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Yang, G.

Publications and source records attributed to Yang, G..

At least 163 records · Page 9Linked to original sources
bioRxiv2021

Modeling autism-associated SHANK3 deficiency using human cortico-striatal organoids generated from single neural rosettes

Our understanding of the human brain is limited by the lack of experimental models to mechanistically probe the properties of brain cells at different developmental stages under normal and pathological conditions. We developed a new method for generating human cortico-striatal organoids from stem cell-derived single neural rosettes (SNRs) and used it to investigate cortico-striatal development and deficits caused by the deficiency of an autism- and intellectual disability-associated gene SHANK3. We show that SNR-derived organoids consist of different cortico-striatal cells, including pallial and subpallial progenitors, primary cortical and striatal neurons, interneurons, as well as macroglial and mural cells. We also demonstrate that neurons in SNR-derived organoids are predictably organized, functionally mature, and capable of establishing functional neural networks. Interestingly, we found that the cellular and electrophysiological deficits in SHANK3-deficient SNR-derived organoids are dependent on the level of SHANK3 expression and that organoids with complete hemizygous SHANK3 deletion have disrupted expression of several clustered protocadherins and multiple primate-specific zinc-finger genes. Together, this study describes a new method for using SNRs to generate organoids, provides new insights into the cell lineages associated with human cortico-striatal development, and identifies specific molecular pathways disrupted by hemizygous SHANK3 deletion, which is the most common genetic abnormality detected in patients with 22q13 deletion syndrome.

neuroscience↗
bioRxiv2020

Body site-specific and disease-specific virulome in the human microbiome

Human body habitats are home to a diverse array of microbes, and within these microbial ecosystems, there are exchanges of genetic material, including virulence factors (VFs). Little is known about the diversity and abundance of VFs in different body sites and different types of diseases. We developed a virulome analysis pipeline using the species-specific sequence identity inferred from intraspecies ANI values to precisely assign reads to virulence factors. We characterized the human virulome from four body habitats, including the gut, oral cavity, skin, and vagina. Specifically, the diversity and abundance of VFs in the oral cavity were significantly higher than those in other body sites, including stool. We highlight the importance of sex-specific analysis when studying the human virulome. We analyzed data from more than 4,000 samples across healthy and diseased subjects and 13 types of diseases from different metagenomic sequencing studies to characterize the disease-specific virulome. Atherosclerotic cardiovascular disease (ACVD) has a more diverse virulome than other diseases tested. Notably, many VFs, including genes for secretion systems and toxins, are more abundant in diseased subjects than in healthy controls. We present, to our knowledge, the most comprehensive healthy and diseased virulome dataset yet created.

genomics↗
bioRxiv2020

Molecular basis of functional compatibility between ezrin and other actin-membrane associated proteins during cytokinesis

The mechanism that mediates the interaction between the contractile ring and the plasma membrane during cytokinesis remains elusive. We previously found that ERM (Ezrin/Radixin/Moesin) proteins, which usually mediate cellular pole contraction, become over-accumulated at the cell equator and support furrow ingression upon the loss of other actin-membrane associated proteins, anillin and supervillin. In this study, we addressed the molecular basis of the semi-compatibility between ezrin and other actin-membrane associated proteins in mediating cortical contraction during cytokinesis. We found that depletion of supervillin and anillin caused over-accumulation of the membrane-associated FERM domain and actin-binding C-terminal domain (C-term) of ezrin at the cleavage furrow, respectively. This finding suggests that ezrin differentially shares its binding sites with these proteins on the actin cytoskeleton or inner membrane surface. Using chimeric mutants, we found that ezrin C-term, but not the FERM domain, can substitute for the corresponding anillin domains in cytokinesis and cell proliferation. On the other hand, either the membrane-associated or the actin/myosin-binding domains of anillin could not substitute for the corresponding ezrin domains in controlling cortical blebbing at the cell poles. Our results highlight specific designs of actin- or membrane-associated moieties of different actin-membrane associated proteins with limited compatibility, which enables them to support diverse cortical activities on the shared actin-membrane interface during cytokinesis.

