. Hence, we propose that targeting NET-generation or -function counteracts post-injury B cell contraction in PP and thereby maintains immune homeostasis at mucosal barriers. In briefHigh numbers of B cells reside in the intestinal Peyers patches. Tuz et al. revealed that in response to sterile tissue injury, activated neutrophils release histone-decorated DNA into the circulation which induces B cell death. The loss of B cells results in the shrinkage of Peyers patches and reduced amounts of secretory IgA. HighlightsO_LIStroke and myocardial infarction induce the melting of Peyers patch C_LIO_LILight-sheet microscopy and cytometry revealed B cell loss in Peyers patch C_LIO_LIPost-injury activated neutrophils release NETs and trigger B cell death C_LIO_LIInhibition of NETs rescues B cell loss and degeneration of Peyers patch C_LI

immunology↗

bioRxiv2022

Oral Feeding of Nanoplastics reduces Brain function of Mice by Inducing Intestinal IL-1β-producing Macrophages

Background and AimsNanoplastics (NPs) as contaminants in food and water have drawn an increasing public attention. However, little is known about how NPs shape the gut immune landscape after entering the body. The objective of the study was to explore indirect effects caused by the interaction of NPs with the mammalian gut and whole immune system after entering the body. MethodsIn this study, we fabricated NPs ([~]500 nm) and microplastics (MPs) ([~]2 m) and aimed to evaluate their in vivo effects by feeding them in mice. The mechanism was then investigated by various technology including single-cell RNA sequencing of gut and brain tissue. ResultsThe results suggested that NPs showed a better ability to induce gut macrophage activation than did MPs. In addition, NPs triggered gut interleukin 1 beta (IL-1{beta})-producing macrophage reprogramming via inducing lysosomal damage after phagocytosis. More importantly, IL-1{beta} released from the intestine could affect brain immunity, leading to microglial activation and Th17 differentiation, all of which correlated with a decline in cognitive and short-term memory in NPs-fed mice ConclusionsThus, this study provides new insight into the mechanism of action of the gut-brain axis and delineates the way NPs reduce brain function, highlights the importance to fix the plastic pollution problem worldwide.

immunology↗

bioRxiv2022

LSR Targets YAP to Modulate Intestinal Paneth Cell Differentiation

Lipolysis-stimulated lipoprotein receptor (LSR) is a multi-functional protein that is best known for its roles in assembly of epithelial tricellular tight junctions and hepatic clearance of lipoproteins. Here, we investigated whether LSR contributes to intestinal epithelium homeostasis and pathogenesis of intestinal disease. By using multiple conditional deletion mouse models and ex vivo cultured organoids, we find that LSR elimination in intestinal stem cells results in disappearance of Paneth cell without affecting the differentiation of other cell lineages. Mechanistic studies reveal that LSR deficiency increases abundance and nuclear localization of YAP by modulating its phosphorylation and proteasomal degradation. Using gain- and loss-of-function studies we show that LSR protects against necrotizing enterocolitis through enhancement of Paneth cell differentiation in small intestinal epithelium. Thus, this study identifies LSR as an upstream negative regulator of YAP activity, an essential factor for Paneth cell differentiation, and a potential novel therapeutic target for inflammatory bowel disease.

cell biology↗

bioRxiv2022

BrainPy: a flexible, integrative, efficient, and extensible framework towards general-purpose brain dynamics programming

The neural mechanisms underlying brain functions are extremely complicated. Brain dynamics modeling is an indispensable tool for elucidating these mechanisms by modeling the dynamics of the neural circuits that execute brain functions. To ease and facilitate brain dynamics modeling, a general-purpose programming framework is needed to enable users to freely define neural models across multiple scales; efficiently simulate, train, and analyze model dynamics; and conveniently extend new modeling approaches. By utilizing the advanced just-in-time (JIT) compilation, we developed BrainPy. BrainPy provides a rich infrastructure tailored for brain dynamics programming, which supports an integrated platform for brain dynamics model building, simulation, training, and analysis. Models in BrainPy can be JIT compiled into binary instructions for multiple devices (including CPU, GPU, and TPU) to achieve a high running performance comparable to native C or CUDA. Moreover, BrainPy features an extensible architecture allowing easy expansion of new infrastructure, utilities, and machine learning approaches.

neuroscience↗

bioRxiv2022

Determination of insulin secretion from stem cell-derived islets with liquid chromatography-tandem mass spectrometry

