Biology subjects

Zhang, S.

Publications and source records attributed to Zhang, S..

At least 1,171 records · Page 65Linked to original sources

bioRxiv2019

De novo mutations in fetal brain specific enhancers play a significant role in severe intellectual disability

PurposeThe genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood.\n\nMethodsWe sequenced 70 whole genomes from 24 ID probands and their unaffected parents and analyzed 30 previously sequenced genomes from exome-negative ID probands.\n\nResultsWe found that DNVs were selectively enriched in fetal brain-specific enhancers that show purifying selection in human population. DNV containing enhancers were associated with genes that show preferential expression in the pre-frontal cortex, have been previously implicated in ID or related disorders, and exhibit intolerance to loss of function variants. DNVs from ID probands preferentially disrupted putative binding sites of neuronal transcription factors, as compared to DNVs from healthy individuals and most showed allele-specific enhancer activity. In addition, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1 and POU3F3). Moreover, CRISPR-based perturbation of a DNV-containing enhancer caused CSMD1 overexpression and abnormal expression of neurodevelopmental regulators.\n\nConclusionOur results, therefore, provide new evidence to indicate that DNVs in constrained fetal brain-specific enhancers play a role in the etiology of ID.

genomics↗

bioRxiv2019

Sing cell RNA-seq reveals cellular diversity and developmental characteristics of human infant retina

Retina, located in the innermost layer of the eye of human, holds the decisive role in visual perception. Dissecting the heterogeneity of retina is essential for understanding the mechanism of vision formation and even the development of central nervous system (CNS). Here, we performed single cell RNA-seq, analyzed 57,832 cells from human infant donors, resulting in 20 distinct clusters representing major cell types in retina: rod photoreceptors, cone photoreceptors, bipolar cells, horizontal cells, amacrine cells, Muller glia cells and microglia. We next constructed extensive networks of intercellular communication and identified ligand-receptor interactions playing crucial roles in regulating neural cell development and immune homeostasis in retina. Though re-clustering, we identified known subtypes in cone PRs and additional unreported subpopulations and corresponding markers in rod PRs as well as bipolar cells. Additionally, we linked inherited retinal disease to certain cell subtypes or subpopulations through enrichment analysis. Intriguingly, we found that status and functions of photoreceptors changed drastically between early and late retina. Overall, our study offers the first retinal cell atlas in human infants, dissecting the heterogeneity of retina and identifying the key molecules in the developmental process, which provides an important resource that will pave the way for retina development mechanism research and regenerative medicine concerning retinal biology.

cell biology↗

bioRxiv2019

NK cells force cytomegalovirus to use hematopoietic cells and immune evasion for dissemination after mucosal infection

Cytomegalovirus (CMV) infects most people in the world and causes clinically important disease in immune compromised and immune immature individuals. How the virus disseminates from the initial site of infection is poorly understood. We used an innovative approach, involving insertion of target sites for the haematopoietic specific miRNA miR-142-3p into an essential viral gene in murine cytomegalovirus. This virus was unable to disseminate to the salivary gland following intranasal infection, demonstrating a strict need for hematopoietic cells for dissemination from the natural site of infection. Viral immune evasion genes that modulate MHC-I expression and NKG2D activation were also required in this setting, as MCMV lacking these genes exhibited impaired dissemination of the viral genome to the salivary gland, and there was no detectable viral replication in the salivary gland. Depletion of T cells rescued the replication of this evasion-deficient virus in the salivary gland. Surprisingly however, the early dissemination to the salivary gland of this evasion-deficient virus, could be rescued by depletion of NK cells, but not T cells. These data are the first to show a profound loss of MCMV fitness in the absence of its MHC-I evasion genes and suggest that they protect the virus from NK cells during hematopoietic dissemination to the salivary gland, where they continued to need the three evasion genes to avoid T cell responses. Remarkably, we found that depletion of NK cells also freed the virus from the need to infect hematopoietic cells in order to reach the salivary gland. Thus, our data show that MCMV adapts to NK cell pressure after intranasal infection by using hematopoietic cells for dissemination while immune evasion genes protect the virus from NK cells during dissemination and from T cells within mucosal tissues.

