Biology subjects

Xie, H.

Publications and source records attributed to Xie, H..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Ciliary length regulation by intraflagellar transport in zebrafish

How cells regulate the size of their organelles remains a fundamental question in cell biology. Cilia, with their simple structure and surface localization, provide an ideal model for investigating organelle size control. However, most studies on cilia length regulation are primarily performed on several single-celled organisms. In contrast, the mechanism of length regulation in cilia across diverse cell types within multicellular organisms remains a mystery. Similar to humans, zebrafish contain diverse types of cilia with variable lengths. Taking advantage of the transparency of zebrafish embryos, we conducted a comprehensive investigation into intraflagellar transport (IFT), an essential process for ciliogenesis. By generating a transgenic line carrying Ift88-GFP transgene, we observed IFT in multiple types of cilia with varying lengths. Remarkably, cilia exhibited variable IFT speeds in different cell types, with longer cilia exhibiting faster IFT speeds. This increased IFT speed in longer cilia is likely not due to changes in common factors that regulate IFT, such as motor selection, BBSome proteins, or tubulin modification. Interestingly, longer cilia in the ear cristae tend to form larger IFT compared to shorter spinal cord cilia. Reducing the size of IFT particles by knocking down Ift88 slowed IFT speed and resulted in the formation of shorter cilia. Our study proposes an intriguing model of cilia length regulation via controlling IFT speed through the modulation of the size of the IFT complex. This discovery may provide further insights into our understanding of how organelle size is regulated in higher vertebrates.

cell biology↗

bioRxiv2023

Aberrant connective tissue sheath contraction drives premature hair follicle regression by inducing progenitor cell depletion in androgenetic alopecia

Androgenetic alopecia (AGA) is characterized by progressive miniaturization of hair, forming a distinctive patterned baldness in the scalp; yet, the mechanisms for hair miniaturization in this disease remain largely unknown. Here by single-cell transcriptome analysis, we describe a concise single-cell atlas, and identify the early changes in cell subpopulations, hair follicle (HF) stem cell fate determination and cell-cell communications in AGA anagen HF units. Thereinto, apoptotic loss of HF progenitor cells is significantly increased, correlated with HF miniaturization in AGA. Mechanistically, enhanced contraction of connective tissue sheath (CTS) activates the mechanosensitive channel PIEZO1, which triggers ectopic apoptosis of progenitor cells in human anagen HFs. Continuous CTS contraction during AGA causes long-term loss of progenitor cells via inducing persistent ectopic apoptosis through PIEZO1, eventually leading to premature hair regression. Most importantly, we show that targeting CTS contraction by ML-7, a selective myosin light chain kinase (MLCK) inhibitor, can obviously improve the growth of HFs from balding scalps of AGA patients. Our study reveals the cellular hierarchies and identifies CTS with increased muscle contraction activity as a driver of premature hair regression in AGA, highlighting CTS surrounding human HF as the therapeutic target for treating this disorder.

pathology↗

bioRxiv2023

PNLDC1 catalysis and postnatal germline function are required for piRNA trimming, LINE1 silencing, and spermatogenesis in mice

PIWI-interacting RNAs (piRNAs) play critical and conserved roles in transposon silencing and gene regulation in the animal germline. Two distinct piRNA populations are present during mouse spermatogenesis: pre-pachytene piRNAs in fetal/neonatal testes and pachytene piRNAs in adult testes. PNLDC1 is required for both pre-pachytene piRNA and pachytene piRNA 3 end maturation in multiple species. However, whether PNLDC1 is the bona fide piRNA trimmer and the physiological role of 3 trimming of two distinct piRNA populations in spermatogenesis remain unclear. Here, by inactivating Pnldc1 exonuclease activity in vitro and in mice, we reveal that PNLDC1 trimmer activity is required for both pre-pachytene piRNA and pachytene piRNA 3 end trimming and male fertility. Furthermore, conditional inactivation of Pnldc1 in postnatal germ cells causes LINE1 transposon de-repression and spermatogenic arrest in mice. This indicates that pachytene piRNA trimming, but not pre-pachytene piRNA trimming, is essential for mouse germ cell development and transposon silencing. Our findings highlight the potential of inhibiting germline piRNA trimmer activity as a potential means for male contraception.

