Biology subjects

Wang, C.

Publications and source records attributed to Wang, C..

At least 631 records · Page 35Linked to original sources

bioRxiv2023

High Resolution Salmonella Subtyping by the MLSTnext Method

The food industry needs a straightforward, efficient, widely applicable and cost-efficient method to not only detect, but also determine serovar and potential sources of multiple strains in food and environment. While Whole Genome Sequencing (WGS) can generate complete genomic profile of food pathogens, it is a laborious, time-consuming, and expensive method that necessitates pure isolates. As a result, it is unsuitable for samples with complex background, limiting its widespread application by food industry. However, traditional multilocus sequence typing (MLST) approaches do not provide sufficient single nucleotide polymorphism (SNP) information to effectively track- and-trace sources of contamination. In contrast, ChapterDx MLSTnext-NGS (next-generation sequencing) Salmonella assay amplifies and sequences 47 polymorphic loci, evenly spanning the Salmonella enterica genome. As demonstrated in this study, the ChapterDx MLSTnext-NGS Salmonella can identify serovar with high resolution, distinguishing between various strains of the same serovar and resolve co-presence of different strains in a single sample. Additionally, this assay can analyze up to thousand samples in a single sequencing run within 22 hours, making it a highly efficient and scalable method for the food industry. Moreover, the cost per sample of the ChapterDx MLSTnext-NGS Salmonella assay is comparable to that of quantitative Polymerase Chain Reaction (qPCR), making it an affordable option. The assay uses ChapterDx amplification technology, allowing for the amplification of all 47 loci in a single-tube, single-step PCR reaction. This makes it one of the simplest NGS applications available. In summary, ChapterDx MLSTnext-NGS Salmonella assay can be implemented in many diagnostic laboratories to address increasingly complex food safety issues.

microbiology↗

bioRxiv2023

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

genomics↗

bioRxiv2023

Unfolded Protein Response Factor ATF6 Augments T Helper Cell Responses and Promotes Mixed Granulocytic Airway Inflammation

The unfolded protein response (UPR) is associated with the risk of asthma, including treatment- refractory severe asthma. Several recent studies demonstrated a pathogenic role of activating transcription factor 6 (ATF6 or ATF6), one of the essential arms of UPR, in airway structural cells. However, its role in T helper (TH) cells has not been well examined. In this study, we found that ATF6 was selectively induced by STAT6 and STAT3 in TH2 and TH17 cells, respectively. ATF6 upregulated UPR genes and promoted the differentiation and cytokine secretion of TH2 and TH17 cells. T cell-specific Atf6-deficiency impaired TH2 and TH17 responses in vitro and in vivo and attenuated mixed granulocytic experimental asthma. ATF6 inhibitor Ceapin A7 suppressed ATF6 downstream gene expression and TH cell cytokine expression in both murine and human memory CD4+ T cells. At the chronic stage of asthma, administration of Ceapin A7 lessened TH2 and TH17 responses in vivo, leading to alleviation of both airway neutrophilia and eosinophilia. Thus, our results demonstrate a critical role of ATF6 in TH2 and TH17 cell-driven mixed granulocytic airway disease, suggesting a novel option to combat steroid-resistant mixed and even T2-low endotypes of asthma by targeting ATF6.

immunology↗

bioRxiv2023

Endothelial cell-derived lactate triggers mesenchymal stem cell histone lactylation to attenuate osteoporosis

