Biology subjects

Xu, C.

Publications and source records attributed to Xu, C..

At least 307 records · Page 17Linked to original sources

bioRxiv2021

Cross-tissue immune cell analysis reveals tissue-specific adaptations and clonal architecture across the human body

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. Here, we surveyed the immune compartment of 15 tissues of six deceased adult donors by single-cell RNA sequencing and paired VDJ sequencing. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of 45 finely phenotyped immune cell types and states, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. In summary, our multi-tissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis and antigen receptor sequencing. One Sentence SummaryWe provide an immune cell atlas, including antigen receptor repertoire profiling, across lymphoid and non-lymphoid human tissues.

immunology↗

bioRxiv2021

A suite of activity-based probes to dissect the KLK activome in drug-resistant prostate cancer

Kallikrein-related peptidases (KLKs) are a family of secreted serine proteases, which form a network - the KLK activome - with an important role in proteolysis and signaling. In prostate cancer (PCa), increased KLK activity promotes tumor growth and metastasis through multiple biochemical pathways, and specific quantification and tracking of changes in the KLK activome could contribute to validation of KLKs as potential drug targets. Herein we report a technology platform based on novel activity-based probes (ABPs) and inhibitors with unprecedented potency and selectivity enabling simultaneous orthogonal analysis of KLK2, KLK3 and KLK14 activity in hormone-responsive PCa cell lines and tumor homogenates. Using selective inhibitors and multiplexed fluorescent activity-based protein profiling (ABPP) we dissect the KLK activome in PCa cells and show that increased KLK14 activity leads to a migratory phenotype. Furthermore, using biotinylated ABPs we show that active KLK molecules are secreted into the bone microenvironment by PCa cells following stimulation by osteoblasts suggesting KLK-mediated signaling mechanisms could contribute to PCa metastasis to bone. Together our findings show that ABPP is a powerful approach to dissect dysregulation of the KLK activome as a promising and previously underappreciated therapeutic target in advanced PCa.

biochemistry↗

bioRxiv2021

Salt-induced first-order structural transition in a DNA-interacting protein

Thermodynamics and structural transitions on protein surfaces remain relatively understudied and poorly understood. Wrapping of DNA on proteins provides a paradigm for studying protein surfaces. We used magnetic tweezers to investigate a prototypical DNA-interacting protein, i.e., the single-stranded DNA binding protein (SSB). SSB binds DNA with distinct binding modes the mechanism of which is still elusive. The measured thermodynamic parameters relevant to the SSB-DNA complex are salt-dependent and discontinuous at the bind-mode transitions. Our data indicate that free SSB undergoes salt-induced first-order structural transitions. The conclusion was supported by the infrared spectroscopy of SSB in salt solutions. Ultrafast infrared spectroscopy further suggests that the transitions are correlated with surface salt bridges. Our work not only unravels a long-standing mystery of the different binding site sizes of SSB, but also would inspire interests in thermodynamics of protein surfaces.

biophysics↗

bioRxiv2021

Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins

Present in all bacteria, lipoproteins are central in bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of cytoplasmic membrane. In Gram-negative bacteria, many lipoproteins are transported to the outer membrane (OM), a process dependent on the ATP-binding cassette (ABC) transporter LolCDE which extracts the OM-targeted lipoproteins from the cytoplasmic membrane for subsequent trafficking across the periplasm. Lipid-anchored proteins pose a unique challenge for transport machinery as they have both hydrophobic lipid moieties and soluble protein component, and the underlying mechanism is poorly understood. Here we determined the cryo-EM structures of nanodisc-embedded LolCDE in the nucleotide-free and nucleotide-bound states at 3.8-[A] and 3.5-[A] resolution, respectively. The structural analyses, together with biochemical and mutagenesis studies, uncover how LolCDE specifically recognizes its substrate by establishing multiple interactions with the lipid and N-terminal peptide moieties of the lipoprotein, and identify the amide-linked acyl chain as the key element for LolCDE interaction. Upon nucleotide binding, the transmembrane helices and the periplasmic domains of LolCDE undergo large-scale, asymmetric movements, resulting in extrusion of the captured lipoprotein. Comparison of LolCDE and MacB reveals the conserved mechanism of type VII ABC transporters and emphasizes the unique properties of LolCDE as a molecule extruder of triacylated lipoproteins.

microbiology↗

bioRxiv2021

An intein-split transactivator for intersectional neural imaging and optogenetic manipulation