Organoids are laboratory-grown 3D organ models, mimicking human organs for e.g. drug development and personalized therapy. Islet organoids (typically 100-200 m), which can be grown from the patients own cells, are emerging as prototypes for transplantation-based therapy of diabetes. Selective methods for quantifying insulin production from islet organoids are needed, but sensitivity and carry-over have been major bottlenecks in previous efforts. We have developed a reverse phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) method for studying the insulin secretion of islet organoids. In contrast to our previous attempts using nano-scale LC columns, conventional 2.1 mm inner diameter LC column (combined with triple quadrupole mass spectrometry) was well suited for sensitive and selective measurements of insulin secreted from islet organoids with low microliter-scale samples. Insulin is highly prone to carry-over, so standard tubings and injector parts were replaced with shielded fused silica nanoViper connectors. As samples were expected to be very limited, an extended Box-Behnken experimental design for the MS settings was conducted to maximize performance. The finale method has excellent sensitivity, accuracy and precision (limit of detection: [≤] 0.2 pg/L, relative error: [≤] {+/-}10%, relative standard deviation: < 10%), and was well suited for measuring 20 L amounts of Krebs buffer containing insulin secreted from islet organoids.

bioengineering↗

bioRxiv2022

Microsecond pulse electrical stimulation modulates cell migration

Wound healing is a complicated process for maintaining skin integrity after injury, for which electrical stimulations (ES) are ascribed to promote wound healing by facilitating cell migration. Time-shortening of the stimulation treatment from current hours to minutes for efficient wound healing but free of cell damage in return, is however rather a challenge. Here, a novel mechanism of ultrashort pulse electric field (PEF), microsecond PEF at higher voltage, is proposed and realized to promote wound healing under a much short time (seconds) for the total treatment. We revealed that microsecond PEF regulated actin cytoskeleton reorganization and focal adhesion turnover, promoting fibroblasts migration in 2D cell cultures under the pulse stimulation. This accelerated fibroblast migration was accompanied by the mutual promotion with extracellular matrix (ECM) alignment in 3D microenvironments, which cooperatively benefit the eventual wound healing, and these findings were further confirmed by the enhanced skin wound healing in a classic mouse model. Additionally, we coined an actin- and collagen-dependent mechanism of microsecond PEF-mediated wound healing. The quantitative mechanism proposed here for our novel microsecond pulse electric filed (sPEF) methodology orients the new practical electric treatment in a wide range of biomedical applications, such as wound healing, regenerative medicine, and tissue engineering.

bioengineering↗

bioRxiv2022

Macaque Brainnetome Atlas with Fine-grained Parcellations and Reliable Connections

The rhesus macaque (Macaca mulatta) is a crucial experimental animal that shares many genetic, brain organizational, and behavioral characteristics with humans. A macaque brain atlas that identifies anatomically and functionally distinct regions is fundamental to biomedical and evolutionary research. However, even though connectivity information is vital for understanding brain functions, a connectivity-based whole-brain atlas of the macaque has not previously been made. In this study, we created a new whole-brain map, the Macaque Brainnetome Atlas (MacBNA), based on the anatomical connectivity profiles provided by high angular and spatial resolution ex vivo diffusion MRI data. The new atlas consists of 248 cortical and 56 subcortical regions as well as their structural and functional connections. The parcellation and the diffusion-based tractography were comprehensively evaluated with multi-contrast MRI, invasive neuronal-tracing, and Nissl-stained images collected from a single subject and with open-access datasets from other cohorts. As a demonstrative application, the structural connectivity divergence between macaque and human brains was mapped using the Brainnetome atlases of those two species to uncover the genetic underpinnings of the evolutionary changes in brain structure. The resulting resource includes (1) the thoroughly delineated Macaque Brainnetome Atlas (MacBNA), (2) regional connectivity profiles, (3) the postmortem high resolution macaque diffusion and T2-weighted MRI dataset (Brainnetome-8), and (4) multi-contrast MRI, block-face, and section images collected from a single macaque. MacBNA can serve as a common reference frame for mapping multifaceted features across modalities and spatial scales and for integrative investigation and characterization of brain organization and function. Therefore, it will enrich the collaborative resource platform for nonhuman primates and facilitate translational and comparative neuroscience research.

neuroscience↗

bioRxiv2022

A reversible SRC-relayed COX2-inflammatory program drives therapeutic resistance in BRAF(V600E) colorectal tumors

BRAFV600E mutation confers a poor prognosis in metastatic colorectal cancer (CRC) despite combinatorial targeted therapies based on the latest understanding of signaling circuitry. To identify parallel resistance mechanisms induced by BRAF/MEK/EGFR co-targeting, we used a high throughput kinase activity mapping platform. We found that SRC kinases are systematically activated in BRAFV600E CRC following targeted inhibition of BRAF {+/-} EGFR, and that coordinated targeting of SRC with BRAF {+/-} EGFR increases efficacy in vitro and in vivo. SRC drives resistance to BRAF {+/-} anti-EGFR therapy independently of ERK signaling by inducing transcriptional reprogramming via beta-catenin (CTNNB1). The EGFR-independent compensatory activation of SRC kinases is mediated by an autocrine prostaglandin E2-loop that can be blocked with cyclooxygenase-2 (COX2) inhibitors. Co-targeting of COX2 with BRAF+EGFR promotes durable suppression of tumor growth in patient-derived tumor xenograft (PDX) models. COX2 inhibition represents a novel drug-repurposing strategy to overcome therapeutic resistance in BRAFV600E CRC.