Blood vessels play a role in osteogenesis and osteoporosis; however, the role of vascular metabolism is unclear. The present study found that ovariectomized mice exhibit reductions in bone blood vessel density and expression of endothelial glycolytic regulator pyruvate kinase M2 (PKM2). Additional data showed that endothelial cell (EC)-specific deletion of Pkm2 impair osteogenesis and worsen osteoporosis in mice. This was attributed to the impaired differentiation ability toward osteoblast of bone mesenchymal stem cells (BMSCs). Mechanistically, EC-specific deletion of Pkm2 reduce serum lactate levels secreted by ECs, which affect histone lactylation of BMSCs. We identified collagen type I alpha 2 chain, cartilage oligomeric matrix protein, ectonucleotide pyrophosphatase/phosphodiesterase 1, and transcription factor 7 like 2 as histone H3K18 lactylation-regulated osteogenic genes using joint CUT&Tag and RNA-sequencing analyses. The overexpression of PKM2 in ECs, addition of lactate, and exercise were observed to restore the phenotype of endothelial Pkm2-deficient mice. Furthermore, metabolomics of the serum indicated that osteoporosis patients showed a relatively low lactate level. The histone lactylation and related osteogenic genes of BMSCs in osteoporosis patients also decreased. In conclusion, the glycolysis of ECs fuels the differentiation of BMSCs into osteoblasts through histone lactylation, and exercise partially ameliorates osteoporosis through increased serum lactate.

cell biology↗

bioRxiv2023

Glutamatergic neurons in the infralimbic cortex for motivational response of pain relief induced by electroacupuncture

Peripheral neuromodulation by electroacupuncture (EA) is a promising tool for both experimental and clinical applications. However, whether EA signals reflect a multidimensional composite and evoke affective and motivational processes remains largely elusive. Here, we demonstrated that EA at ST.36 acupuncture point considerably attenuated pain hypersensitivity at 24h and 48h postincision. In conditioned place preference (CPP) model, one chamber becomes associated with EA through three-day repeated pairings, whereas the other chamber is associated with no EA stimulation. EA stimulation resulted in strong preference for the chamber paired with EA in incisional injury (INP) rats. In contrast, EA at non-acupuncture points in INP rats did not relief pain and produce CPP. Notably, EA with the context in sham-operated animals did not induce CPP. Next, we identified neurons activation in brain associated with affective and motivational aspects of pain after EA stimulation using immediate early gene c-Fos expression in SNI rats. EA stimulation increased c-Fos positive neurons in the IL, but not cingulate (Cg1) and prelimbic (PL) subregion of the mPFC. Sham EA did not increase c-Fos expression in the IL in spared nerve injury (SNI) rats. Using reversible inactivation of IL in rats, inactivation of the IL significantly abolished CPP of pain relief induced by EA. Optogenetic activation of IL glutamatergic neurons mimicked EA-induced analgesia and CPP behaviors, and inhibition of glutamatergic neurons in the IL reversed the effects of EA. The study directly demonstrates a novel and important role for glutamatergic neurons in the infralimbic cortex in acupuncture-induced motivational response of pain relief and provides a new perspective for investigating acupuncture analgesia.

neuroscience↗

bioRxiv2023

Fast and accurate DNASeq Variant Calling workflow composed of LUSH toolkit

BackgroundWhole genome sequencing (WGS) is becoming increasingly prevalent for molecular diagnosis, staging and prognosis because of its declining costs and the ability to detect nearly all genes associated with a patients disease. The currently widely accepted variant calling pipeline, GATK, is limited in terms of its computational speed and efficiency, which cannot meet the growing analysis needs. MethodsIn this study, we propose a fast and accurate DNASeq variant calling workflow that is purely composed of tools from LUSH toolkit. The LUSH pipeline is highly optimized for the WGS pipeline based on SOAPnuke, BWA and GATK which can be deployed on any general-purpose CPU-based computing system. We validated the accuracy, speed and scalability of the LUSH pipeline on several standard WGS datasets. ResultsOur test results show that the LUSH pipeline and the GATK pipeline are highly consistent in terms of accuracy, achieving over 99% precision and recall on NA12878. For speed, the LUSH pipeline completes 30x WGS data in 1.6 hours, which is about 17x faster than the GATK pipeline. From BAM to VCF, LUSH_HC even takes only 12 minutes, about 76x faster than GATK. Moreover, the LUSH pipeline shows favorable scalability in terms of thread and sequencing depth. ConclusionThe LUSH pipeline provides far superior computational speed to GATK while maintaining a high level of accuracy comparable to that of GATK, which greatly facilitates bedside analysis of acute patients, large-scale cohort data analysis, and variant calling in crop breeding programs.

