Biology subjects

Bian, S.

Publications and source records attributed to Bian, S..

18 recordsLinked to original sources

bioRxiv2026

Nucleoporin1 maintains male germ unit organization and transport in Arabidopsis pollen tubes, likely through shaping nuclear morphology

The male germ unit (MGU) in Arabidopsis pollen is comprised of one vegetative nucleus (VN) and two sperm nuclei (SN). It is evolutionarily specialized to deliver immotile sperm nuclei to an ovule for fertilization. Despite some progress in research on MGU, its organization and transport remain only partially understood. Here, we identified Nucleoporin1/136 as a new player in the structural organization and positioning of MGU in pollen tubes. We and others have previously reported the reduced fertility of nup1-1 plants; however, the mechanism remains unknown. In this work, we further examined the role of NUP1 in fertility using two mutant alleles, nup1-1 and nup1-2-/+. The reciprocal crosses between the nup1 mutants and the Col-0 wild type indicate that the nup1 mutant pollen is defective. To study the effect of a complete NUP1 knockout on pollen, we generated a transgenic line that produces pollen with and without NUP1 expression. This work led to the surprising discovery that the NUP1 protein is inherited from the pollen mother cell to the daughter cell during microgametophyte development. Subsequent in vitro experiments showed that NUP1 is required for pollen germination and pollen tube elongation. Further microscopic studies demonstrated that NUP1 is highly expressed in VN and essential for maintaining nuclear shape and size. We also demonstrated that NUP1 is required for proper MGU organization and transport, likely through maintaining VN morphology. Notably, our finding of nuclear morphology-mediated regulation of MGU may also explain the mechanistic details underlying the defective MGU movement in previously reported mutants such as kaku4, wit, and wip, which have abnormal nuclear morphology.

plant biology↗

bioRxiv2026

Mitochondrial activity directs nutrient uptake and patterning in human gastrula models.

How a uniform field of cells responds to inductive cues to form distinct, spatially organised, lineages is a question of much interest. In human gastruloids, a BMP4 signalling gradient directs the self-organization of embryonic stem cells (hESCs) into the three germ-layers. But what regulates differential responses to BMP4 is poorly understood. Here we demonstrate that mitochondrial activity is key, as by directing nutrient uptake it determines the threshold of BMP signalling. We show that decreased mitochondrial activity stimulates fatty acid uptake via macropinocytosis and subsequent {beta}-oxidation and that this increases the BMP4 response. However, we also find that disease causing mitochondrial DNA mutations impair dynamic switching between glucose and fatty acid utilisation, causing hESCs to be unable to spatially organise the mesoderm, endoderm and ectoderm layers in gastruloids. These results suggest that the correct interpretation of morphogen gradients during gastrulation emerges through the crosstalk of signalling inputs and nutrient utilisation.

developmental biology↗

bioRxiv2026

Generation of Genetically Identical Mammalian Oocytes from Parthenogenetic Double-Haploid Embryonic Stem Cells

Generating genetically identical mammalian oocytes is challenging due to stochastic meiotic recombination. Here, we established parthenogenetic double-haploid embryonic stem cells (PG-DhESCs) possessing complete homozygosity. By employing blastocyst complementation in Prdm14-deficient embryos, we generated chimeric females that produced oocytes derived exclusively from these donor cells. Fertilization of these oocytes yielded viable, fertile, maternally semi-cloned (MSC) mice of both sexes. Although DNA methylation was largely restored during gametogenesis, subtle epigenetic defects correlated with increased body weight in MSC offspring. This study establishes a robust platform combining PG-DhESCs with blastocyst complementation to generate isogenic mammalian oocytes, overcoming traditional limitations in mammalian cloning.

developmental biology↗

bioRxiv2025

CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies

Causal mediation analysis investigates whether the effect of an exposure on an outcome operates through intermediate variables known as mediators. Although progress has been made in high-dimensional mediation analysis, current methods do not reliably control the false discovery rate (FDR) in finite samples, especially when mediators are moderately to highly correlated or follow non-Gaussian distributions. These challenges frequently arise in DNA methylation studies. We introduce CoxMDS, a multiple data splitting method that uses Cox proportional hazards models to identify putative causal mediators for survival outcomes. CoxMDS ensures finite-sample FDR control even in the presence of correlated or non-Gaussian mediators. Through simulations, CoxMDS is shown to maintain FDR control and achieve higher statistical power compared with existing approaches. In applications to DNA methylation data with survival outcomes, CoxMDS identified eight CpG sites in The Cancer Genome Atlas (TCGA) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on lung cancer survival, and two CpG sites in the Alzheimers Disease Neuroimaging Initiative (ADNI) that are consistent with the hypothesis that DNA methylation may mediate the effect of smoking on time to Alzheimers disease conversion.

bioinformatics↗

bioRxiv2025

Genome-Wide Investigation of Transcription Factor Occupancy and Dynamics Using cFOOT-seq

Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences. Notably, cFOOT-seq, combined with FootTrack analysis, predicts TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.