immunology↗

bioRxiv2019

PSC-RED, an Albumin-Free Robust Erythroid Differentiation Method to Produce Enucleated Red Blood Cells from Human Pluripotent Stem Cells

Cultured red blood cells (cRBCs) have many potential applications in transfusion medicine and drug delivery. We report that we have developed chemically defined, albumin-free Robust Erythroid Differentiation (RED) methods to produce enucleated cRBCs from human induced pluripotent stem cells (iPSCs). Human iPSC-derived cRBCs produced with either the short or long variation of the RED protocol respectively express embryonic/fetal or a mixture of fetal and adult hemoglobins. The long version of the protocol produces up to 50% of enucleated cells at an unprecedented yield. RED is scalable and relies on inexpensive components and therefore dramatically increases the feasibility and economic viability of all translational applications of cRBCs.\n\nHighlightsO_LIPSC-RED: A chemically-defined, albumin-free Robust Erythroid Differentiation (RED) methods to produce cRBCs from human induced pluripotent stem cells.\nC_LIO_LIPSC-RED produces up to 50% enucleated cells at an unprecedented yield.\nC_LIO_LIPSC-RED is scalable and relies on inexpensive components and therefore increases the feasibility and economic viability of translational applications of cRBCs.\nC_LI

bioengineering↗

bioRxiv2019

Single cell RNA sequencing reveals cellular diversity of trisomy 21 retina

Retina is a crucial tissue for the capturing and processing of light stimulus. Characterization of the retina at single cell level is essential for the understanding of its biological functions. A variety of abnormalities in terms of morphology and function were reported in T21 retina. To evaluate the effects of chromosome aneuploidy on retina development, we characterized single cell transcriptional profiles of a T21 fetus and performed comprehensive bioinformatic analyses. Our data revealed the diversity and heterogeneity of cellular compositions in T21 retina. In total, we identified seven major cell types, and detected several subtypes within each cell type, followed by the detection of corresponding molecular markers including previously reported ones and a series of novel markers. Our analyses identified extensive communication networks between distinct cellular types, among which a few ligand-receptor interactions were associated with the development of retina and immunoregulatory interactions. Taken together, our data provided the first single cell transcriptome profile for human T21 retina which facilitates our understanding on the dosage effects of chromosome 21 on the development of retina.

cell biology↗

bioRxiv2019

piRNA-mediated silencing of an invading transposable element evolves rapidly through abundant beneficial de novo mutations

The regulation of transposable element (TE) activity by small RNAs is a ubiquitous feature of germlines. However, despite the obvious benefits to the host in terms of ensuring the production of viable gametes and maintaining the integrity of the genomes they carry, it remains controversial whether TE regulation evolves adaptively. We examined the emergence and evolutionary dynamics of repressor alleles after P-elements invaded the Drosophila melanogaster genome in the mid 20th century. In many animals including Drosophila, repressor alleles are produced by transpositional insertions into piRNA clusters, genomic regions encoding the Piwi-interacting RNAs (piRNAs) that regulate TEs. We discovered that [~]94% of recently collected isofemale lines in the Drosophila Genetic Reference Panel (DGRP) contain at least one P-element insertion in a piRNA cluster, indicating that repressor alleles are produced by de novo insertion at an exceptional rate. Furthermore, in our sample of [~]200 genomes, we uncovered no fewer than 80 unique P-element insertion alleles in at least 15 different piRNA clusters. Finally, we observe no footprint of positive selection on P-element insertions in piRNA clusters, suggesting that the rapid evolution of piRNA-mediated repression in D. melanogaster was driven primarily by mutation. Our results reveal for the first time how the unique genetic architecture of piRNA production, in which numerous piRNA clusters can encode regulatory small RNAs upon transpositional insertion, facilitates the non-adaptive rapid evolution of repression.

evolutionary biology↗

bioRxiv2019

Quantifying the mechanics of locomotion of the schistosome pathogen with respect to changes in its physical environment