developmental biology↗

bioRxiv2023

Ca2+ Oscillation in Vascular Smooth Muscle Cells Control Myogenic Spontaneous Vasomotion and Counteract Post-ischemic No-reflow

Ischemic stroke produces the highest adult disability. Despite successful recanalization, no-reflow, or the futile restoration of the cerebral perfusion after ischemia, is a major cause of brain lesion expansion. However, the vascular mechanism underlying this hypoperfusion is largely unknown, and no approach is available to actively promote optimal reperfusion to treat no-reflow. Here, by combining two-photon laser scanning microscopy (2PLSM) and a mouse middle cerebral arteriolar occlusion (MCAO) model, we found myogenic vasomotion deficits correlated with post-ischemic cerebral circulation interruptions and no-reflow. Transient occlusion-induced transient loss of mitochondrial membrane potential ({Delta}{Psi}m) permanently impaired mitochondria-endoplasmic reticulum (ER) contacts and abolished Ca2+ oscillation in smooth muscle cells (SMCs), the driving force of myogenic spontaneous vasomotion. Furthermore, tethering mitochondria and ER by specific overexpression of ME-Linker in SMCs restored cytosolic Ca2+ homeostasis, remotivated myogenic spontaneous vasomotion, achieved optimal reperfusion, and ameliorated neurological injury. Collectively, the maintaining of arteriolar myogenic vasomotion and mitochondria-ER contacts in SMCs, are of critical importance in preventing post-ischemic no-reflow.

neuroscience↗

bioRxiv2023

Rapid and prolonged response of oligodendrocyte lineage cells in standard acute cuprizone demyelination model revealed by in situ hybridization

Dietary administration of a copper chelator, cuprizone (CPZ), has long been reported to induce intense and reproducible demyelination of several brain structures such as the corpus callosum (CC) in mice, followed by spontaneous remyelination after drug withdrawal. Despite the widespread use of CPZ as an animal model for demyelinating diseases such as multiple sclerosis (MS), the mechanism by which it induces demyelination and then allows robust remyelination is still unclear. An intensive mapping of the oligodendrocyte (OL) lineage cell dynamics during the de-and remyelination course would be of particular importance for a deeper understanding of this model. Here, using a panel of OL lineage cell markers as in situ hybridization (ISH) probes, including Pdgfra, Plp, Mbp, Mog, Enpp6, combined with immunofluorescence staining of CC1, SOX10, we provide a detailed dynamic profile of OL lineage cells during the entire course of the model from 3.5 days, 1, 2, 3, 4,5 weeks of CPZ treatment, i.e. the demyelination period, as well as after 1, 2, 3, 4 weeks of recovery (drug withdrawal) from 5 weeks of CPZ treatment, i.e. the remyelination period. The result showed an unexpected early death of mature OLs and response of OL progenitor cells (OPCs) in vivo upon CPZ challenge, and a prolonged upregulation of myelin-forming OLs compared to the intact control even 4 weeks after CPZ withdrawal. These data may point to the need to optimize the timing windows for the introduction of pro-remyelination therapies in demyelinating diseases such as MS, and may serve as a basic reference system for future studies of the effects of any intervention on demyelination and remyelination using the CPZ model.

neuroscience↗

bioRxiv2023

High-resolution vasomotion analysis reveals novel venous physiological features and progressive modulation of cerebral vascular networks by stroke

