Biology subjects

Wang, D.

Publications and source records attributed to Wang, D..

At least 559 records · Page 31Linked to original sources

bioRxiv2021

Intracellular glycosyl hydrolase PslG shapes bacterial cell fate, signaling, and the biofilm development of Pseudomonas aeruginosa

Biofilm formation is one of most important causes leading to persistent infections. Exopolysaccharides are usually a main component of biofilm matrix. Genes encoding for glycosyl hydrolases are often found in gene clusters that are involved in the exopolysaccharide synthesis. It remains elusive about the functions of intracellular glycosyl hydrolase and why a polysaccharide synthesis gene cluster requires a glycosyl hydrolase. Here we systematically studied the role of intracellular PslG, a glycosyl hydrolase that is co-transcribed with 15 psl genes, which is responsible for the synthesis of exopolysaccharide Psl (ePsl), a key biofilm matrix polysaccharide in opportunistic pathogen Pseudomonas aeruginosa. We showed that lacking of PslG in this opportunistic pathogen alters the signaling function and structure of ePsl, changes the relative level of cyclic-di-GMP within daughter cells during cell division and shapes the localization of ePsl on bacterial periphery, thus results in long chains of bacterial cells, fast-forming and compact biofilm microcolonies. Our results reveal the important roles of intracellular PslG on the cell fate and biofilm development.

microbiology↗

bioRxiv2021

Single-cell lineage trajectories and chromatin regulators that initialize antiviral CD8 T cell ontogeny

Individual naive CD8 T cells activated in lymphoid organs differentiate into functionally diverse and anatomically distributed T cell phylogenies in response to intracellular microbes. During infections that resolve rapidly, including live viral vaccines1, distinct effector (TEFF) and memory (TMEM) cell populations develop that ensure long term immunity2. During chronic infections, responding cells progressively become dysfunctional and "exhaust"3. A diverse taxonomy of TEFF, TMEM and exhausted (TEX) CD8 T cell populations is known, but the initial developmental basis of this phenotypic variation remains unclear4-10. Here, we defined single-cell trajectories and identified chromatin regulators that establish antiviral CD8 T cell heterogeneity using unsupervised analyses of single-cell RNA dynamics11-13 and an in vivo RNAi screen14. Activated naive cells differentiate linearly into uncommitted effector-memory progenitor (EMP) cells, which initially branch into an analogous manifold during either acute or chronic infection. Disparate RNA velocities in single EMP cells initiate divergence into stem, circulating, and tissue-resident memory lineages that generate diverse TMEM and TEX precursor states in specific developmental orders. Interleukin-2 receptor (IL-2R) signals are essential for formation and transcriptional heterogeneity of EMP cells, and promote trajectories toward TEFF rather than TEX states. Nucleosome remodelers Smarca4 and Chd7 differentially promote transcription that delineates divergent TMEM lineages before cooperatively driving terminal TEFF cell differentiation. Thus, the lineage architecture is established by specific chromatin regulators that stabilize diverging transcription in uncommitted progenitors.

immunology↗

bioRxiv2021

Integrative annotation of genomic features reveal functional elements and epigenetic landscapes in the developing zebrafish

Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals.

developmental biology↗

bioRxiv2021

Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma

CD38 is a surface ectoenzyme expressed at high levels on myeloma plasma cells and is the target for the monoclonal antibodies (mAbs) daratumumab and isatuximab. Pre-treatment CD38 density on tumor cells is an important determinant of mAb efficacy. Several small molecules have been found to increase tumor surface CD38, with the goal of boosting mAb efficacy in a co-treatment strategy. Numerous other CD38-targeting therapeutics are currently in preclinical or clinical development. Here we sought to extend our currently limited insight into CD38 surface expression by using a multi-omics approach. Genome-wide CRISPR-interference screens integrated with patient-centered epigenetic analysis confirmed known regulators of CD38, such as RARA, while revealing XBP1 and SPI1 as other key transcription factors governing surface CD38 levels. CD38 knockdown followed by cell surface proteomics demonstrated no significant remodeling of the myeloma "surfaceome" after genetically-induced loss of this antigen. Integrated transcriptome and surface proteome data confirmed high specificity of all-trans retinoic acid in upregulating CD38 in contrast to broader effects of azacytidine and panobinostat. Finally, unbiased phosphoproteomics identified inhibition of MAP kinase pathway signaling in tumor cells after daratumumab treatment. Our work provides a resource to design strategies to enhance efficacy of CD38-targeting immunotherapies in myeloma.