The complexity of brain circuitry is manifested by numerous cell types based on genetic marker, location and neural connectivity. Cell-type specific recording and manipulation is essential to disentangle causal neural mechanisms in physiology and behavior; however, many current approaches are largely limited by number of intersectional features, incompatibility of common effectors and insufficient gene expression. To tackle these limitations, we devise an intein-based intersectional synthesis of transactivator (IBIST) to selectively control gene expression of common effectors in specific cell types defined by a combination of multiple features. We validate the specificity and sufficiency of IBIST to control common effectors including fluorophores, optogenetic opsins and Ca2+ indicators in various intersectional conditions in vivo. Using IBIST-based Ca2+ imaging, we show that the IBIST can intersect up to five features, and that hippocampal cells tune differently to distinct emotional valences depending on the pattern of projection targets. Collectively, the IBIST multiplexes the capability to intersect cell-type features and is compatible with common effectors to effectively control gene expression, monitor and manipulate neural activities.

neuroscience↗

bioRxiv2021

Enhancing the localization precision of single molecule localization microscopy by analyzing Brownian motion of individual fluorescent probe

Single-molecule localization microscopy (SMLM) boosts its applications when combined with the studies of cells, in which nanometer-sized biomolecules are irresolvable due to diffraction limit unless being subjected to SMLM. Although being well immobilized, given the nanometer sizes of biological molecules, they are still capable of movement stochastically around their immobilized sites. The influence of such motion on image quality and possible improvements have not yet been systematically investigated. Here, we accessed the biomolecule stochastic motion in SMLM by calculating the displacements between different localizations from the same molecule in single-molecule samples of Alexa Fluor-647-conjugated oligonucleotides. We found that, for most molecules, localization displacements at random frame intervals are remarkably larger than those between temporally neighbouring frames despite of drift correction, showing that biomolecule stochastic motion is involved in SMLM. Furthermore, the localization displacements were observed to increase with frame intervals and then saturate, suggesting biomolecule stochastic motion is confined within a finite area. Moreover, we showed that the localization precision is deteriorated by enlarging molecule sizes and improved by sample post-fixation. This study reveals confined stochastic motion of biomolecules increase localization uncertainty in SMLM, and improved localization precision can be achieved via restricting biomolecule stochastic motion.

biophysics↗

bioRxiv2021

FastTomo: A SerialEM Script for Collecting Electron Tomography Data

FastTomo is a SerialEM script for collecting tilted specimen images in transmission electron microscopes to be further used in tomographic reconstruction. It achieves a speedup over conventional tracking methods by minimizing the usage of off-target tracking shots, and instead applies proportional control to the specimen images. Movement in the Z coordinate is estimated prior to each tilt series in a separate calibration routine. Overall, this method is fast and reliable when the field of view is at least 1 um, and can tolerate minor errors in setting eucentric height. The implemented tilt series schemes include the unidirectional, bidirectional, and dose-symmetric schemes.

bioengineering↗

bioRxiv2021

A specialized bone marrow microenvironment for fetal haematopoiesis

Local signals provided by cells in specialized niche microenvironments regulate stem cell behaviour in many different organs and species. In adult mammalian bone marrow (BM), leptin receptor-positive (LepR+) reticular cells express secreted factors that control the function of haematopoietic stem and progenitor cells (HSPCs). During fetal development, the developing skeletal system is colonized by c-Kit+ haematopoietic cells de novo after a transient phase of liver haematopoiesis. The cellular and molecular mechanisms regulating de novo haematopoietic cell colonization and expansion remain largely unknown. Here, we report that fetal and adult BM exhibit fundamental differences both in terms of cellular composition and molecular interactions by single cell RNA sequencing (scRNA-seq) analysis. While LepR+ reticular cells are almost completely absent in fetal femur, arterial endothelial cells (AECs) are a source of signals controlling the initial HSPC expansion during BM development. Long-term haematopoietic stem cells (HSCs) and other c-Kit+ HSPCs are reduced when Wnt ligand secretion by AECs is genetically blocked. We identify Wnt2 as an AEC-derived signal that directly activates {beta}-catenin dependent proliferation of fetal HSPCs. Treatment of HSPCs ex vivo with Wnt2 promotes their proliferation and improves engraftment in vivo after transplantation. Our work reveals a fundamental switch in the cellular organization and molecular regulation of BM niches in the embryonic and adult organism.

developmental biology↗

bioRxiv2021

Modeling gene x environment interactions in PTSD using glucocorticoid-induced transcriptomics in human neurons