cell biology↗
bioRxiv2020

Dynamic modelling of the PI3K/mTOR signalling network uncovers biphasic dependence of mTORC1 activation on the mTORC2 subunit Sin1

The PI3K/mTOR signalling network critically regulates a broad array of important biological processes, including cell growth, metabolism and autophagy. Dysregulation of PI3K/mTOR signalling is associated with a variety of human diseases, including cancer and metabolic disorders. The mechanistic target of rapamycin (mTOR) is a kinase that functions as a core catalytic subunit in two physically and functionally distinct complexes termed mTOR complex 1 (mTORC1) and mTORC2, which also share other common components such as mLTS8 (also known as G{beta}L) and DEPTOR. Despite being the subject of intensive research, a full picture of how mTORC1/2 assembly and activity are coordinated, and how they are functionally connected remain to be fully characterised. This is due primarily to the complex network wiring, featuring a growing number of intricate feedback loops and post-translational modifications, which require quantitative systems-level approaches to decipher. Here, we integrate predictive computational modelling, in vitro experiments and -omics data analysis to elucidate the dynamic and emergent features of the PI3K/mTOR network behavior. We construct new mechanistic models of the network that encapsulate novel critical mechanistic details, including mTORC1/2 coordination by mLTS8 (de)ubiquitination, and Akt-to-mTORC2 positive feedback loop. Model simulations subsequently confirmed by experimental validation revealed a previously unknown biphasic, threshold-gated dependence of mTORC1 activity on the key mTORC2 subunit Sin1, which is robust against cell-to-cell variation in protein expression. Furthermore, our results support the essential role of mLST8 in both mTORC1 and 2 activity, and suggest mLST8 could serve as a viable therapeutic target in breast cancer. Overall, our integrated analyses provide fresh systems-level insights into the dynamic behavior of PI3K/mTOR signalling and shed new light on the complexity of this important network. AUTHOR SUMMARYSignalling networks are the key information-processing machineries that underpin the ability of living cells to respond proportionately to extra- (and intra-) cellular cues. The PI3K/mTOR signalling network is one of the most important signalling networks in human cells that regulates cellular response to hormones such as insulin, yet our understanding of the network behaviour remains far from complete. Here, we employed a highly integrative approach that combines predictive mathematical modelling, biological experimentation, and data analysis to gain novel systems-level insights into PI3K/mTOR signalling. We constructed new mathematical models of this complex network incorporating important regulatory mechanisms. In contrary to commonly held views that mTORC2 lies upstream and is a positive regulator of mTORC1, we found that their relationship is highly nonlinear and dose dependent. This finding has major implications for mTORC2-directed anti-cancer strategies as depending on the cellular contexts, blocking mTORC2 may reduce or even enhance mTORC1 activation, the latter could inadvertently blunt the effect of mTORC2 blockade. Furthermore, our results demonstrate that mLST8 is required for the assembly and activity of both mTOR complexes, and suggest mLST8 is a viable therapeutic target in breast cancer, notably breast cancer.

