Biology subjects

Huang, Y.

Publications and source records attributed to Huang, Y..

At least 667 records · Page 37Linked to original sources

bioRxiv2022

2,4-Di-tert-butylphenol Induces Adipogenesis in Human Mesenchymal Stem Cells by Activating Retinoid X Receptors

2,4-di-tert-butylphenol (2,4-DTBP) is an important commercial antioxidant and a toxic natural secondary metabolite that has been detected in humans. However, there is scant information regarding its toxicological effects. Here we asked whether 2,4-DTBP is a potential obesogen. Using a human mesenchymal stem cell (MSC) adipogenesis assay, we found that exposure to 2,4-DTBP led to increased lipid accumulation and expression of adipogenic marker genes. Antagonist assays revealed that 2,4-DTBP increased lipid accumulation by activating the peroxisome proliferator-activated receptor {gamma} (PPAR{gamma})-retinoid X receptor (RXR) heterodimer. 2,4-DTBP likely activated the PPAR{gamma}/RXR heterodimer by activating RXR but not directly binding to PPAR{gamma}. We confirmed that 2,4-DTBP directly bound to RXR by solving the crystal structure of this complex, then predicted and demonstrated that related compounds could also activate RXR. Our study demonstrated that 2,4-DTBP and related chemicals could act as obesogens and endocrine disruptors via RXR. These data showed that 2,4-DTBP belongs to a family of compounds whose endocrine-disrupting and obesogenic effects can be strongly modulated by their chemical composition and that structure-activity studies such as the present one could help guide the rational development of safer antioxidants. SYNOPSISLittle research exists on the effects of commercially valuable antioxidants on biological systems. This study reports that di- and tri-tert-butylphenols can act as endocrine disruptors and potential obesogens by activating nuclear hormone receptors.

pharmacology and toxicology↗

bioRxiv2022

Phosphatidylserine controls synaptic targeting and membrane stability of ASIC1a

Phospholipid-protein interaction is highly specialized at the membranous nanodomains and critical for membrane receptor signaling. Calcium-permeable acid-sensing ion channel isoform 1a (ASIC1a) is a major neuronal proton sensor that contributes to synaptic plasticity. The functional outcome of ASIC1a is dependent on its surface targeting in synaptic subdomains; however, the lipid environment for ASIC1a and its role in channel targeting remain poorly understood. Here, we report that anionic phosphatidylserine (PS) is enriched in dendritic spines during neurodevelopment and it directly binds to ASIC1a through an electrostatic interaction with a di-arginine motif at ASIC1a C-terminus. PS regulates the membrane targeting and function of ASIC1a, which are both strongly suppressed by inhibition of PS synthesis. In cortical neuron dendrites, both PS and ASIC1a are predominately localized to peri-synaptic sites of spine heads, surrounding instead of overlapping with postsynaptic markers, PSD-95 and GluN1. Uncoupling the interaction between PS and ASIC1a by changing the charges to neutral or acidic at the di-arginine PS-binding motif, or applying a membrane penetrating competing peptide, caused mistargeting of ASIC1a at the synaptic sites, an overall increase in internalization and/or cytoplasmic accumulation of ASIC1a, and a decrease in its channel function. Together, our results provide novel insights on lipid microenvironment that governs ASIC1a expression and function at the membrane surface, especially peri-synaptic regions of dendritic spines, through an electrostatic interaction with anionic phospholipids.

neuroscience↗

bioRxiv2022

DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer

Large-scale genetic and pharmacologic dependency maps are generated to reveal genetic vulnerabilities and drug sensitivities of cancer. However, user-friendly software is needed to systematically link such maps. Here we present DepLink, an R Shiny server to identify genetic and pharmacologic perturbations that induce similar effects on cell viability or molecular changes. DepLink integrates heterogeneous datasets of genome-wide CRISPR loss-of-function screens, high-throughput pharmacologic screens, and perturbation expression signatures. The datasets are systematically connected by four complementary modules tailored for different query scenarios. In summary, DepLink enables easy navigation, visualization, and linkage of rapidly evolving cancer dependency maps.