Spontaneous cerebral vasomotion, characterized by [~]0.1 Hz rhythmic contractility, is crucial for brain homeostasis. However, our understanding of vasomotion is limited due to a lack of high-precision analytical methods to determine single vasomotion events at basal levels. Here, we developed a novel strategy that integrates a baseline smoothing algorithm, allowing precise measurements of vasodynamics and concomitant Ca2+ dynamics in mouse cerebrovasculature imaged by two-photon microscopy. We identified several previously unrecognized vasomotion properties under different physiological and pathological conditions, especially in ischemic stroke, which is a highly harmful brain disease that results from vessel occlusion. First, the dynamic characteristics between SMCs Ca2+ and corresponding arteriolar vasomotion are interplayed. Second, compared to previous diameter-based estimations, our radius-based measurements reveal nonisotropic vascular movements, enabling a more precise determination of the latency between smooth muscle cell (SMC) Ca2+ activity and vasocontraction. Third, we characterized single vasomotion event kinetics at scales of less than 4 seconds. Finally, following pathological vasoconstrictions induced by ischemic stroke, vasoactive arterioles transitioned to an inert state and persisted despite recanalization. In summary, we developed a highly accurate technique for analyzing spontaneous vasomotion, and we suggest a potential strategy to reduce stroke damage by promoting vasomotion recovery.

neuroscience↗

bioRxiv2023

Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks

In this paper, we aim to build a tool that will help bridge the gap between high-dimensional computation and wet-lab experimentation by allowing users to interrogate genomic signatures at multiple molecular levels and identify best next actionable steps for downstream decision making. We introduce Multioviz: a publicly accessible R package and web application platform to easily perform in silico hypothesis testing of generated gene regulatory networks. We demonstrate the utility of Multioviz by conducting an end-to-end analysis in a statistical genetics application focused on measuring the effect of in silico perturbations of complex trait architecture. By using a real data set from the Wellcome Trust Centre for Human Genetics, we both recapitulate previous findings and propose hypotheses about the genes involved in the percentage of immune CD8+ cells found in heterogeneous stocks of mice. Source code for the Multioviz R package is available at https://github.com/lcrawlab/multio-viz and an interactive version of the platform is available at multioviz.ccv.brown.edu.

bioinformatics↗

bioRxiv2023

BatchEval Pipeline: Batch Effect Evaluation Workflow for Multiple Datasets Joint Analysis

As genomic sequencing technology continues to advance, it becomes increasingly important to perform joint analyses of multiple datasets of transcriptomics. However, batch effect presents challenges for dataset integration, such as sequencing data measured on different platforms, and datasets collected at different times. Here, we report the development of BatchEval Pipeline, a batch effect workflow used to evaluate batch effect on dataset integration. The BatchEval Pipeline generates a comprehensive report, which consists of a series of HTML pages for assessment findings, including a main page, a raw dataset evaluation page, and several built-in methods evaluation pages. The main page exhibits basic information of the integrated datasets, a comprehensive score of batch effect, and the most recommended method for removing batch effect from the current datasets. The remaining pages exhibit evaluation details for the raw dataset, and evaluation results from the built-in batch effect removal methods after removing batch effect. This comprehensive report enables researchers to accurately identify and remove batch effects, resulting in more reliable and meaningful biological insights from integrated datasets. In summary, the BatchEval Pipeline represents a significant advancement in batch effect evaluation, and is a valuable tool to improve the accuracy and reliability of the experimental results. Availability & ImplementationThe source code of the BatchEval Pipeline is available at https://github.com/STOmics/BatchEval.

bioinformatics↗

bioRxiv2023

SARS-CoV-2 Omicron BA.2.86: less neutralization evasion compared to XBB sub-variants

The continual emergence and circulation of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused a great challenge for the coronavirus disease 2019 (COVID-19) pandemic control. Recently, Omicron BA.2.86 was identified with more than 30 amino acid changes on the spike (S) protein, compared to Omicron BA.2 or XBB.1.5. The immune evasion potential of BA.2.86 is of great concern. In this study, we evaluated the neutralizing activities of sera collected from participants and mice. Participants were divided into five groups according to their vaccination (inactivated vaccine, protein subunit vaccine ZF2001 or ZF2202-A) and infection (Omicron BF.7/BA.5.2) status. ZF2202-A is ZF2001 vaccines next-generation COVID-19 vaccine with updated bivalent Delta-BA.5 RBD-heterodimer immunogen. BALB/c mice were immunized with XBB.1.5 RBD-homodimer, BA.5-BA.2, Delta-XBB.1.5 or BQ.1.1-XBB.1.5 RBD-heterodimers protein vaccine candidates for evaluating the neutralizing responses. We found that Omicron BA.2.86 shows stronger immune evasion than BA.2 due to >30 additional mutations on S protein. Compared to XBB sub-variants, BA.2.86 does not display more resistance to the neutralizing responses induced by ZF2001-vaccination, BF.7/BA.5.2 breakthrough infection or a booster dose of ZF2202-A-vaccination. In addition, the mouse experiment results showed that BQ.1.1-XBB.1.5 RBD-heterodimer and XBB.1.5 RBD-homodimer induced high neutralizing responses against XBB sub-variants and BA.2.86, indicating that next-generation COVID-19 vaccine should be developed to enhance the protection efficacy against the circulating strains in the future.