systems biology↗
bioRxiv2020

Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2

The ongoing SARS-CoV-2 pandemic has brought an urgent need for animal models to study the pathogenicity of the virus. Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain, named MASCp36, that causes severe acute respiratory symptoms and mortality in standard laboratory mice. Particularly, this model exhibits age and gender related skewed distribution of mortality akin to severe COVID-19, and the 50% lethal dose (LD50) of MASCp36 was 58 PFU in 9-month-old, male BALB/c mice. Deep sequencing identified three amino acid substitutions, N501Y, Q493H, and K417N, subsequently emerged at the receptor binding domain (RBD) of MASCp36, during in vivo passaging. All three mutations in RBD significantly enhanced the binding affinity to its endogenous receptor, mouse ACE2 (mACE2). Cryo-electron microscopy (cryo-EM) analysis of human ACE2 (hACE2) or mACE2 in complex with the RBD of MASCp36 at 3.1 to 3.7 angstrom resolution elucidates molecular basis for the receptor-binding switch driven by specific amino acid substitutions. Interestingly, N501Y and Q493H enhanced the binding affinity to human ACE2 (hACE2); while triple mutations N501Y/Q493H/K417N decreased affinity to hACE2, thus led to the reduced infectivity of MASCp36 to human cells. Our study not only provides a robust platform for studying the pathogenesis of severe COVID-19 and rapid evaluation of coutermeasures against SARS-CoV-2, but also unveils the molecular mechanism for the rapid adaption and evolution of SARS-CoV-2 in human and animals. One sentence summaryA mouse adapted SARS-CoV-2 strain that harbored specific amino acid substitutions in the RBD of S protein showed 100% mortality in aged, male BALB/c mice.

microbiology↗
bioRxiv2020

SARS-CoV-2 infection causes transient olfactory dysfunction in mice

Olfactory dysfunction caused by SARS-CoV-2 infection represents as one of the most predictive and common symptoms in COVID-19 patients. However, the causal link between SARS-CoV-2 infection and olfactory disorders remains lacking. Herein we demonstrate intranasal inoculation of SARS-CoV-2 induces robust viral replication in the olfactory epithelium (OE), resulting in transient olfactory dysfunction in humanized ACE2 mice. The sustentacular cells and Bowmans gland cells in OE were identified as the major targets of SARS-CoV-2 before the invasion into olfactory sensory neurons. Remarkably, SARS-CoV-2 infection triggers cell death and immune cell infiltration, and impairs the uniformity of OE structure. Combined transcriptomic and proteomic analyses reveal the induction of antiviral and inflammatory responses, as well as the downregulation of olfactory receptors in OE from the infected animals. Overall, our mouse model recapitulates the olfactory dysfunction in COVID-19 patients, and provides critical clues to understand the physiological basis for extrapulmonary manifestations of COVID-19.

microbiology↗
bioRxiv2020

Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago

Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The SARS-CoV-2 pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, we used a combinatorial human antibody library constructed 20 years before the COVID-19 pandemic to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in crystal structures with SARS-CoV-2 spike RBD. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of human immune responses to SARS-CoV-2.

microbiology↗
bioRxiv2020

Comprehensive and scalable quantification of splicing differences with MntJULiP

Alternative splicing of mRNA is an essential gene regulatory mechanism with important roles in development and disease. We present MntJULiP, a method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP implements novel Dirichlet-multinomial and zero-inflated negative binomial models within a Bayesian framework to detect both changes in splicing ratios and in absolute splicing levels of introns with high accuracy, and can find classes of variation overlooked by reference tools. Additionally, a mixture model allows multiple conditions to be compared simultaneously. Highly scalable, it processed hundreds of GTEx samples in <1 hour to reveal splicing constituents of tissue differentiation.

bioinformatics↗
bioRxiv2020

Single-dose intranasal administration of AdCOVID elicits systemic and mucosal immunity against SARS-CoV-2 in mice

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the urgent need for effective preventive vaccination to reduce burden and spread of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) in humans. Intranasal vaccination is an attractive strategy to prevent COVID-19 as the nasal mucosa represents the first-line barrier to SARS-CoV-2 entry before viral spread to the lung. Although SARS-CoV-2 vaccine development is rapidly progressing, the current intramuscular vaccines are designed to elicit systemic immunity without conferring mucosal immunity. Here, we show that AdCOVID, an intranasal adenovirus type 5 (Ad5)-vectored vaccine encoding the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, elicits a strong and focused immune response against RBD through the induction of mucosal IgA, serum neutralizing antibodies and CD4+ and CD8+ T cells with a Th1-like cytokine expression profile. Therefore, AdCOVID, which promotes concomitant systemic and local mucosal immunity, represents a promising COVID-19 vaccine candidate.