bioinformatics↗

bioRxiv2022

Longitudinal characterization of circulating extracellular vesicles and small RNA during simian immunodeficiency virus infection and antiretroviral therapy

ObjectivesLatent infection by human immunodeficiency virus (HIV) hinders viral eradication despite effective antiretroviral treatment (ART), Amongst proposed contributors to viral latency are cellular small RNAs that have also been proposed to shuttle between cells in extracellular vesicles (EVs). Thus, we profiled EV small RNAs during different infection phases to understand the potential relationship between these EV-associated small RNAs and viral infection. DesignA well characterized simian immunodeficiency virus (SIV)/macaque model of HIV was used to profile EV-enriched blood plasma fractions harvested during pre-infection, acute infection, latent infection/ART treatment, and rebound after ART interruption. MethodsMeasurement of EV concentration, size distribution, and morphology was complemented with qPCR array for small RNA expression, followed by individual qPCR validations. Iodixanol density gradients were used to separate EV subtypes and virions. ResultsPlasma EV particle counts correlated with viral load and peaked during acute infection. However, SIV gag RNA detection showed that virions did not fully explain this peak. EV microRNAs miR-181a, miR-342-3p, and miR-29a decreased with SIV infection and remained downregulated in latency. Interestingly, small nuclear RNA U6 had a tight association with viral load peak. ConclusionsThis study is the first to monitor how EV concentration and EV small RNA expression change dynamically in acute viral infection, latency, and rebound in a carefully controlled animal model. These changes may also reveal regulatory roles in retroviral infection and latency.

microbiology↗

bioRxiv2022

Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis

Single-cell level characterization of embryonic development is a major benchmark of human developmental biology. Spatiotemporal analysis of stem-cell-derived embryos offers conceptual and technical advances in the field. Here, we defined the single-cell spatiotemporal gene expression landscape of human embryonic development with stem-cell-derived organoids. We established the human embryonic organoid (HEMO) from expanded potential stem cells and achieved both embryonic and extraembryonic tissues in the same organoid. Time-series single-cell RNA sequencing paired with single-cell resolution spatial revealed human embryonic development signatures such as extraembryonic placenta, yolk sac hematopoiesis neural crest, blood vessels, and cardiac mesoderm. Hematopoietic tissues eventually predominated HEMO with erythropoiesis, mekagaryopiesis, and myelopoiesis. Cell-cell communication network analysis demonstrated that trophoblast-like tissues supplied WNT signaling in neural crest cells to facilitate maturation and migration. Single-cell resolution spatial transcriptomics defined the yolk sac erythro-megakaryopoietic niche. Vitronectin-integrin signaling, a major contributor to megakaryocyte maturation, was predominant in the yolk sac niche in HEMO and to human fetal samples. Overall, our study advances the spatiotemporal analysis of human embryonic development in stem-cell-derived organoids. HighlightsO_LIModeling human embryonic development from stem cells C_LIO_LIUsed of both 10X Chromium and 10X Visium to define the gene expression landscape of embryonic development and hematopoiesis C_LIO_LIWNT signaling as a regulator of neural crest maturation and EMT C_LIO_LIVTN-ITGA2B as the main contributor to Mk maturation within the yolk sac erythro-megakaryopoietic niche C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/505700v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1710d00org.highwire.dtl.DTLVardef@10ca8e0org.highwire.dtl.DTLVardef@2310d1org.highwire.dtl.DTLVardef@252728_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2022

SpatialDM: Rapid identification of spatially co-expressed ligand-receptor reveals cell-cell communication patterns

Cell-cell communication is a key aspect of dissecting the complex cellular microenvironment. Existing single-cell and spatial transcriptomics-based methods primarily focus on identifying cell-type pairs for a specific interaction, while less attention has been paid to the prioritisation of interaction features or the identification of interaction spots in the spatial context. Here, we introduce SpatialDM, a statistical model and toolbox leveraging a bivariant Morans statistic to detect spatially co-expressed ligand and receptor pairs, their local interacting spots (single-spot resolution), and communication patterns. By deriving an analytical null distribution, this method is scalable to millions of spots and shows accurate and robust performance in various simulations. On multiple datasets including melanoma, Ventricular-Subventricular Zone (SVZ), and intestine, SpatialDM reveals promising communication patterns and identifies differential interactions between conditions, hence enabling the discovery of context-specific cell cooperation and signalling.