Post-traumatic stress disorder (PTSD) results from severe trauma exposure, but the extent to which genetic and epigenetic risk factors impact individual clinical outcomes is unknown. We assessed the impact of genomic differences following glucocorticoid administration by examining the transcriptional profile of human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons and live cultured peripheral blood mononuclear cells from combat veterans with PTSD (n=5) and without PTSD (n=5). This parallel examination in baseline and glucocorticoid-treated conditions resolves cell-type specific and diagnosis-dependent elements of stress response, and permits discrimination of gene expression signals associated with PTSD risk from those induced by stress. Computational analyses revealed neuron-specific glucocorticoid-response expression patterns that were enriched for transcriptomic patterns observed in clinical PTSD samples. PTSD-specific signatures, albeit underpowered, accurately stratify veterans with PTSD relative to combat-exposed controls. Overall, in vitro PTSD and glucocorticoid response signatures in blood and brain cells represent exciting new platforms with which to test the genetic and epigenetic mechanisms underlying PTSD, identify biomarkers of PTSD risk and onset, and conduct drug-screening to identify novel therapeutics to prevent or ameliorate clinical phenotypes.

pathology↗

bioRxiv2021

Avalanches During Epithelial Tissue Growth; Uniform Growth and a Drosophila Eye Disc Model

In the physicists perspective, epithelial tissues constitute an exotic type of active matter with non-linear properties reminiscent of amorphous materials. In the context of a circular proliferating epithelium, modeled by the quasistatic vertex model, we identify novel discrete tissue scale rearrangements, i.e. cellular flow avalanches, which are a form of collective cell movement. During the avalanches, the cellular trajectories are radial in the periphery and form a vortex in the core. After the onset of these avalanches, the epithelial area grows discontinuously. The avalanches are found to be stochastic, and their strength is determined by the density of cells in the tissue. Overall, avalanches regularize the spatial tension distribution along tissue. Furthermore, the avalanche distribution is found to obey a power law, with an exponent consistent with sheer induced avalanches in amorphous materials. To decipher the role of avalanches in organ development, we simulate epithelial growth of the Drosophila eye disc during the third instar using a computational model, which includes both signaling and mechanistic signalling. During the third instar, the morphogenetic furrow (MF), a [~]10 cell wide wave of apical area constriction propagates through the epithelium, making it a system with interesting mechanical properties. These simulations are used to understand the details of the growth process, the effect of the MF on the growth dynamics on the tissue scale, and to make predictions. The avalanches are found to depend on the strength of the apical constriction of cells in the MF, with stronger apical constriction leading to less frequent and more pronounced avalanches. The results herein highlight the dependence of simulated tissue growth dynamics on relaxation timescales, and serve as a guide for in vitro experiments.

biophysics↗

bioRxiv2021

scGAE: topology-preserving dimensionality reduction for single-cell RNA-seq data using graph autoencoder

Dimensionality reduction is crucial for the visualization and interpretation of the high-dimensional single-cell RNA sequencing (scRNA-seq) data. However, preserving topological structure among cells to low dimensional space remains a challenge. Here, we present the single-cell graph autoencoder (scGAE), a dimensionality reduction method that preserves topological structure in scRNA-seq data. scGAE builds a cell graph and uses a multitask-oriented graph autoencoder to preserve topological structure information and feature information in scRNA-seq data simultaneously. We further extended scGAE for scRNA-seq data visualization, clustering, and trajectory inference. Analyses of simulated data showed that scGAE accurately reconstructs developmental trajectory and separates discrete cell clusters under different scenarios, outperforming recently developed deep learning methods. Furthermore, implementation of scGAE on empirical data showed scGAE provided novel insights into cell developmental lineages and preserved inter-cluster distances.

bioinformatics↗

bioRxiv2021

Natural variation in GmRAV confers ecological adaptation through photoperiod control of flowering time and maturity in soybean

Photoperiod strictly controlled vegetative and reproductive growth stages in soybean. A soybean GmRAV transcription factor containing both AP2 and B3 domains was shown to be a key component of this process. We identified six polymorphisms in GmRAV promoter that showed significant association with flowering time and maturity of soybean in one or multiple environments. Soybean varieties with minor polymorphism exhibited longer growth period contributing to soybean adaptation to lower latitudes. The cis-acting element GT1CONSENSUS motif of GmRAV promoter controlled the growth period and shortened R5-R7 by reducing the expression level of GmRAV in soybean. Three GmRAV-overexpressing (GmRAV-ox) transgenic lines displayed later flowering time and maturity, shorter height and fewer numbers of leaves compared with control plants, and transgenic inhibition of GmRAV (GmRAV-i) soybean displayed earlier flowering time and maturity, and increased plant heights. 163 GmRAV-target genes were determined to be putatively directly bound and transcriptionally regulated by GmRAV by combining the results from the DAP-seq and RNA-seq analyses. Two GmRAV binding motifs [C(A/G/T)A(C)ACAA(G/T)A(C/T)A(G/T)] and [C(T/A)A(C/T) C(T/G)CTG] were identified. GmRAV acting downstream of E3E4 delayed soybean growth period by repressing GmFT5a transcriptional activity to guaranteed both vegetative and reproductive phase long enough to allow necessary energy reserved to be accumulated.