immunology↗
bioRxiv2020

Ethylenediaminetetraacetic acid promotes the accumulation of nitric oxide

Ethylenediaminetetraacetic acid (EDTA) is a well-established chelating agent used in industry, agriculture, food, and medicine. However, the analysis of an EDTA-sensitive Arabidopsis thaliana mutant revealed that EDTA can significantly promote nitric oxide (NO) accumulation, indicating that EDTA has unexpected biological functions beyond its chelating activity. This finding challenges our current understanding about the effects of EDTA on biological systems. One Sentence SummaryAn analysis of ethylenediaminetetraacetic acid (EDTA)-sensitive mutants suggests that EDTA can promote the accumulation of nitric oxide.

molecular biology↗
bioRxiv2020

Pancreatic α and β cells are globally phase-locked

The Ca2+ modulated pulsatile secretion of glucagon and insulin by pancreatic and {beta} cells plays a key role in glucose homeostasis. However, how and {beta} cells coordinate via paracrine interaction to produce various Ca2+ oscillation patterns is still elusive. Using a microfluidic device and transgenic mice in which and {beta} cells were labeled with different colors, we were able to record islet Ca2+ signals at single cell level for long times. Upon glucose stimulation, we observed heterogeneous Ca2+ oscillation patterns intrinsic to each islet. After a transient period, the oscillations of and {beta} cells were globally phase-locked, i.e., the two types of cells in an islet each oscillate synchronously but with a phase shift between the two. While the activation of cells displayed a fixed time delay of ~20 s to that of {beta} cells, {beta} cells activated with a tunable delay after the cells. As a result, the tunable phase shift between and {beta} cells set the islet oscillation period and pattern. Furthermore, we demonstrated that the phase shift can be modulated by glucagon. A mathematical model of islet Ca2+ oscillation taking into consideration of the paracrine interaction was constructed, which quantitatively agreed with the experimental data. Our study highlights the importance of cell-cell interaction to generate stable but tunable islet oscillation patterns.

systems biology↗
bioRxiv2020

Restoration of β-globin expression with optimally designed lentiviral vector for β-thalassemia treatment in Chinese patients

{beta}-thalassemia is one of the most prevalent genetic diseases worldwide. The current treatment for {beta}-thalassemia is allogeneic hematopoietic stem cell transplantation (HSCT), which is limited due to lack of matched donors. Gene therapy has been developed as an alternative therapeutic option for transfusion-ependent {beta}-thalassemia (TDT). However, successful gene therapy for {beta}-thalassemia patients in China has not been reported. Here we present the results of preclinical studies of an optimally designed LV named LentiHBBT87Q in hematopoietic stem cells (HSCs) derived from Chinese TDT patients. LentiHBBT87Q was selected from a series of LVs with optimized backbone and de novo cloning strategy. It contains an exogenous T87Q {beta}-globin gene (HBBT87Q) driven by a specific reconstituted locus control region (rLCR) and efficiently express HBB mRNA and HBB protein in erythroblasts derived from cord blood (CB) HSCs. To facilitate clinical transformation, we manufactured clinical grade LentiHBBT87Q (cLentiHBBT87Q) and optimized its transduction procedure. Importantly, transduction of cLentiHBBT87Qrestored expression of HBB monomer and adult hemoglobin (HbA) tetramer to relatively normal level in erythroblasts from bone marrow (BM) HSCs of Chinese TDT patients, that carry the most common mutation types and cover various genotypes, including {beta}0/{beta}0. Furthermore, viral integration sites (VIS) of cLentiHBBT87Q were similar to other LVs safely used in previous clinical trials and the associated risk of tumorigenesis was not observed in cLentiHBBT87Q transduced HSCs through comprehensive analysis. Taken together, we have engineered the cLentiHBBT87Q that can restore {beta}-globin expression in the HSCs-derived erythroblasts of Chinese TDT patients with minimal risk on tumorigenesis, providing a favorable starting point for future clinical application.