bioinformatics↗

bioRxiv2023

PRL1 negatively regulates Rho GTPase-independent and -dependent signaling pathways maintaining actin microfilament dynamic for pavement cell morphogenesis

Actin dynamic is critical for cell morphogenesis in plants, but the signaling mechanisms underlying its regulation are not well understood. Here we found PRL1 (Pleiotropic Regulatory Locus1) modulates leaf pavement cell (PC) morphogenesis in Arabidopsis by maintaining the dynamic homeostasis of actin microfilaments (MF). Our previous studies indicated PC shape formation was mediated by the counteracting ROP2 and ROP6 signaling pathways that promote the organization of cortical MF and microtubules (MT), respectively. Our genetic screen for ROP6 enhancers identified prl1 alleles. Genetic analysis suggested that prl1 acted synergistically with ROP2 and ROP6 in regulation of PC morphogenesis. We further found that the activities of ROP2 and ROP6 were increased and decreased in prl1 mutants, respectively. Interestingly prl1 was found to prefer to depolymerize MF independent of ROP2 and ROP6. Stress (high salinity and low temperature) induced similar changes of ROP activities as do prl1 mutations. Together our findings provided evidence that PRL1 governed two signaling pathways that counteractively maintain actin dynamics and resultant cell morphogenesis.

plant biology↗

bioRxiv2023

Pleiotropic Regulatory Locus1 maintains actin microfilament integrity and concomitant cellular homeostasis facilitating root development in Arabidopsis

Cell functions are based on integrity of actin filaments. The Actin cytoskeleton is typically the target but also the source of signals. An evolutionarily conserved WD-40 protein PRL1 (Pleiotropic Regulatory Locus1) in Arabidopsis was investigated with multilayer functions in development, innate immunity, alternative splicing activation, transcription regulation, genome maintenance, ubiquitination-based protein turnover et al., but the underlying mechanisms are undefined. Here, we show PRL1 maintains actin integrity and concomitant cellular homeostasis. To explore causes for developmental root defect, we found depolymerization of cortical actin cytoskeleton and ROS imbalance in prl1 mutant. Further, we revealed that actin de-polymerization was the fundamental cause and dominant to ROS imbalance (H2O2 and O2{middle dot}-) for retarded root of prl1; NAC085 was up-regulated by and cooperated with actin depolymerization to mediate to stele cell death. Moreover, we revealed stress-related differentially expressed genes and alternative splicing defects were mutually independent and were responses to actin depolymerization in prl1. Our work ravels out cause-effect relationships between actin configuration and downstream hierarchical signals and explores underlying mechanism for functions of PRL1.

plant biology↗

bioRxiv2023

CLE11 and CLE10 Suppress Mycorrhizal Colonisation in Tomato

Symbioses with beneficial microbes are widespread in plants, but these relationships must balance the energy invested by the plants with the nutrients acquired. Symbiosis with arbuscular mycorrhizal (AM) fungi occurs throughout land plants but our understanding of the genes and signals that regulate colonisation levels is limited. Here, we demonstrate that in tomato two CLV3/EMBRYO-SURROUNDING REGION (CLE) peptides, SlCLE10 and SlCLE11, act to suppress AM colonisation of roots. Mutant studies and overexpression via hairy transformation indicate SlCLE11 acts locally in the root to limit AM colonisation. Indeed, SlCLE11 expression is strongly induced in AM colonised roots but SlCLE11 is not required for phosphate suppression of AM colonisation. SlCLE11 may act through as yet uncharacterised signalling pathways, as SlCLE11 does not suppress AM colonisation by acting through two previously characterised receptors with roles in regulating AM colonisation, SlFAB (CLAVATA1 orthologue) or SlCLV2. SlCLE10 appears to play a more minor or redundant role, as cle10 mutants did not influence AM, although the fact that ectopic overexpression of SlCLE10 did suppress colonisation suggests SlCLE10 may play a role in regulating AM colonisation. Our findings show that CLE peptides regulate AM colonisation in the non-legume species tomato.