Schistosomiasis is a chronic and morbid disease of poverty affecting approximately 200 million people worldwide. Mature schistosome flatworms wander in the hosts hepatic portal and mesenteric venous system where they encounter a range of blood flow conditions and geometrical confinement. However, the mechanisms that support schistosome locomotion and underlie the pathogens adaptation to its physical environment are largely unknown. By combining microfabrication and traction force microscopy, we developed various in vitro assays to quantify the mechanics of locomotion of adult male S. mansoni in different physiologically relevant conditions. We show that in unconfined settings, the parasite undergoes two-anchor marching mediated by the coordinated action of its oral and ventral suckers. This mode of locomotion is maintained when the worm faces an external flow, to which it responds by adjusting the strength of its suckers. In geometrically confined conditions, S. mansoni switches to a different crawling modality by generating retrograde peristaltic waves along its body, a mechanism shared with terrestrial and marine worms. But while the surface of most worms has backward-pointing bristles that rectify peristaltic waves and facilitate forward locomotion, S mansoni has isotropically oriented tubercles. This requires tight coordination between muscle contraction and substrate friction but confers S. mansoni the ability to reverse its direction of locomotion without turning its body, which is likely advantageous to maneuver in narrow bore vessels. We show that the parasite can also coordinate the action of its suckers with its peristaltic body contractions to increase crawling speed. Throughout this study, we report on a number of biomechanical parameters to quantify the motility of adult schistosomes (e.g. sucker grabbing strength, rate of detachment under flow, peristaltic wave properties and traction stresses). The new series of in vitro assays make it possible to quantify key phenotypical aspects of S. mansoni motility that could guide the discovery of new drugs to treat schistosomiasis.

biophysics↗

bioRxiv2019

Single amino acid changes decouple two opposite activities of a viral auxiliary replication protein

We recently reported that the p28 auxiliary replication protein encoded by turnip crinkle virus (TCV) is also responsible for eliciting superinfection exclusion (SIE) against superinfecting TCV. However, it remains unresolved whether the replication function of p28 could be separated from its ability to elicit SIE. Here we report the identification of two single amino acid (aa) mutations that decouple these two functions. Using an Agrobacterium infiltration-based delivery system, we transiently expressed a series of p28 deletion and point mutants, and tested their ability to elicit SIE against a co-introduced TCV replicon. We found that substituting alanine (A) for valine (V) and phenylalanine (F) at p28 positions 181 and 182, respectively, modestly compromised SIE in transiently expressed p28 derivatives. Upon incorporation into TCV replicons, V181A and F182A decoupled TCV replication and SIE diametrically. While V181A impaired SIE without detectably compromising replication, F182A abolished TCV replication but had no effect on SIE once the replication of the defective replicon was restored through complementation. Both mutations diminished accumulation of p28 protein, suggesting that p28 must reach a concentration threshold in order to elicit a strong SIE. Importantly, the severe reduction of F182A protein levels correlated with a dramatic loss in the number of intracellular p28 foci formed by p28-p28 interactions. Together these findings not only decouples the replication and SIE functions of p28, but also unveils a concentration dependence for p28 coalescence and SIE elicitation. These data further highlight the role of p28 multimerization in driving the exclusion of secondary TCV infections.\n\nIMPORTANCESuperinfection exclusion (SIE) insulates virus-infected cells from subsequent invasion by the same or closely related viruses. SIE has been observed in both animal and plant virus-infected cells. Therefore, a thorough understanding of how SIE is achieved at the molecular level is expected to inspire novel strategies for combating virus infections in humans, animals, and plants. Our group has been using turnip crinkle virus (TCV) to elucidate the molecular interactions critical for SIE elicitation. The current study builds on the previous observation that TCV SIE is elicited by one single TCV-encoded protein (p28), and further identifies key regions and amino acids that are needed for SIE. We unravel key amino acid changes that decouple the replication and SIE functions of p28, and provides novel mechanistic insights of SIE.