immunology↗

bioRxiv2023

Neutralization of SARS-CoV-2 EG.5/EG.5.1 by sera from ZF2001 RBD-dimer and its next-generation vaccines

SARS-CoV-2 Omicron EG.5 and EG.5.1 are surging in several areas of the world, including China. Compared with XBB.1, EG.5 contains additional mutations of F456L and S486P in the spike protein receptor binding domain (RBD) and its subvariant EG.5.1 carries a further spike mutation Q52H. The immune escape potential of EG.5/EG.5.1 is of great concern. In this study, we evaluated the neutralization activities of sera from participants who received COVID-19 inactivated vaccines, protein subunit vaccine ZF2001 or a booster vaccination of Delta-BA.5 RBD-heterodimer protein vaccine, and participants who had a breakthrough infection during a wave of BF.7/BA.5.2 circulation in December 2022. Neutralization profiles elicited by bivalent RBD-heterodimer vaccine candidates containing XBB.1.5 antigen were evaluated in a murine model. We found that EG.5 and EG.5.1 displayed similar immune evasion potential to XBB.1 and XBB.1.5. The Delta-BA.5 RBD-heterodimer booster induced higher neutralizing titers against the tested XBB subvariants, including EG.5 and EG.5.1, than breakthrough infection by BF.7 or BA.5.2. In addition, Delta-XBB.1.5 and BQ.1.1-XBB.1.5 RBD-heterodimer vaccines induced high neutralizing activities against XBB sub-variants in a murine model, suggesting that next-generation COVID-19 vaccines with updated components must be developed to enhance the protection efficacy against the circulating SARS-CoV-2 strains.

immunology↗

bioRxiv2023

CRISPR-based Genome Editing of a Diurnal Rodent, Nile Grass Rat (Arvicanthis niloticus)

Diurnal and nocturnal mammals have evolved distinct pathways to optimize survival for their chronotype-specific lifestyles. Conventional rodent models, being nocturnal, may not sufficiently recapitulate the biology of diurnal humans in health and disease. Although diurnal rodents are potentially advantageous for translational research, until recently, they have not been genetically tractable. Here, we address this major limitation by demonstrating the first successful CRISPR genome editing of the Nile grass rat (Arvicanthis niloticus), a valuable diurnal rodent. We establish methods for superovulation; embryo development, manipulation, and culture; and pregnancy maintenance to guide future genome editing of this and other diurnal rodent species.

genomics↗

bioRxiv2023

SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics

The basic analysis steps of spatial transcriptomics involve obtaining gene expression information from both space and cells. This process requires a set of tools to be completed, and existing tools face performance issues when dealing with large data sets. These issues include computationally intensive spatial localization, RNA genome alignment, and excessive memory usage in large chip scenarios. These problems affect the applicability and efficiency of the process. To address these issues, a high-performance and accurate spatial transcriptomics data analysis workflow called Stereo-Seq Analysis Workflow (SAW) has been developed for the Stereo-Seq technology developed by BGI. This workflow includes mRNA spatial position reconstruction, genome alignment, gene expression matrix generation and clustering, and generate results files in a universal format for subsequent personalized analysis. The excutation time for the entire analysis process is [~]148 minutes on 1G reads 1*1 cm chip test data, 1.8 times faster than unoptimized workflow.

bioinformatics↗

bioRxiv2023

Large-scale population genomics of Malayan pangolins reveals deep diversification and a new species