plant biology↗

bioRxiv2023

Differentially Expressed Heterogeneous Overdispersion Genes Testing for Count Data

The mRNA-seq data analysis is a powerful technology for inferring information from biological systems of interest. Specifically, the sequenced RNA fragments are aligned with genomic reference sequences, and we count the number of sequence fragments corresponding to each gene for each condition. A gene is identified as differentially expressed (DE) if the difference in its count numbers between conditions is statistically significant. Several statistical analysis methods have been developed to detect DE genes based on RNA-seq data. However, the existing methods could suffer decreasing power to identify DE genes arising from overdispersion and limited sample size. We propose a new differential expression analysis procedure: heterogeneous overdispersion genes testing (DEHOGT) based on heterogeneous overdispersion modeling and a post-hoc inference procedure. DEHOGT integrates sample information from all conditions and provides a more flexible and adaptive overdispersion modeling for the RNA-seq read count. DEHOGT adopts a gene-wise estimation scheme to enhance the detection power of differentially expressed genes. DEHOGT is tested on the synthetic RNA-seq read count data and outperforms two popular existing methods, DESeq and EdgeR, in detecting DE genes. We apply the proposed method to a test dataset using RNAseq data from microglial cells. DEHOGT tends to detect more differently expressed genes potentially related to microglial cells under different stress hormones treatments.

genomics↗

bioRxiv2023

Comparison between Canine and Porcine Models of Chronic Deep Venous Thrombosis

Venous thromboembolism(VTE) refers to deep venous thrombosis(DVT) and pulmonary embolism(PE), which is a worldwide problem and has very high morbidity and mortality. The research of venous thrombosis involves pathogenesis, pathophysiology, and therapeutic attempt. Alternative experimental animal models have changed dramatically over the past 20 years, from small murine models to large ones. Larger animal models offer more options and are more consistent with human physiology. This article aims to induce chronic deep venous thrombosis in the left iliac vein in canine and porcine models and compare these two models. We think that feasible large animal models can better translate the results of therapeutic research into clinical application.

animal behavior and cognition↗

bioRxiv2023

Pharmacological PINK1 activation ameliorates Pathology in Parkinson's Disease models

PINK1 loss-of-function mutations and exposure to mitochondrial toxins are causative for Parkinsons disease (PD) and Parkinsonism, respectively. We demonstrate that pathological -synuclein deposition, the hallmark pathology of idiopathic PD, induces mitochondrial dysfunction and impairs mitophagy, driving accumulation of the PINK1 substrate pS65-Ubiquitin (pUb) in primary neurons and in vivo. We synthesized MTK458, a brain penetrant small molecule that binds to PINK1 and stabilizes an active heterocomplex, thereby increasing mitophagy. MTK458 mediates clearance of -synuclein pathology in PFF seeding models in vitro and in vivo and reduces pUb. We developed an ultrasensitive assay to quantify pUb levels in plasma and observed an increase in pUb in PD subjects that correlates with disease progression, paralleling our observations in PD models. Our combined findings from preclinical PD models and patient biofluids suggest that pharmacological activation of PINK1 is worthy of further study as a therapeutic strategy for disease modification in PD. HighlightsO_LIDiscovery of a plasma Parkinsons Disease biomarker candidate, pS65-Ubiquitin (pUb) C_LIO_LIPlasma pUb levels correlate with disease status and progression in PD patients. C_LIO_LIIdentification of a potent, brain penetrant PINK1 activator, MTK458 C_LIO_LIMTK458 selectively activates PINK1 by stimulating dimerization and stabilization of the PINK1/TOM complex C_LIO_LIMTK458 drives clearance of -synuclein pathology and normalizes pUb in in vivo Parkinsons models C_LI