molecular biology↗

bioRxiv2019

Treatment of Murine Lupus with TIGIT-Ig

The TIGIT (T cell immunoreceptor with Ig and ITIM domains) protein is a co-inhibitory receptor that has been reported to suppress autoreactive T and B cells to trigger immunological tolerance. We generated a new recombinant protein by connecting the extracellular domain of murine TIGIT to the Fc region of the rat immunoglobulin IgG2a. The fusion protein was then characterized. The results suggested that among mice with lupus that were treated with the TIGIT-Ig fusion protein, the onset of proteinuria was delayed, serum concentrations of autoantibodies, such as antinuclear antibodies, were reduced without a decrease in the total IgG concentrations, and the survival rate was significantly increased compared to those of the controls. In conclusion, TIGIT-Ig administration showed promising results for both the prevention and treatment of autoimmune diseases in mice. This indicates that treatment with recombinant human TIGIT-Ig shows promise as an effective way to treat human autoimmune diseases.

immunology↗

bioRxiv2019

Membrane association of VAMP2 SNARE motif in cells and its regulation by different lipid phases of synaptic vesicle membrane

Vesicle associated membrane protein 2 (VAMP2) contains a conserved SNARE motif that forms helix bundles with the homologous motifs of syntaxin-1 and SNAP25 to assemble into a SNARE complex for the exocytosis of synaptic vesicles (SV). Prior to SNARE assembly, the structure of VAMP2 is unclear. Here, using in-cell NMR spectroscopy, we described the dynamic membrane association of VAMP2 SNARE motif in mammalian cells at atomic resolution, and further tracked the intracellular structural changes of VAMP2 upon the lipid environmental changes. The underlying mechanistic basis was then investigated by solution NMR combined with mass-spectrometry-based lipidomic profiling. We analyzed the lipid compositions of lipid-raft and non-raft phases of SV membrane and revealed that VAMP2 configures distinctive conformations in different phases of SV membrane. The phase of cholesterol-rich lipid rafts could largely weaken the association of SNARE motif with SV membrane and thus, facilitate vesicle docking; While in the non-raft phase, the SNARE motif tends to hibernate on SV membrane with minor activity. Our work provides a spatial regulation of different lipid membrane phases to the structure of core SNARE proteins, which deepens our knowledge on the modulation of SNARE machinery.

biophysics↗

bioRxiv2019

Whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants

Predicting the functional or pathogenic regulatory variants in the human non-coding genome facilitates the interpretation of disease causation. While numerous prediction methods are available, their performance is inconsistent or restricted to specific tasks, which raises the demand of developing comprehensive integration for those methods. Here, we compile whole genome base-wise aggregations, regBase, that incorporate largest prediction scores. Building on different assumptions of causality, we train three composite models to score functional, pathogenic and cancer driver non-coding regulatory variants respectively. We demonstrate the superior and stable performance of our models using independent benchmarks and show great success to fine-map causal regulatory variants. We believe that regBase database together with three composite models will be useful in different areas of human genetic studies, such as annotation-based casual variant fine-mapping, pathogenic variant discovery as well as cancer driver mutation identification. regBase is freely available at https://github.com/mulinlab/regBase.

genomics↗

bioRxiv2019

Coloring Single Nanoparticle Trajectory on Live Cell Membrane with its Own History: a Presuppositionless Approach

Analyzing single particle trajectories is a prominent issue in understanding complex dynamics such as nanoparticle-cell interactions. Existing methods treat data points as isolated \"atoms\" and use predefined mechanical models to \"frame\" their complicated relationship. Herein, we propose a \"historical evolution\" based model-free strategy. It allows spatiotemporal heterogeneity embedded in a trajectory to self-emerge as consecutive colored segments before any model assumption, provide both an overall picture and local state transitions on the particle movement with minimum information loss, and inspire further model-based investigation. We demonstrate with simulations and experiments that the underlying mechanisms of various time-series and motion states of single nanoparticles on live cell membranes could all be revealed successfully. Since complexity studies at different levels of molecules, particles, cells, human beings, vehicles, and even stars could all be reduced to analyzing spatiotemporal trajectories of \"single particles\", this presuppositionless approach will help fundamental researches on many important systems.\n\nImpact StatementA preprocessing strategy for single particle trajectory analysis is established by providing an intuitive global pattern from \"historical experiences\" of the particle without predefining any mechanical models.