bioinformatics↗

bioRxiv2022

A premotor microcircuit to generate behavior-specific muscle activation patterns in Drosophila larvae

Animals can use a common set of muscles and motor neurons (MNs) to generate diverse locomotor behaviors, but how this is accomplished remains poorly understood. Previously, we characterized the muscle activity patterns for Drosophila larval forward and backward locomotion and found that ventral oblique (VO) muscles become active earlier in backward than in forward locomotion (Zarin et al. 2019). Here, we describe how premotor circuits generate differential activation timing of VO muscles. We identify inhibitory (A06c) and excitatory (A27h) premotor neurons (PMNs) with the greatest number of synapses with VO MNs. Strikingly, A06c is a bi-modal PMN that fires before and after VO MNs in forward locomotion but fires only after MNs in backward locomotion. Further, A27h is a forward-dedicated PMN active only in forward locomotion. These two PMNs interconnect with another forward-dedicated excitatory PMN (A18b3), to create feedforward inhibitory microcircuits that define the activity window for VO MNs/muscles, producing precise VO muscle patterns underlying forward locomotion. Silencing A06c, A27h, or A18b3 PMN results in premature VO muscle activation in forward locomotion, resembling early VO activation in backward locomotion. Our results identify PMN micro-circuits that produce unique MN/muscle activity patterns to create behavior-specific motor output.

neuroscience↗

bioRxiv2022

Lipids Maintain Genomic Stability and Developmental Potency of Murine Pluripotent Stem Cells

Lipids play vital roles in cellular homeostasis and regulate pluripotency of human stem cells. However, the impact of lipids on murine pluripotent stem cells is unclear. While Mek1/2 and Gsk3{beta} inhibition ("2i") supports the maintenance of murine embryonic stem cells (ESCs) in a homogenous naive state, prolonged culture in 2i results in aneuploidy and DNA hypomethylation that impairs developmental potential. Additionally, 2i fails to support derivation and culture of fully potent female ESCs. Here we find that mouse ESCs cultured in 2i/LIF supplemented with lipid-rich albumin (AlbuMAX) undergo pluripotency transition yet maintain genomic stability and full potency over long-term culture. Mechanistically, lipids in AlbuMAX impact intracellular metabolism including nucleotide biosynthesis, lipid biogenesis, and TCA cycle intermediates, with enhanced expression of ZCAN4 and DNMT3s that prevent telomere shortening and DNA hypomethylation. In concert with 2i, lipids induce a formative-like pluripotent state through direct stimulation of Mek-mediated Erk2 phosphorylation, which also alleviates X chromosome loss in female ESCs. Importantly, both male and female "all-ESC" mice can be generated from de novo derived ESCs using AlbuMAX-based media. Our findings underscore the importance of lipids to pluripotency and link nutrient cues to genome integrity in early development.

developmental biology↗

bioRxiv2022

Engineering precise adenine base editor with infinitesimal rates of bystander mutations and off-target editing

Adenine base editors (ABEs) catalyze A-to-G transitions showing broad applications, but their bystander mutations and off-target editing effects raise the concerns of safety issues. Through structure-guided engineering, we found ABE8e with an N108Q mutation reduced both adenine and cytosine bystander editing, and introduction of an additional L145T mutation (ABE9), further refined the editing window to 1-2nt with eliminated cytosine editing. Importantly, ABE9 induced very minimal RNA and undetectable Cas9-independent DNA off-target effects, which mainly installed desired single A-to-G conversion in mouse and rat embryos to efficiently generate disease models. Moreover, ABE9 accurately edited A5 position of the protospacer sequence in pathogenic homopolymeric adenosine sites (up to 342.5-fold precision than ABE8e) and was further confirmed through a library of guide RNA-target sequence pairs. Due to the minimized editing window, ABE9 could further broaden the targeting scope for precise correction of pathogenic SNVs when fused to Cas9 variants with expanded PAM compatibility.