neuroscience↗

bioRxiv2023

RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac4C modification

NAT10 is dysregulated and plays an essential role in various types of cancers. However, the exact machenism of how NAT10 regulates cancer progression remains debatable. In this report, we show that NAT10 affects tumorigeneis mainly based on its acetylation function on tRNA. In addition, we found NAT10 regulate the ac4C of tRNA in cancer via interaction with RNPS1, which in turn protect NAT10 from degradation by E3 ubiquitin ligase ZSWIM6. We developed TRMC-seq method to compreshensively profile tRNA ac4C sites and uncovered the presence of ac4C in a broader range of tRNA isoacceptors than previous studies. Multi-omics analysis identified AP-1 signaling pathway as a major downstream mediator of NAT10. Mechanistically, we found NAT10 is responsible for the translation efficiency genes which contain higher ac4C-tRNA codon. Importantly, our genetic mouse model validated our in vitro findings of NAT10 in cancer. Our study highlights a role of NAT10 in mediating tRNA ac4C to regulate the translation and tumorigenesis of cancer.

molecular biology↗

bioRxiv2023

The Alfin-like transcription factor GmAlfin09 regulates endoplasmic reticulum stress in soybean via a peroxidase GmPRDX6

Soybean is a valuable oil crop cultivated throughout the world, but also highly susceptible to environmental stressors. The development of approaches to enhancing soybean stress resistance is thus vital to improving yields. In prior studies, Alfin has been shown to serve as an epigenetic regulator of plant growth and development. No studies of Alfin have yet been reported in soybean, however. In this study, the endoplasmic reticulum (ER) stress- and reactive oxygen species (ROS)-related transcription factor GmAlfin09 was identified. Screening of genes co-expressed with GmAlfin09 unexpectedly led to the identification of the peroxidase GmPRDX6. Further analyses revealed that both GmAlfin09 and GmPRDX6 were responsive to ER stress, with GmPRDX6 localizing to the ER under stress. Promoter binding experiments confirmed the ability of GmAlfin09 to directly bind the GmPRDX6 promoter. When GmAlfin09 and GmPRDX6 were overexpressed in soybean, enhanced ER stress resistance and decreased ROS levels were observed. Together, these findings suggest that GmAlfin09 can promote the upregulation of GmPRDX6, which subsequently localizes to the ER, reduced ROS levels, promotes ER homeostasis, and helps ensure the normal growth of soybean even under ER stress. This study highlights a novel genetic target for the future molecular breeding of stress-resistant soybean cultivars. HIGHLIGHTGmAlfin09 can increase the expression of GmPRDX6 to reduce ROS level under ER stress.

plant biology↗

bioRxiv2023

Ferroptosis is determined by chloride ions

Ferroptosis has emerged as a deliberate type of programmed cell death that manifests marked importance ubiquitously in health and diseases. However, after a decade of research, the mechanisms of ferroptosis execution remain unclear. Here we identify chloride ions (Cl-) as essential determinants of ferroptosis. Water homeostasis manipulated by extracellular solute concentration disrupts ferroptotic cell death. Hyperosmotic stress attenuates ferroptosis and endues cells with high lipid peroxidation. Analyses of a fluorescent chloride probe show that Cl- fluxes into the cytoplasm during ferroptosis, substantiating a role for Cl- to drive water flow. Depletion of extracellular chloride ions ([Cl-]o) from culture media congruously confers resistance to ferroptosis. The [Cl-]o-depleted ferroptotic cells fall into two populations: cells with low lipid peroxidation; cells with high lipid peroxidation but not cell swelling or cell rupture. Contrarily, solitary [Cl-]o overload is sufficient to elicit ferroptosis without canonical ferroptosis inducers. Further experiments show that ferroptotic cells depolarize and [Cl-]o is positively correlated with this process. Membrane depolarization upregulates the level of lipid peroxidation, suggesting that membrane potential may be a universal mechanism governing ferroptosis. Together, our findings reveal that ferroptosis is determined by chloride ions.