BackgroundArchipelagos and oceanic islands often present high percentage of endemism due to rapid speciation. The Malayan pangolin is a species distributing at both mainland (southern Yunnan, China) and oceanic islands via Malayan peninsula, which may result in deep differentiation among populations. In-depth investigation of population structure and genetic consequences for such species is of vital importance for their protection and conservation, practically for the critically endangered Malayan pangolin that is suffering from poaching, illegal trade, and habitat loss. ResultsHere we carried out a large-scale population genomic analysis for Malayan pangolins, and revealed three highly distinct genetic populations in this species, two of which are now being reported for the first time. Based on multiple lines of genomic and morphological evidence, we postulate the existence of a new pangolin species (Manis_1). Genetic diversity and recent inbreeding were both at a moderate level for both Malayan pangolins and Manis_1, but mainland Malayan pangolins presented relatively lower genetic diversity, higher inbreeding and fitness cost than island populations. ConclusionsWe found extremely deep and graded differentiation in Malayan pangolins, with two newly discovered genetic populations and a new pangolin species that is closely related to the Philippine pangolin than the typical Malayan pangolin, but a distant relative of the Indian pangolin. Anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins, but mainland Malayan pangolins should be paid more attention for conservation due to higher genetic risks than island populations.

genomics↗

bioRxiv2023

The anti-tubercular callyaerins target the Mycobacterium tuberculosis-specific non-essential membrane protein Rv2113

Spread of antimicrobial resistances in the pathogen Mycobacterium tuberculosis remains a public health challenge. Thus, there is a continuous need for new therapeutic options with modes-of-action differing from current antibiotics. Previously, bioactivity-guided isolation identified the callyaerins, a class of hydrophobic cyclopeptides with an unusual (Z)-2,3-di-aminoacrylamide unit, as promising antitubercular agents. In this study, we investigated the molecular mechanisms underlying their antimycobacterial properties. Structure-activity relationship studies enabled the identification of the structural determinants relevant for their antibacterial activity. The antitubercular callyaerins are bacteriostatics selectively active against M. tuberculosis, including extensively drug-resistant (XDR) strains, with minimal cytotoxicity against human cells and a promising intracellular activity in a macrophage infection model. Via spontaneous resistance mutant screens and various chemical proteomics approaches, we showed that they act by direct targeting of the non-essential, M. tuberculosis-specific putative membrane protein Rv2113, thereby triggering a complex stress response in M. tuberculosis characterized by global downregulation of lipid biosynthesis, cell division, DNA repair and replication. Our study thus not only identifies Rv2113 as a new M. tuberculosis-specific target for antitubercular drugs, which should result in less harm of the microbiome and weaker resistance development in off-target pathogens. It furthermore demonstrates that also non-essential proteins may represent efficacious targets for antimycobacterial drugs.

microbiology↗

bioRxiv2023

Defining Dementia Subtypes Through Neuropsychiatric Symptom-Linked Brain Connectivity Patterns

BACKGROUNDDementia is highly heterogeneous, with pronounced individual differences in neuropsychiatric symptoms (NPS) and neuroimaging findings. Understanding the heterogeneity of NPS and associated brain abnormalities is essential for effective management and treatment of dementia. METHODSUsing large-scale neuroimaging data from the Open Access Series of Imaging Studies (OASIS-3), we conducted a multivariate sparse canonical correlation analysis to identify functional connectivity-informed symptom dimensions. Subsequently, we performed a clustering analysis on the obtained latent connectivity profiles to reveal neurophysiological subtypes and examined differences in abnormal connectivity and phenotypic profiles between subtypes. RESULTSWe identified two reliable neuropsychiatric subsyndromes - behavioral and anxiety in the connectivity-NPS linked latent space. The behavioral subsyndrome was characterized by the connections predominantly involving the default mode and somatomotor networks and neuropsychiatric symptoms involving nighttime behavior disturbance, agitation, and apathy. The anxiety subsyndrome was mainly contributed by connections involving the visual network and the anxiety neuropsychiatric symptom. By clustering individuals along these two subsyndromes-linked connectivity latent features, we uncovered three subtypes encompassing both dementia patients and healthy controls. Dementia in one subtype exhibited similar brain connectivity and cognitive-behavior patterns to healthy individuals. However, dementia in the other two subtypes showed different dysfunctional connectivity profiles involving the default mode, frontoparietal control, somatomotor, and ventral attention networks, compared to healthy individuals. These dysfunctional connectivity patterns were associated with differences in baseline dementia severity and longitudinal progression of cognitive impairment and behavioral dysfunction. CONCLUSIONSOur findings shed valuable insights into disentangling the neuropsychiatric and brain functional heterogeneity of dementia, offering a promising avenue to improve clinical management and facilitate the development of timely and targeted interventions for dementia patients.