bioengineering↗

bioRxiv2022

ATF3 Preserves Skeletal Muscle Stem Cell Quiescence by Preventing Precocious Activation

Skeletal muscle stem cells (also called satellite cells, SCs) are important for maintaining muscle tissue homeostasis and damage-induced regeneration. However, it remains poorly understood how the SC quiescence is preserved. Here we report that AP-1 family member ATF3 preserves the SC quiescence by preventing their premature activation. Atf3 is rapidly and transiently induced in SCs upon activation. Short-term deletion of Atf3 in SCs accelerates acute injury-induced regeneration, and however, its long-term deletion exhausts the SC pool and thus impairs muscle regeneration. The Atf3 loss also provokes SC activation during voluntary exercise and enhances SC activation during resistance exercise. Mechanistically, ATF3 directly activates the transcription of Histone 2B genes, which reduction accelerates nucleosome displacement and gene transcription required for SC activation. Finally, the ATF3-dependent H2B expression also prevents genome instability and replicative senescence in SCs. Therefore, this study has revealed a novel mechanism for preserving the SC population by actively suppressing precocious activation, in which ATF3 is a key regulator.

cell biology↗

bioRxiv2022

An efficient and robust tool for colocalisation: Pair-wise Conditional and Colocalisation (PWCoCo)

Genetic colocalisation is an important tool to test for shared genetic aetiology and is commonly used to strengthen causal inference in genetic studies of molecular traits and drug targets. However, the single causal variant assumption of the original colocalization method is a considerable limitation in genomic regions with multiple causal effects. We integrated conditional analyses (GCTA-COJO) and colocalisation analyses (coloc), into a novel analysis tool called Pair-Wise Conditional Colocalization (PWCoCo). PWCoCo performs conditional analyses to identify independent signals for the two tested traits in a genomic region and then conducts colocalisation of each pair of conditionally independent signals for the two traits using summary-level data. This allows for the stringent single-variant assumption to hold for each pair of colocalisation analysis. We found that the computational efficiency of PWCoCo is on average better than colocalisation with Sum of Single Effects Regression using Summary Stats (SuSiE-RSS), with greater gains in efficiency for high-throughput analysis. In a case study using GWAS data for multiple sclerosis and brain cortex-derived eQTLs (MetaBrain), we recapitulated all previously identified genes, which showcased the robustness of the method. We further found colocalisation evidence for secondary signals in nine additional loci, which was not identifiable in conventional GWAS and/or colocalisation. PWCoCo offers key improvements over existing methods, including: (1) robust colocalisation when the single variant assumption is violated; (2) independent colocalisation of secondary signals, which enables identification of novel disease-causing variants; (3) an easy-to-use and computationally efficient tool to test for colocalisation of high-dimensional omics data.

bioinformatics↗

bioRxiv2022

Decoding Subject's Own Name in the Primary Auditory Cortex

Current studies have shown that perception of subjects own name (SON) involves multiple multimodal brain regions, while activities in unimodal sensory regions (i.e., primary auditory cortex) and their interaction with multimodal regions during the self-processing remain unclear. To answer this, we combined multivariate pattern analysis and dynamic causal modelling analysis to explore the regional activation pattern and inter-region effective connection during the perception of SON. We found that SON and other names could be decoded from the activation pattern in the primary auditory cortex. In addition, we found an excitatory effect of SON on connections from the anterior insula/inferior frontal gyrus to the primary auditory cortex, and to the temporal parietal junction. Our findings extended the current knowledge of self-processing by showing that primary auditory cortex could discriminate SON from other names. Furthermore, our findings highlighted the importance of influence of the insula on the primary auditory cortex during self-processing.