biophysics↗

bioRxiv2019

Specific oligodendrocyte populations have differential spatial distribution and susceptibility to injury

Oligodendrocytes (OLs), the myelinating cells of the central nervous system, are transcriptionally heterogeneous,1 the origin and functional consequences of which are unknown. Functional heterogeneity of MOLs might correlate with the local environment or their interactions with different neuron types.2 Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system and differential susceptibility to traumatic spinal cord injury. We also show that the generation of distinct MOL populations is independent of the OPC developmental origin. We found that OPCs originating from the previously described developmental waves3-5 have comparable potential to differentiate into the main MOL populations. Furthermore, we found that MOL type 2 (MOL2) is enriched in the spinal cord and almost absent in the brain, while MOL5/6 is enriched with age in all analyzed regions. MOL2 and MOL5/6 also have differential preference for motor and sensory tracts in the spinal cord. In the context of disease, we found that MOL2 and MOL5/6 have differential susceptibility to traumatic spinal cord injury, where MOL2 are lost and MOL5/6 increased their contribution to the OL lineage. Importantly, MOL2 susceptibility is disease specific, as we found MOL2 is not lost in a mouse model of multiple sclerosis. Our results demonstrate that the MOL populations, previously described by single-cell transcriptomics,1 have distinct spatial preference and responses. We anticipate our study to pave the way for a better understanding of the MOL populations-specific functional roles in development, health, and disease, allowing for better targeting of the OL subtypes important for the regeneration and repair of the central nervous system.

neuroscience↗

bioRxiv2019

Deep Learning of Representations for Transcriptomics-based Phenotype Prediction

The ability to predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. This task is complicated because expression data are high dimensional whereas each experiment is usually small (e.g.,[~] 20,000 genes may be measured for[~] 100 subjects). However, thousands of transcriptomics experiments with hundreds of thousands of samples are available in public repositories. Can representation learning techniques leverage these public data to improve predictive performance on other tasks? Here, we report a comprehensive analysis using different gene sets, normalization schemes, and machine learning methods on a set of 24 binary and multiclass prediction problems and 26 survival analysis tasks. Methods that combine large numbers of genes outperformed single gene methods, but neither unsupervised nor semi-supervised representation learning techniques yielded consistent improvements in out-of-sample performance across datasets. Our findings suggest that using l2-regularized regression methods applied to centered log-ratio transformed transcript abundances provide the best predictive analyses.

bioinformatics↗

bioRxiv2019

Afucosylated maternal anti-dengue IgGs are a biomarker for susceptibility to dengue disease in their infants

Infant mortality from dengue disease is a devastating global health burden that could be minimized with the ability to identify susceptibility for severe disease prior to infection. While most primary infant dengue infections are asymptomatic, maternally derived anti-dengue IgGs present during infection can trigger progression to severe disease through antibody-dependent enhancement mechanisms. Importantly, specific characteristics of maternal IgGs that herald progression to severe infant dengue are unknown. Here, we define [≥]10% afucosylation of maternal anti-dengue IgGs as a biomarker for susceptibility of infants to symptomatic dengue infections. Mechanistic experiments show that anti-dengue afucosylation, a modification that enhances Fc affinity for the activating receptor Fc{gamma}RIIIa, promotes infection of Fc{gamma}RIIIa+ monocytes. Fc{gamma}RIIIa signaling, in turn, enhances a post-entry step of dengue virus replication. These studies identify a biomarker that can be applied to reduce mortality associated with dengue viruses and define a mechanism by which afucosylated antibodies and Fc{gamma}RIIIa enhance dengue infections.

immunology↗

bioRxiv2019

Positive feedback loop of regulating ERK phosphorylation in mESCs mediated by Etv5-Tet2-Fgfr2 axis