cell biology↗

bioRxiv2023

Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno

In the analysis of both single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data, classifying cells/spots into cell/domain types is an essential analytic step for many secondary analyses. Most of the existing annotation methods have been developed for scRNA-seq datasets without any consideration of spatial information. Here, we present SpatialAnno, an efficient and accurate annotation method for spatial transcriptomics datasets, with the capability to effectively leverage a large number of non-marker genes as well as "qualitative" information about marker genes without using a reference dataset. Uniquely, SpatialAnno estimates low-dimensional embeddings for a large number of non-marker genes via a factor model while promoting spatial smoothness among neighboring spots via a Potts model. Using both simulated and four real spatial transcriptomics datasets from the 10x Visium, ST, Slide-seqV1/2, and seqFISH platforms, we showcase the methods improved spatial annotation accuracy, including its robustness to the inclusion of marker genes for irrelevant cell/domain types and to various degrees of marker gene misspecification. SpatialAnno is computationally scalable and applicable to SRT datasets from different platforms. Furthermore, the estimated embeddings for cellular biological effects facilitate many downstream analyses.

bioinformatics↗

bioRxiv2023

NLRP1 inflammasome modulates senescence and senescence-associated secretory phenotype

Senescence is a cellular aging-related process triggered by different stresses and characterized by the secretion of various inflammatory factors referred to as the senescence-associated secretory phenotype (SASP). Here, we present evidence that the inflammasome sensor, NLRP1, is a key mediator of senescence induced by irradiation both in vitro and in vivo. The NLRP1 inflammasome promotes senescence by regulating the expression of p16, p21, p53, and SASP in Gasdermin D (GSDMD)-dependent manner as these responses are reduced in conditions of NLRP1 insufficiency or GSDMD inhibition. Mechanistically, the NLRP1 inflammasome is activated downstream of the cytosolic DNA sensor cGMP-AMP (cGAMP) synthase (cGAS) in response to genomic damage. These findings provide a rationale for inhibiting the NLRP1 inflammasome-GSDMD axis to treat senescence-driven disorders.

immunology↗

bioRxiv2023

Sequential restoring O2 then unloading CO2 is beneficial against reperfusion injury: role of CO2 in metabolism

CO2 is one of main byproducts during mitochondrial oxidation. Under the acute occlusion of coronary artery situation, the intra-tissue pCO2 of heart could be extremely high. This CO2 accumulation will be acutely unloaded and discharged by blood reperfusion. However, the effect of this intra-tissue CO2 accumulation then unloading process on cardiac ischemic reperfusion injury has not been well investigated yet. In the present study, we show that the perfusion with a high level of pCO2 and normal pO2 in the initial 30min followed by a 30min normal pCO2 and normal pO2 is better than the perfusion with 1h normal pCO2 and normal pO2 simultaneously during the reperfusion after a 45min global ischemia in isolated rat hearts. To observe the effect of high pCO2 on cellular metabolism, we exposed C2C12 cells under about 370mmHg pCO2 to observe the mitochondrial substrate switch and TCA cycle flux change, by using 13C tracers. We show that a short time exposure to the extremely high level of pCO2 is not completely destructive for cellular metabolism but has specific effects. The high pCO2 inhibits pyruvate transport into mitochondria and the next oxidation, switching to more reliance on fatty acid oxidation and enhancing the glutamine oxidation to maintain the TCA cycle. Intriguingly, the high pCO2 significantly activates the reductive carboxylation from glutamine, fixation of mitochondrial excessive CO2. The mechanism under the beneficial effect of the high-then-low CO2 sequential reperfusion strategy is discussed further.

biochemistry↗