cell biology↗
bioRxiv2020

Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy

Coronavirus disease 2019 (COVID-19) threatens global public health and economy. In order to develop safe and effective vaccines, suitable animal models must be established. Here we report the rapid adaption of SARS-CoV-2 in BALB/c mice, based on which a convenient, economical and effective animal model was developed. Specifically, we found that mouse-adapted SARS-CoV-2 at passage 6 (MACSp6) efficiently infected both aged and young wild-type BALB/c mice, resulting in moderate pneumonia as well as inflammatory responses. The elevated infectivity of MACSp6 in mice could be attributed to the substitution of a key residue (N501Y) in the receptorbinding domain (RBD). Using this novel animal model, we further evaluated the in vivo protective efficacy of an RBD-based SARS-CoV-2 subunit vaccine, which elicited highly potent neutralizing antibodies and conferred full protection against SARS-CoV-2 MACSp6 challenge. This novel mouse model is convenient and effective in evaluating the in vivo protective efficacy of SARS-CoV-2 vaccine. SummaryThis study describes a unique mouse model for SARS-CoV-2 infection and confirms protective efficacy of a SARS-CoV-2 RBD subunit vaccine.

microbiology↗
bioRxiv2020

Molecularly Targeted Magnetic Resonance Imaging and Spectroscopy

Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) have tremendous utility in many fields, such as clinical diagnosis, medical research and brain science. MRI provides high resolution anatomic images of tissues/organs, and MRS provides functional molecular information related to specific regions of tissues/organs. However, it is often difficult for conventional MRI/MRS to selectively image/probe a specific metabolite molecule other than water and fat. This greatly limits study of the molecular mechanisms underlying metabolism and disease. Herein, we report a novel method for obtaining an exact molecularly targeted MRI and MRS. This method uses the nuclear spin singlet state to select the signals from a specific molecule. Several endogenous molecules in living organism such as N-acetylaspartate and dopamine have been exemplarily imaged and probed as the targeted molecules in the MRI and MRS experiments, demonstrating the unique molecular selectivity of the developed method. Endogenous-molecule-targeted MRI and MRS can be achieved by using the new pulse sequences O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/026252v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@483ca2org.highwire.dtl.DTLVardef@84d4c0org.highwire.dtl.DTLVardef@abca24org.highwire.dtl.DTLVardef@6423ae_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗
bioRxiv2020

Cellular senescence and quiescence are associated with altered ribosomal RNA methylation and processing

The 2-O-methylation (2-O-Me) of ribosomal RNA (rRNA) shows plasticity potentially associated with specific cell phenotypes. We used RiboMeth-seq profiling to reveal 2-O-Me patterns specific to stress induced premature senescent (SIPS), quiescent and proliferating human dermal fibroblasts. The altered methylation levels in SIPS and quiescence partially correlated with the expression of specific snoRNAs but not fibrillarin. Senescence and quiescence were accompanied by a trend towards preferred usage of one of the two alternative ribosome biogenesis pathways.

molecular biology↗
bioRxiv2020

Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex

Nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC from Xenopus laevis oocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes, and a Grid domain, which serves as a rigid base for the Finger domain. Two neighbouring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighbouring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC.

biophysics↗
bioRxiv2020

Multiple approaches for massively parallel sequencing of HCoV-19 genomes directly from clinical samples

COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. We also examine and compare the bias, sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. This is, to date, the first work systematically implements amplicon and capture approaches in sequencing HCoV-19, as well as the first comparative study across methods. Our work offers practical solutions for genome sequencing and analyses of HCoV-19 and other emerging viruses.

genomics↗