Dynamic equilibrium of extracellular signal-regulated kinase (ERK) activity is regulated elaborately by multiple feedback loops to ensure the normal self-renewal of mouse embryonic stem cells (mESCs). Previous studies on mESCs have demonstrated that the negative feedback loops are engaged to prevent the overactivated ERK phosphorylation (pERK). It is not clear whether there is any positive feedback loop involved to maintain a minimum of pERK in mESCs. Here, we found that blocking fibroblast growth factor (FGF)-ERK pathway by chemical PD0325901 downregulated the transcription of E26 transformation-specific (ETS) family transcription factor Etv5 in mESCs. In turn, knockout (KO) of Etv5 by CRISPR/Cas9 decreased pERK. Moreover, Etv5 KO enhanced the DNA methylation at promoter of fibroblast growth factor receptor 2 (Fgfr2) by downregulating DNA hydroxylase Tet2, which further decreased the expression of Fgfr2 in mESCs. Collectively, a positive feedback loop of regulating pERK was revealed in mESCs, which was mediated by Etv5-Tet2-Fgfr2 axis. Our findings provide a new paradigm for pERK regulation in mESCs and will be useful to understand the cell fate determination during early embryo development.

developmental biology↗

bioRxiv2019

Chiroptical Kirigami Modulators for Terahertz Circular Dichroism Spectroscopy of Biomaterials

ABSTRACTSTerahertz circular dichroism (TCD) offers spectroscopic capabilities for understanding mesoscale chiral architecture and low-energy vibrations of macromolecules in (bio)materials1-5. However, the lack of dynamic polarization modulators comparable to polarization optics for other parts of electromagnetic spectrum impedes proliferation of TCD spectroscopy6-10. Here we show that tunable optical elements fabricated from patterned plasmonic sheets with periodic kirigami cuts make possible polarization modulation of THz radiation under application of mechanical strain. A herringbone pattern of microscale metal stripes enables dynamic range of polarization rotation modulation exceeding 80{degrees} over thousands of cycles. Upon out-of-plane buckling, the plasmonic stripes function as reconfigurable semi-helices of variable pitch aligned along the THz propagation direction. Several biomaterials, exemplified by elytrons of Chrysina gloriosa beetles, revealed distinct TCD fingerprints associated with the helical substructure in the biocomposite. Analogous kirigami modulators will also enable other applications in THz optics, such as polarization-based terahertz imaging and phase-encrypted telecommunication.

biophysics↗

bioRxiv2019

Screening for neurotoxic potential of 15 flame retardants using freshwater planarians

Asexual freshwater planarians are an attractive invertebrate model for high-throughput neurotoxicity screening, because they possess multiple quantifiable behaviors to assess distinct neuronal functions. Planarians uniquely allow direct comparisons between developing and adult animals to distinguish developmentally selective effects from general neurotoxicity. In this study, we used our automated planarian screening platform to compare the neurotoxicity of 15 flame retardants (FRs), consisting of representative phased-out brominated (BFRs) and replacement organophosphorus FRs (OPFRs). OPFRs have emerged as a proposed safer alternative to BFRs; however, limited information is available on their health effects. We found 11 of the 15 FRs (3/6 BFRs, 7/8 OPFRs, and Firemaster 550) caused adverse effects in both adult and developing planarians with similar nominal lowest-effect-levels for BFRs and OPFRs. This suggests that replacement OPFRs are comparably neurotoxic to the phased-out compounds. BFRs were primarily systemically toxic, whereas OPFRs, except Tris(2-chloroethyl) phosphate, shared a behavioral phenotype in response to noxious heat at sublethal concentrations, indicating specific neurotoxic effects. By directly comparing effects on adult and developing planarians, we further found that one BFR (3,3,5,5-Tetrabromobisphenol A) caused a developmental selective defect. Together, these results demonstrate that our planarian screening platform yields high content data resulting from assaying various behavioral and morphological endpoints, allowing us to distinguish selective neurotoxic effects and effects specific to the developing nervous system. Ten of these 11 bioactive FRs were previously found to be bioactive in other models, including cell culture and alternative animal models (nematodes and zebrafish). This level of concordance across different platforms emphasizes the urgent need for further evaluation of OPFRs in mammalian systems.

pharmacology and toxicology↗