cancer biology↗

bioRxiv2021

The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) and its phylogenetic position in Decapoda

In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. We compared the order of genes of Decapoda ancestor and found that the positions of the two tRNAs genes (trnA and trnR) of the L. vittata were translocated. The phylogenetic tree showed that L. vittata was an independent clade, namely Hippolytidae.

molecular biology↗

bioRxiv2021

SUITOR: selecting the number of mutational signatures through cross-validation

For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. In vitro studies and in silico simulations demonstrated that SUITOR can correctly identify signatures, some of which were missed by other widely used methods. Applied to 2,540 whole-genome sequenced tumors across 22 cancer types, SUITOR selected signatures with the smallest prediction errors and almost all signatures of breast cancer selected by SUITOR were validated in an independent breast cancer study. SUITOR is a powerful tool to select the optimal number of mutational signatures, facilitating downstream analyses with etiological or therapeutic importance.

bioinformatics↗

bioRxiv2021

N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry

N-glycosylation plays an important role in the structure and function of membrane and secreted proteins. The spike protein on the surface of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is heavily glycosylated and the major target for developing vaccines, therapeutic drugs and diagnostic tests. The first major SARS-CoV-2 variant carries a D614G substitution in the spike (S-D614G) that has been associated with altered conformation, enhanced ACE2 binding, and increased infectivity and transmission. In this report, we used mass spectrometry techniques to characterize and compare the N-glycosylation of the wild type (S-614D) or variant (S-614G) SARS-CoV-2 spike glycoproteins prepared under identical conditions. The data showed that half of the N-glycosylation sequons changed their distribution of glycans in the S-614G variant. The S-614G variant showed a decrease in the relative abundance of complex-type glycans (up to 45%) and an increase in oligomannose glycans (up to 33%) on all altered sequons. These changes led to a reduction in the overall complexity of the total N-glycosylation profile. All the glycosylation sites with altered patterns were in the spike head while the glycosylation of three sites in the stalk remained unchanged between S-614G and S-614D proteins.

biochemistry↗

bioRxiv2021

An ancestral burst of regulatory and protein innovation drives divergent implantation in eutherian mammals.

Summary paragraphThe origin of live birth in mammals [~]148 million years ago was a dramatic shift in reproductive strategy, yet the molecular changes that established mammal viviparity are largely unknown. Although progesterone receptor signalling predates the origin of mammals andis highly conserved in, and critical for, successful mammal pregnancy, it alone cannot explain the origin and subsequent diversity of implantation strategies throughout the placental mammal radiation. MiRNAs are known to be flexible and dynamic regulators with a well established role in the pathophysiology of mammal placenta. We propose that a dynamic core microRNA (miRNA) network originated early in placental mammal evolution, responds to conserved mammal pregnancy cues (e.g. progesterone), and facilitates species-specific responses. Here we identify 13 miRNAs that arose at the origin of placental mammals and were subsequently retained in all descendent lineages. The expression of these 13 miRNAs in response to early pregnancy molecules is regulated in a species-specific manner in endometrial epithelia of species with extremes of implantation strategies. Furthermore, these 13 miRNAs preferentially target 84 proteins under positive selective pressure on ancestral eutherian. Discovery of this core "live-birth" toolkit and specifically adapted proteins helps explain the origin and evolution of the placenta in mammals.

evolutionary biology↗

bioRxiv2021

Chemically Induced Senescence in Human Stem Cell-Derived Neurons Promotes Phenotypic Presentation of Neurodegeneration

Modeling age-related neurodegenerative disorders with human stem cells is difficult due to the embryonic nature of stem cell derived neurons. We developed a chemical cocktail to induce senescence of iPSC-derived neurons to address this challenge. We first screened small molecules that induce embryonic fibroblasts to exhibit features characteristic of aged fibroblasts. We then optimized a cocktail of small molecules that induced senescence in fibroblasts and cortical neurons without causing DNA damage. The utility of the "senescence cocktail" was validated in motor neurons derived from ALS patient iPSCs which exhibited protein aggregation and axonal degeneration substantially earlier than those without cocktail treatment. Our "senescence cocktail" will likely enhance the manifestation of disease-related phenotypes in neurons derived from iPSCs, enabling the generation of reliable drug discovery platforms.

neuroscience↗

bioRxiv2021

Isonicotinamide extends yeast chronological lifespan through a mechanism that diminishes nucleotides