plant biology↗

bioRxiv2021

Activation of GSDME compensates for GSDMD deficiency in a mouse model of NLRP3 inflammasomopathy

The D301N NLRP3 mutation in mice (D303N in humans) causes severe multi-organ damage and early death driven by the constitutively activated NLRP3 (NLRP3ca) inflammasome. Triggered inflammasomes activate caspase-1 to process IL-1 family cytokines and gasdermin D (GSDMD), generating N-terminal fragments, which oligomerize within the plasma membrane to form pores, which cause inflammatory cell death (pyroptosis) and through which IL-1{beta} and IL-18 are secreted. GSDMD activation is central to disease symptoms since spontaneous inflammation in Nlrp3ca;Gsdmd-/- mice is negligible. Unexpectedly, when Nlrp3ca;Gsdmd-/- mice were challenged with LPS or TNF-, they secreted high amounts of IL-1{beta} and IL-18, suggesting an alternative GSDMD-independent inflammatory pathway. Here we show that GSDMD deficient macrophages subjected to inflammatory stimuli activate caspase-8, -3 and GSDME-dependent cytokine release and pyroptosis. Caspase-8, -3 and GSDME also activated pyroptosis when NLRP3 was stimulated in caspase-1 deficient macrophages. Thus, a salvage caspase-8, -3-GSDME inflammatory pathway is activated following NLRP3 activation when the canonical NLRP3-caspase-1-GSDMD is blocked. Surprisingly, the active metabolite of the GSDMD-inhibitor disulfiram, inhibited not only GSDMD but also GSDME-mediated inflammation in vitro and suppressed severe inflammatory disease symptoms in Nlrp3ca mice, a model for severe neonatal multisystem inflammatory disease. Although disulfiram did not directly inhibit GSDME, it suppressed inflammasome activation in GSDMD-deficient cells. Thus, the combination of inflammatory signals and NLRP3ca overwhelmed the protection provided by GSDMD deficiency, rewiring signaling cascades through caspase-8, -3 and GSDME to propagate inflammation. This functional redundancy suggests that concomitant inhibition of GSDMD and GSDME may be necessary to suppress disease in inflammasomopathy patients.

immunology↗

bioRxiv2021

Impact of Meteorological factors on wheat growth period and irrigation water requirement --A case study of the Beijing-Tianjin-Hebei region in China

This study analyzes the irrigation water requirement of wheat in the growth stage in the Beijing-Tianjin-Hebei region under the changes of meteorological factors conditions, using the growth period data, and meteorological data from 80 meteorological stations, from 2000 to 2019. The results show that: (1) The annual average precipitation, average wind speed, and average relative humidity of the growth period in the Beijing-Tianjin-Hebei region show a downward variation trend, while the temperature variation shows an upward trend. Moreover, relative humidity and radiation exhibit a negative spatial correlation. (2) Wheat irrigation water requirement in the Beijing-Tianjin-Hebei region gradually decreases from north to south and east to west. However, the eastern region shows a gradually increasing trend, while the western region shows a decreasing trend. (3) Meteorological factors are negatively correlated with irrigation water requirement, potential evapotranspiration, effective precipitation, and relative humidity, and significantly positively correlated with sunshine hours, average temperature, and wind speed. The overall variation in irrigation water requirement has the highest correlation with potential evapotranspiration. However, the yearly variations in regional irrigation water requirement are dependent on factors such as wind speed, relative humidity, and radiation.

plant biology↗

bioRxiv2020

Evaluation of exosome-encapsulated miR-23a/b in the diagnosis of human coronary heart diseases