cancer biology↗

bioRxiv2022

FGFR1 governs iron metabolism via regulating post-translational modification of IRP2 in prostate cancer cells

The acquisition of ectopic fibroblast growth factor receptor 1 (FGFR1) expression is well documented in prostate cancer (PCa) progression. However, how FGFR1 facilitates PCa progression is not fully revealed, although it is known to confer tumor growth advantage and metastasis. Here we report that FGFR1 deletion in DU145 human PCa cells retards the iron metabolism and reduces transferrin receptor 1 (TFR1), which synergistically enhances the anti-cancer effect of iron chelator. FGFR1 and TFR1 are highly expressed in PCa, and FGFR1 overexpression increased TFR1 in PCa cell lines. Furthermore, we first time demonstrate that FGFR1 deletion boosts and shifts the degradation of iron regulatory proteins 2 (IRP2) to downregulate TFR1. Detailed characterization revealed that based on FGFR1 deletion the stability of IRP2 is broken, whose degradation is accelerated, which can be not observed without FGFR1 deletion. In addition, IRP2 overexpression rescue the malignancy degree of DU145 cells. Our results here unravel a novel mechanism by which FGFR1 promotes PCa progression by upregulating iron metabolism, and that the FGFR1/IRP2/TFR1 axis can be a potential target for managing PCa progression.

cancer biology↗

bioRxiv2022

Manipulating Oxalate Decarboxylase Provides the Basis of Antilithic Therapy by Acting on the Gut Microbiota

A high concentration of oxalate is associated with an increased risk of kidney calcium oxalate (CaOx) stones, and the degradation of exogenous oxalate mainly depends on oxalate-degrading enzymes from the intestinal microbiome. We found that Zinc Gluconate supplement to patients with CaOx kidney stones could significantly improve the abundance of oxalate metabolizing bacteria in human body through clinical experiments on the premise of simultaneous antibiotic treatment and the imbalance of Lactobacillus and OxDC was involved in CaOx kidney stones through clinical sample analysis. Then, we identified that Zn2+ could be used as an external factor to improve the activity of OxDC and protect Lactobacillus, achieved the preventive effect on rats with stones aggravated by antibiotics. Finally, by analyzing the three-dimensional structure of OxDC and some in vitro experiments, we propose a hypothesis Zn2+ increases the metabolism of oxalate in humans through its positive effects on Lactobacillus and OxDC to reduce CaOx kidney stone symptoms in rats. IMPORTANCEUrinary stone disease is one of the most common urological disorders, and 70%-80% of urinary stones are calcium oxalate (CaOx) stones. We found the structural basis and metabolic mechanism by which oxalate decarboxylase metabolizes oxalate were elucidated, and Zn2+ was illustrated to have therapeutic effects on CaOx stones by improving the tolerance of Lactobacillus to antibiotics. According to that, proper Zn2+ levels in the diet, the consumption of more probiotic food and avoidance of the antibiotic overuse might be desirable measures for the prevention and treatment of kidney stones. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/512337v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@d3df85org.highwire.dtl.DTLVardef@1f7b3f5org.highwire.dtl.DTLVardef@147d861org.highwire.dtl.DTLVardef@1cf046e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Mechanism of dual pharmacological correction and potentiation of human CFTR

Cystic fibrosis (CF) is caused by mutations in a chloride channel called the human Cystic Fibrosis Transmembrane Conductance Regulator (hCFTR). We used cryo-EM global conformational ensemble reconstruction to characterize the mechanism by which the breakthrough drug VX445 (Elexacaftor) simultaneously corrects both protein-folding and channel-gating defects caused by CF mutations. VX445 drives hCFTR molecules harboring the gating-defective G551D mutation towards the open-channel conformation by binding to a site in the first transmembrane domain. This binding interaction reverses the usual pathway of allosteric structural communication by which ATP binding activates channel conductance, which is blocked by the G551D mutation. Our ensemble reconstructions include a 3.4 [A] non-native structure demonstrating that detachment of the first nucleotide-binding domain of hCFTR is directly coupled to local unfolding of the VX445 binding site. Reversal of this unfolding transition likely contributes to its corrector activity by cooperatively stabilizing NBD1 and the transmembrane domains of hCFTR during biogenesis. SummaryCryo-EM global conformational ensemble reconstruction has been used to characterize the mechanism-of-action of a breakthrough pharmaceutical that corrects fatal protein-folding and channel-gating defects in the human cystic fibrosis transmembrane conductance regulator (CFTR).

biophysics↗