Isonicotinamide (INAM) is an isomer of the NAD+ precursor nicotinamide (NAM) that stimulates the enzymatic activity of Sir2, an NAD+-dependent histone deacetylase from the budding yeast, Saccharomyces cerevisiae. Supplementing INAM into growth media promotes the replicative lifespan (RLS) of this single cell organism by maintaining intracellular NAD+ homeostasis. INAM also extends yeast chronological lifespan (CLS), but the underlying mechanisms remain largely uncharacterized. To identify interacting genes, a chemical genomics screen of the yeast knockout (YKO) collection was performed for mutants sensitized to growth inhibition by INAM. Significant Gene Ontology (GO) terms included transcription elongation factors, metabolic pathways converging on one-carbon metabolism, and de novo purine biosynthesis, collectively suggesting that INAM may perturb nucleotide metabolism. Indeed, INAM caused dose-dependent depletion of intracellular cytidine, uridine and guanosine, ribonucleosides derived from the breakdown of nucleotide monophosphates by a set of nucleotidases (Phm8, Sdt1, Isn1) or the alkaline phosphatase Pho8. Direct inhibition of recombinant Sdt1 and Phm8 nucleotidase activity by INAM was confirmed in vitro, as was inhibition of alkaline phosphatase activity. Each of these enzymes can also convert nicotinamide mononucleotide (NMN) to nicotinamide riboside (NR), consistent with an accumulation of NMN and NAD+ upon inhibition by INAM. Taken together, the findings suggest a model whereby partial impairment of nucleotide salvage pathways can trigger a hormetic stress response that supports enhanced quiescence during chronological aging.

biochemistry↗

bioRxiv2021

Hyperdirect connectivity of opercular speech network to the subthalamic nucleus

The importance of the basal ganglia in modulating cognitive and motor behaviors is well known, yet how the basal ganglia participate in the uniquely human behavior of speech is poorly understood. The subthalamic nucleus (STN) is well positioned to facilitate two basal ganglia functions critical for speech: motor learning and gain modulation. Using a novel paradigm to study cortical-subcortical interactions during speech in patients undergoing awake DBS surgery, we found evidence for a left opercular hyperdirect pathway in humans by stimulating in the STN and examining antidromic evoked activity in the left temporal, parietal and frontal opercular cortex. These high resolution cortical and subcortical mapping data provided evidence for hyperdirect connectivity between Brocas area (typically corresponding to pars triangularis and pars opercularis of the inferior frontal gyrus) and the STN. In addition, we observed evoked potentials consistent with the presence of monosynaptic projections from areas of opercular speech cortex that are primarily sensory, including auditory cortex, to the STN. These connections may be unique to humans, evolving alongside the ability for speech. SIGNIFICANCEUsing intracranial recordings from the basal ganglia and cortex in subjects undergoing deep brain stimulation, this study provides evidence for monosynaptic cortical inputs from motor planning, motor sensory, and auditory sensory cortices to the subthalamic nucleus. These observations suggest that in humans, the cortical-basal ganglia hyperdirect pathway is uniquely positioned to participate in speech production. Moreover, the existence of a monosynaptic connection between human sensory cortical areas and the subthalamic nucleus indicates a need to update traditional models of information transfer within cortical-basal ganglia-thalamocortical circuitry, which has significant implications for understanding other human cognitive behavior or dysfunction.

neuroscience↗

bioRxiv2021

Integrative analysis of multi-omics reveals gene regulatory networks across brain regions from risk variants to phenotypes of Alzheimer's disease and Covid-19