ObjectiveCoronary heart disease (CHD) is currently one of the major causes of death with high morbidity. Due to the increasing heterogeneity and complexity in the CHDs progression, biomarkers for specific diagnosis and monitoring of disease progression need to be developed. The study was aimed to investigate the roles of serum exosomal miR-23a and miR-23b in diagnosis of CHDs. Methods16 healthy individuals and 56 patients with CHDs were enrolled in this study, including the CHDs of stable angina, unstable angina, non-ST elevation myocardial infarction (NSTEMI), ST elevation myocardial infarction (STEMI) and acute myocardial infarction (AMI). Serum exosomal miR-23a and miR-23b were quantified by Q-PCR. The associations of miR-23a/b with multiple clinical parameters were analyzed. ResultsSerum exosomal miR-23a was downregulated in the 56 CHD patients. In the specific prediction of stable angina and AMI, miR-23a achieved the area under the receiver operating characteristic (AUC-ROC) of 0.809 and 0.783, respectively. The levels of serum creatinine (CREA) and miR-23a were associated, which was consistent with risk of kidney injury in CHDs patients. Exosomal miR-23b levels showed no difference among CHD groups. ConclusionsmiR-23a may serve as a non-invasive marker in predicting stable angina and AMI. The level of miR-23a was implicated in CREA-dependent CHD-renal damage.

pathology↗

bioRxiv2020

Distinguish virulent and temperate phage-derived sequences in metavirome data with a deep learning approach

BackgroundProkaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing virulent and temperate phage-derived sequences in metavirome data is important for their role in interactions with bacterial hosts and regulations of microbial communities. However there is no experimental or computational approach to classify sequences of these two in culture-independent metavirome effectively, we present a new computational method DeePhage, which can directly and rapidly judge each read or contig as a virulent or temperate phage-derived fragment. FindingsDeePhage utilizes a "one-hot" encoding form to have an overall and detailed representation of DNA sequences. Sequence signatures are detected via a deep learning algorithm, namely a convolutional neural network to extract valuable local features. DeePhage makes better performance than the most related method PHACTS. The accuracy of DeePhage on five-fold validation reach as high as 88%, nearly 30% higher than PHACTS. Evaluation on real metavirome shows DeePhage annotated 54.4% of reliable contigs while PHACTS annotated 44.5%. While running on the same machine, DeePhage reduces computational time than PHACTS by 810 times. Besides, we proposed a new strategy to explore phage transformations in the microbial community by direct detection of the temperate viral fragments from metagenome and metavirome. The detectable transformation of temperate phages provided us a new insight into the potential treatment for human disease. ConclusionsDeePhage is the first tool that can rapidly and efficiently identify two kinds of phage fragments especially for metagenomics analysis with satisfactory performance. DeePhage is freely available via http://cqb.pku.edu.cn/ZhuLab/DeePhage or https://github.com/shufangwu/DeePhage.

bioinformatics↗

bioRxiv2020

Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperature

BackgroundElevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown. ResultsHere we report that multigenerational exposure of Arabidopsis to extreme heat and moderate warming resulted in significantly increased mutation rates in single-nucleotide variants (SNVs) and small indels. We observed distinctive mutational spectra under extreme and moderately elevated temperatures, with significant increases in transition (C:G[->]T:A) and transversion (A:T[->]T:A) frequencies. Mutation occurred more frequently in intergenic regions, coding regions (especially nonsynonymous mutations), and transposable elements (TEs). At elevated temperatures, more mutations accumulated in genes associated with defense responses, DNA repair, and signaling, including the transcriptional response-related genes HSP70 and HSFA1A. Methylation was observed more frequently at mutation sites, indicating that it contributed significantly to the mutation process at elevated temperatures. Moreover, the mutations in lines and populations grown under elevated temperatures were significantly biased toward low gene density regions, special trinucleotides (GC context), tandem repeats, and adjacent simple repeats. Additionally, 24% (n = 64) of SNVs and 43% (n = 40) of indels found in all mutation accumulation lines overlapped significantly with genetic variations reported in 1001 Genomes, suggesting a non-uniform distribution of de novo mutations through the genome. ConclusionCollectively, our results suggest that elevated temperatures can accelerate the accumulation, and alter the molecular profiles, of DNA mutations in plants, thus providing significant insight into how environmental temperatures fuel plant evolution.

genetics↗

bioRxiv2020

Molecular topography of an entire nervous system

Nervous systems are constructed from a deep repertoire of neuron types but the underlying gene expression programs that specify individual neuron identities are poorly understood. To address this deficit, we have produced an expression profile of all 302 neurons of the C. elegans nervous system that matches the single cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses unique codes of [~]23 neuropeptide-encoding genes and [~]36 neuropeptide receptors thus pointing to an expansive "wireless" signaling network. To demonstrate the utility of this uniquely comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression across the nervous system and (2) reveal adhesion proteins with potential roles in synaptic specificity and process placement. These data are available at cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity and function throughout the C. elegans nervous system.

neuroscience↗