neuroscience↗

bioRxiv2022

Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75

The SARS-CoV-2 Omicron subvariant BA.2.75 emerged recently and appears to be spreading rapidly. It has nine mutations in its spike compared to BA.2, raising concerns it may further evade vaccine-elicited and therapeutic antibodies. Here, we found BA.2.75 to be moderately more neutralization resistant to sera from vaccinated/boosted individuals than BA.2 (1.8-fold), similar to BA.2.12.1 (1.1-fold), but more neutralization sensitive than BA.4/5 (0.6-fold). Relative to BA.2, BA.2.75 showed heightened resistance to class 1 and class 3 monoclonal antibodies to the receptor-binding domain, while gaining sensitivity to class 2 antibodies. The resistance was largely conferred by the G446S and R460K mutations. Of note, BA.2.75 was slightly resistant (3.7-fold) to bebtelovimab, the only therapeutic antibody with potent activity against all Omicron subvariants. BA.2.75 also exhibited higher receptor binding affinity than other Omicron subvariants. BA.2.75 provides yet another example of the ongoing evolution of SARS-CoV-2 as it gains transmissibility while incrementally evading antibody neutralization.

microbiology↗

bioRxiv2022

ZmWRKY82-ZmSLG regulate seed development by modulating brassionsteroid homeostasis in maize

Seed development is a crucial biological process affecting crop yield. Brassionsteroids (BRs) plays essential role in seed development. Although part of genes participated in BR regulate seed development have been cloned in maize, their genetic and mechanisms are still unclear. In the previous experiment, we found that exogenous spray BL promote seed development. Here, RNA-sequence analysis of BL treated seeds revealed that 12 candidate function genes and 62 candidate transcription factors among the differentially expressed genes (DEGs) were regulated by BL. Combining with previous QTL and GWAS research results in maize and homologous gene analysis, ZmSLG1 was screened out from 12 candidate function genes for further study. Overexpression of ZmSLG1 displayed round seed and delayed embryo development in maize. Moreover, overexpression of ZmSLG1 decreased BR content and increased expression of BR synthesis related genes in seed. To understand the mechanism of BL regulating ZmSLG1 expression, ZmWRKY82 was identified from 62 candidate transcription factors and examined its function. Transient expression, EMSA and ChIP analysis showed ZmWRKY82 can directly bind to the ZmSLG1 promoter to regulate ZmSLG1 expression. Collectively, exogenous BL regulate the ZmSLG1 gene expression through ZmWRKY82 transcription factor, and ZmSLG1 negatively regulates the endogenous BR contents in seed. HighlightWe conclude that ZmWRKY82-ZmSLG1 is required for BR homeostasis and that modification of ZmSLG1 expression to an appropriate level may provide a way to increase yield.

molecular biology↗

bioRxiv2022

Pathogen effector-associated nuclear-localization of RPW8.2 amplifies its expression to boost immunity in Arabidopsis

RESISTANCE TO POWDERY MILDEW 8 (RPW8) defines a unique N-terminal coiled-coil domain of nucleotide-binding and leucine-rich repeat immune receptors required for immune signaling in plants. Arabidopsis RPW8.2 is specifically induced by the powdery mildew (PM) fungus (Golovinomyces cichoracearum) in the infected epidermal cells to activate immunity. The mechanism of RPW8.2-induction is not well understood. Here, we identify a G. cichoracearum factor delivered to the nucleus of the host cell, named Gc-RPW8.2 interacting protein 1 (GcR8IP1). Ectopic expression of GcR8IP1 in Arabidopsis or Nicotiana benthamiana suppressed host immune responses and enhanced susceptibility to PM. Host-induced gene silencing of GcR8IP1 compromised PM infectivity in susceptible Arabidopsis plants. Co-expression of GcR8IP1 with RPW8.2 increased nuclear localization of RPW8.2, which in turn, promoted transcriptional amplification of RPW8.2. Thus, RPW8.2-dependent defense strengthening is due to altered partitioning of RPW8.2 by an effector of a PM fungus, which exemplifies an atypical form of effector-triggered immunity.

plant biology↗

bioRxiv2022

SARS-CoV-2 omicron variants succumb in vitro to Artemisia annua hot water extracts