BackgroundGenome-wide association studies have found many genetic risk variants associated with Alzheimers disease (AD). However, how these risk variants affect deeper phenotypes such as disease progression and immune response remains elusive. Also, our understanding of cellular and molecular mechanisms from disease risk variants to various phenotypes is still limited. To address these problems, we performed an integrative multi-omics analysis of genotype, transcriptomics, and epigenomics for revealing gene regulatory mechanisms from disease variants to AD phenotypes. MethodFirst, given the population gene expression data of a cohort, we construct and cluster its gene co-expression network to identify gene co-expression modules for various AD phenotypes. Next, we predict transcription factors (TFs) regulating co-expressed genes and AD risk SNPs that interrupt TF binding sites on regulatory elements. Finally, we construct a gene regulatory network (GRN) linking SNPs, interrupted TFs, and regulatory elements to target genes and gene modules for each phenotype in the cohort. This network thus provides systematic insights into gene regulatory mechanisms from risk variants to AD phenotypes. ResultsOur analysis predicted GRNs in three major AD-relevant regions: Hippocampus, Dorsolateral Prefrontal Cortex (DLPFC), Lateral Temporal Lobe (LTL). Comparative analyses revealed cross-region-conserved and region-specific GRNs, in which many immunological genes are present. For instance, SNPs rs13404184 and rs61068452 disrupt SPI1 binding and regulation of AD gene INPP5D in the Hippocampus and LTL. However, SNP rs117863556 interrupts bindings of REST to regulate GAB2 in DLPFC only. Driven by emerging neuroinflammation in AD, we used Covid-19 as a proxy to identify possible regulatory mechanisms for neuroimmunology in AD. To this end, we looked at the GRN subnetworks relating to genes from shared AD-Covid pathways. From those subnetworks, our machine learning analysis prioritized the AD-Covid genes for predicting Covid-19 severity. Decision Curve Analysis also validated our AD-Covid genes outperform known Covid-19 genes for classifying severe Covid-19 patients. This suggests AD-Covid genes along with linked SNPs can be potential novel biomarkers for neuroimmunology in AD. Finally, our results are open-source available as a comprehensive functional genomic map for AD, providing a deeper mechanistic understanding of the interplay among multi-omics, brain regions, gene functions like neuroimmunology, and phenotypes.

genomics↗

bioRxiv2021

The gravitation-driven stress-reduced urothelial barrier in toad bladder urothelium

The urinary bladder urothelial are highly specialized epithelia that protect the underlying tissues from mechanical stress and seal them from the overlying fluid space. To better understand the maintaining permeability induced electrical potential roles played by urothelial in the bladder, we established a protocol of gravitation stress in toad urothelial, observed the transmembrane potential difference variation. MethodThe toad urothelial were mounted in a using chamber which the chamber was separated to two solution spaces, and stable with 0.9% saline solution. The electrodes were settled on the surface of each side of the preparation, serosal side definite as cathode. The using chamber was settled in the centrifugal rotor and under 300 rpm rotation to obtain a vertically +4G gravitation on serosal chamber 5min. Resulta transient transmembrane potential difference increasing was observed after adding CaCl2 (3% solution) in serosal chamber. The amplitude increasing phase included a rapid and a slowly ascending phase. In gravitation stressed urothelial preparation, CaCl2 induced transient phase was significantly increased, furthermore the secondary slowly ascending phase was much more amplified on its amplitude axis and significantly prolonged on the time scale than that evoked in control preparations. The evoked total amplitude increasing were 10 times higher than that in control. ConclusionThe urinary bladder epithelial layer has a structure which regulates ion permeability as a barrier. The tight junction plays an important role as the intercellular coupling in the apical side of the epithelial cell. On the other hand, it is known that the ion channel exists on the epithelial cell membrane and regulates the physiological process. The gravitation stress weakened the tight junction. The transmembrane potential difference was enhanced both on its amplitude and prolonged time. The gravitation stress induced hyperpolarization that evoked by CaCl2 is one kind of Cl- transfer from serosal chamber in which high Ca2+ in the urothelial basal membrane activated the calcium-activated chloride channels. This outwardly rectifying chloride channel induced hyperpolarization can be blocked by Nppb.

physiology↗

bioRxiv2021

A genotype independent DMP-HI system in dicot crops

Doubled haploid (DH) technology is used to obtain homozygous lines in a single generation, which significantly accelerates the crop breeding trajectory. Traditionally, in vitro culture is used to generate DHs, but is limited by species and genotype recalcitrance. In vivo haploid induction (HI) through seed is been widely and efficiently used in maize and was recently extended to several monocot crops. However, a similar generic and efficient HI system is still lacking in dicot crops. Here we show that genotype-independent in vivo HI can be triggered by mutation of DMP genes in tomato, rapeseed and tobacco with HI rates of ~1.9%, 2.4% and 1.2%, respectively. The DMP-HI system offers a robust DH technology to facilitate variety improvement in these crops. The success of this approach and the conservation of DMP genes paves the way for a generic and efficient genotype-independent HI system in other dicot crops.

plant biology↗

bioRxiv2021

Targeting a proteolytic neo-epitope of CUB-domain containing protein 1 in RAS-driven cancer