neuroscience↗

bioRxiv2023

Monitoring norepinephrine release in vivo using next-generation GRABNE sensors

Norepinephrine (NE) is an essential biogenic monoamine neurotransmitter, yet researches using prototype NE sensors were limited by their low sensitivities. Here, we developed next-generation versions of GPCR activation-based NE sensors (GRABNE2m and GRABNE2h) with a superior response, high sensitivity and selectivity to NE both in vitro and in vivo. Notably, these sensors can detect NE release triggered by either optogenetic or behavioral stimuli in freely moving mice, producing robust signals in the locus coeruleus and hypothalamus. With the development of a novel transgenic mouse line, we recorded both NE release and calcium dynamics with dual-color fiber photometry throughout the sleep-wake cycle; moreover, dual-color mesoscopic imaging revealed cell type-specific spatiotemporal dynamics of NE and calcium during sensory processing and locomotion. Thus, these new GRABNE sensors are valuable tools for monitoring the precise spatiotemporal release of NE in vivo, providing new insights into the physiological and pathophysiological roles of NE.

neuroscience↗

bioRxiv2023

Humanized yeast to study the role of human ECE-1 isoforms in apoptosis in congenital heart diseases

Endothelin convert enzyme-1(ECE-1) plays a significant role in cardiovascular development including four isoforms with unclear function. Therefore, we are interested in studying the function of ECE-1 isoforms through mitochondria due to the high correlation between congenital heart disease (CHD) and apoptosis. Since the expression of human Bax and Bcl-xL in budding yeast (Saccharomyces cerevisiae) results in similar effects in mammalian cells, a yeast system was generated for mimicking human Bax-induced apoptosis and the expression of human ECE-1 isoforms was involved. The correlation between Bax-induced growth defect and the candidates of apoptosis via mitochondrial pathway was preliminarily investigated in this system. Furthermore, the phenotypes of ECE-1 isoforms have been identified through yeast growth defect. Individual ECE-1 isoform does not affect yeast growth but act as enhancers for the Bax-induced growth defect. ECE-1c is the strongest enhancer that affect the expression of candidates of outer membrane translocases. This study indicates that ECE-1 might play an important role in inducing apoptosis and we speculate these findings are possible to provide new perspectives with clarifying the mechanism of CHD.

molecular biology↗

bioRxiv2023

C1q Enables Influenza HA Stem Binding Antibodies to Block Viral Attachment and Broadens the Antibody Escape Repertoire

Broadly neutralizing, anti-hemagglutinin stem antibodies (Abs) are a promising universal influenza vaccine target. While anti-stem Abs are not believed to block viral attachment, we show that C1q confers attachment inhibition and boosts fusion and neuraminidase inhibition, greatly enhancing virus neutralization activity in vitro and in mice challenged with influenza virus via the respiratory route. These effects reflect increased steric interference and not increased Ab avidity. Remarkably, C1q greatly expands the anti-stem Ab viral escape repertoire to include residues throughout the hemagglutinin. Some substitutions cause antigenic alterations in the globular region or modulate HA receptor avidity. We also show that C1q enhances the neutralization activity of non-RBD anti-SARS-CoV-2 Spike Abs, an effect dependent on Spike density on the virion surface. Together, our findings show that first, Ab function must be considered in a physiological context and second, inferring the exact selection pressure for Ab-driven viral evolution is risky business, at best.

microbiology↗