The SARS-CoV-2 (COVID-19) global pandemic continuous to infect and kill millions while rapidly evolving new variants that are more transmissible and evading vaccine-elicited antibodies. Artemisia annua L. extracts have shown potency against all previously tested variants. Here we further queried extract efficacy against omicron and its recent subvariants. Using Vero E6 cells, we measured the in vitro efficacy (IC50) of stored (frozen) dried-leaf hot-water A. annua L. extracts of four cultivars (A3, BUR, MED, and SAM) against SARS-CoV-2 variants: original WA1 (WT), BA.1.1.529+R346K (omicron), BA.2, BA.2.12.1, and BA.4. IC50 values normalized to the extract artemisinin (ART) content ranged from 0.5-16.5 {micro}M ART. When normalized to dry mass of the extracted A. annua leaves, values ranged from 20-106 {micro}g. Although IC50 values for these new variants are slightly higher than those reported for previously tested variants, they were within limits of assay variation. There was no measurable loss of cell viability at leaf dry weights [≤]50 {micro}g of any cultivar extract. Results continue to indicate that oral consumption of A. annua hot-water extracts (tea infusions) could potentially provide a cost-effective approach to help stave off this pandemic virus and its rapidly evolving variants.

pharmacology and toxicology↗

bioRxiv2022

Single Cell Epigenetics Reveal Cell-Cell Communication Networks in Normal and Abnormal Cardiac Morphogenesis

Communication between myriad cell types during organ formation underlies proper morphogenesis1. In cardiac development, reciprocal signaling between mesoderm progenitors and neural crest cells is essential, and its disruption leads to congenital heart malformations, the most common human birth defect. However, mechanistic interrogation of temporal gene networks and cis regulatory elements in this crosstalk is limited2,3. Here, we integrated single cell chromatin accessibility and transcriptomics to establish an unbiased and temporal epigenomic map of the embryonic mouse heart over multiple stages and developed machine learning models to predict enhancers for heart and neural crest. We leveraged these advances to determine the consequences of dysregulated signaling at single cell resolution caused by deletion of TBX1, a transcription factor that causes morphogenetic defects of the cardiac outflow tract in humans and functions non-cell autonomously in cardiac mesodermal progenitors to direct pharyngeal neural crest differentiation4-6. Loss of Tbx1 in mice led to broad closure of chromatin regions enriched in cardiac progenitor transcription factor motifs within a narrow subset of cardiac mesodermal progenitors and correlated with diminished expression of numerous members of the fibroblast growth factor, retinoic acid, Notch and Semaphorin pathways. In affected progenitors, ectopic accessibility and expression of posterior heart field factors in the anterior heart field suggested impaired axial patterning. In response, a subset of cardiac neural crest cells displayed epigenomic and transcriptional defects, indicating a failure of differentiation corresponding to dysregulation of the anterior-posterior gradient of pharyngeal Hox gene expression. This study demonstrates that single-cell genomics and machine learning can generate a mechanistic model for how disruptions in cell communication selectively affect spatiotemporally dynamic regulatory networks in cardiogenesis.

developmental biology↗

bioRxiv2022

Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes

Birth defects occur in [~]6% of all live births and can be caused by combinations of genetic and environmental influences1. Large-scale DNA sequencing efforts are revealing genetic influences2,3, but investigations into the contributions of environmental factors have largely been limited to association studies with limited mechanistic insight. Hyperglycemia present in pre-gestational diabetic mothers is among the most frequent environmental contributor to congenital defects and results in an increased incidence of congenital heart defects and craniofacial anomalies4. However, the cell types involved and underlying mechanisms by which maternal hyperglycemia affects these regions are unknown. Here, we utilized multi-modal single cell analyses to reveal that maternal diabetes affects the epigenomic and transcriptomic state of specific subsets of cardiac and craniofacial progenitors during embryogenesis. A previously unrecognized subpopulation of anterior heart field progenitors expressing Alx3 acquired a more posterior identity in response to maternal hyperglycemia, based on gene expression and chromatin status. Similarly, a sub-population of neural crest-derived cells in the second pharyngeal arch, which contributes to craniofacial structures, also displayed abnormalities in cell specification and patterning. Analysis of differentially accessible chromatin regions demonstrated that disrupted patterning was associated with increased intrinsic retinoic acid signaling in affected cell types in response to maternal diabetes and hyperglycemia. This work demonstrates how an environmental insult can have highly selective epigenomic consequences on discrete cell types leading to developmental patterning defects.

developmental biology↗