A central challenge for any therapeutic is targeting diseased over normal cells. Proteolysis is frequently upregulated in disease and can generate proteoforms with unique neo-epitopes. We hypothesize that targeting proteolytic neo-epitopes can enable more effective and safer treatments, reflecting a conditional layer of disease-specific regulation. Here, we characterized the precise proteolytic isoforms of CUB domain containing protein 1 (CDCP1), a protein overexpressed and specifically cleaved in RAS-driven cancers. We validated that the N-terminal and C-terminal fragments of CDCP1 remain associated after proteolysis in vitro and on the surface of pancreatic cancer cells. Using a differential phage display strategy, we generated exquisitely selective recombinant antibodies that target cells harboring cleaved CDCP1 and not the full-length form using antibody-drug conjugates or a bi-specific T-cell engagers. We show tumor-specific localization and anti-tumor activity in a syngeneic pancreatic tumor model having superior safety profiles compared to a pan-CDCP1-targeting antibody. Our studies show proteolytic neo-epitopes can provide an orthogonal "AND" gate for disease-specific targeting. One-Sentence SummaryAntibody-based targeting of neo-epitopes generated by disease-associated proteolysis improves the therapeutic index

biochemistry↗

bioRxiv2021

Megakaryocyte derived immune-stimulating cells regulate host-defense immunity against bacterial pathogens

Megakaryocytes (MKs) continuously produce platelets to support hemostasis and form a niche for hematopoietic stem cell maintenance in the bone marrow. MKs are also involved in inflammation responses; however, the mechanism remains poorly understood. Here, using single-cell sequencing we identified an MK-derived immune-stimulating cell (MDIC) population exhibiting both MK-specific and immune characteristics, which highly expresses CXCR4 and immune response genes to participate in host-protective response against bacteria. MDICs interact with myeloid cells to promote their migration and stimulate the bacterial phagocytosis of macrophages and neutrophils by producing TNF and IL-6. CXCR4high MDICs egress circulation and infiltrate into the spleen, liver, and lung upon bacterial infection. Ablation of MKs suppresses the innate immune response and T cell activation to impair the anti-bacterial effects in mice under the Listeria monocytogenes challenge. Using hematopoietic stem/progenitor cell lineage-tracing mouse line, we show that MDICs are generated from infection-induced emergency megakaryopoiesis in response to bacterial infection. Overall, we identify MDICs as an MK subpopulation, which regulates host-defense immune response against bacterial infection.

cell biology↗

bioRxiv2021

Discovery, diversity and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts

The crAss-like phages are a diverse group of related viruses that includes one of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyzed gut metagenomic data collected from more than 2000 individuals from the Netherlands. We discovered 125 novel species-level and 32 novel genus-level clusters of crAss-like phages, all belonging to five previously recognized groups associated with the human gut. Analysis of their genomic features revealed that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts pointed primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explored the temporal stability of crAss-like phages over a 4-year period and identified associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients. HighlightsO_LI125 tentative new species of crAss-like phages were discovered C_LIO_LIClosely related crAss-like phages often possess highly divergent transcription gene modules possibly acquired via recombination C_LIO_LICrAss-like fraction of the human gut virome remains relatively stable over the period of 4 years C_LIO_LIPrevalence of crAss-like phages in the human gut is associated with several metabolic, dietary and health phenotypes C_LIO_LIGut crAss-like phages are depleted in inflammatory bowel disease patients C_LI

microbiology↗

bioRxiv2021

Functional connectome reorganization relates to post-stroke motor recovery and structural disconnection

Motor recovery following ischemic stroke is contingent on the ability of surviving brain networks to compensate for damaged tissue. In rodent models, sensory and motor cortical representations have been shown to remap onto intact tissue around the lesion site, but remapping to more distal sites (e.g. in the contralesional hemisphere) has also been observed. Resting state functional connectivity (FC) analysis has been employed to study compensatory network adaptations in humans, but mechanisms and time course of motor recovery are not well understood. Here, we examine longitudinal FC in 23 first-episode ischemic pontine stroke patients (34-74 years old; 8 female, 15 male) and utilize a graph matching approach to identify patterns of regional functional connectivity reorganization during recovery. We quantified functional reorganization between several intervals ranging from 1 week to 6 months following stroke, and demonstrated that the areas that undergo functional reorganization most frequently are in cerebellar/subcortical networks. Brain regions with more structural connectome disruption due to the stroke also had more functional remapping over time. Finally, we show that the amount of functional reorganization between time points is correlated with the extent of motor recovery observed between those time points in the early to late subacute phases, and, furthermore, individuals with greater baseline motor impairment demonstrate more extensive early subacute functional reorganization (from one to two weeks post-stroke) and this reorganization correlates with better motor recovery at 6 months. Taken together, these results suggest that our graph matching approach can quantify recovery-relevant, whole-brain functional connectivity network reorganization after stroke.

neuroscience↗