molecular biology↗

bioRxiv2025

Aptamer-Enabled Discovery and Clinical Analysis of Exosomal Surface Biomarkers in Hepatocellular Carcinoma

Exosomal membrane proteins hold promise as cancer biomarkers but face detection challenges due to low abundance and conformational sensitivity. We developed AptEx-ID, a microbead-displayed aptamer platform enabling high- throughput screening of hepatocellular carcinoma (HCC)-specific exosomal surface proteins. Aptamers, selected via competitive binding to tumor-derived versus healthy exosomes, demonstrated high affinity and specificity. Clinical validation using 50 HCC and 30 control plasma samples identified a 7-aptamer panel via machine learning, achieving 93.75% accuracy and 0.95 ROC-AUC. These aptamers further revealed HCC-associated biomarkers (e.g., IMPDH1, ASCC3, GTSE1), validated by siRNA knockdown and biophysical assays. Post-treatment monitoring showed aptamer signal reduction in responsive patients, highlighting their prognostic utility. This platform integrates biomarker discovery, diagnostics, and therapeutic monitoring, offering a robust approach for HCC management through exosomal surface proteome profiling.

molecular biology↗

bioRxiv2024

SCAMPI: A scalable statistical framework for genome-wide interaction testing harnessing cross-trait correlations

Family-based heritability estimates of complex traits are often considerably larger than their single-nucleotide polymorphism (SNP) heritability estimates. This discrepancy may be due to non-additive effects of genetic variation, including variation that interacts with other genes or environmental factors to influence the trait. Variance-based procedures provide a computationally efficient strategy to screen for SNPs with potential interaction effects without requiring the specification of the interacting variable. While valuable, such variance-based tests consider only a single trait and ignore likely pleiotropy among related traits that, if present, could improve power to detect such interaction effects. To fill this gap, we propose SCAMPI (Scalable Cauchy Aggregate test using Multiple Phenotypes to test Interactions), which screens for variants with interaction effects across multiple traits. SCAMPI is motivated by the observation that SNPs with pleiotropic interaction effects induce genotypic differences in the patterns of correlation among traits. By studying such patterns across genotype categories among multiple traits, we show that SCAMPI has improved performance over traditional univariate variance-based methods. Like those traditional variance-based tests, SCAMPI permits the screening of interaction effects without requiring the specification of the interaction variable and is further computationally scalable to biobank data. We employed SCAMPI to screen for interacting SNPs associated with four lipid-related traits in the UK Biobank and identified multiple gene regions missed by existing univariate variance-based tests. SCAMPI is implemented in software for public use.

genetics↗

bioRxiv2024

scCancerExplorer: a comprehensive database for interactively exploring single-cell multi-omics data of human pan-cancer

Genomic, epigenomic, and transcriptomic alterations are hallmarks of cancer cells, and are closely connected. Especially, epigenetic regulation plays a critical role in tumorigenesis and progression. The growing single-cell epigenome data in cancer research provide new opportunities for data mining from a more comprehensive perspective. However, there is still a lack of databases designed for interactively exploring the single-cell multi-omics data of human pan-cancer, especially for the single-cell epigenome data. To fill in the gap, we developed scCancerExplorer, a comprehensive and user-friendly database to facilitate the exploration of the single-cell genome, epigenome (chromatin accessibility and DNA methylation), and transcriptome data of 50 cancer types. Five major modules were provided to explore those data interactively, including "integrated multi-omics analysis", "single-cell transcriptome", "single-cell epigenome", "single-cell genome", and "TCGA analysis". By simple clicking, users can easily investigate gene expression features, chromatin accessibility patterns, transcription factor activities, DNA methylation states, copy number variations, and TCGA survival analysis results. Taken together, scCancerExplorer is distinguished from previous databases with rich and interactive functions for exploring the single-cell multi-omics data of human pan-cancer. It bridges the gap between single-cell multi-omics data and the end-users, and will facilitate progress in the field of cancer research. scCancerExplorer is freely accessible via https://bianlab.cn/scCancerExplorer.

cancer biology↗

bioRxiv2023

Universal protection against SARS-CoV-2 viruses by multivalent mRNA vaccine in mice

The continual emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges available SARS-CoV-2 vaccines for adequate control of outbreaks. Currently, universal vaccines capable of obviating the need for exact strain matching between mRNA vaccines and circulating viruses are absent. In this study, we designed, manufactured, and evaluated a nucleoside-modified lipid nanoparticle mRNA vaccine, aimed for offering broad-spectrum protection against recent SARS-CoV-2 variants. Additionally, the protection efficiency of monovalent, bivalent, quadrivalent, and XBB.1.5 mRNA vaccines was compared with the proposed universal vaccine. The neutralizing antibody activity against wuhan-1, BA.4/5, XBB.1.5, B.1.1.529, BQ.1.1, EG.5.1 and JN.1 was assessed using enzyme-linked immunosorbent assay, rapid fiber-optic biolayer interferometry-based biosensor, and pseudovirus neutralization test. Our results reveal that the proposed multivalent vaccine affords comprehensive protection against previously circulating, current and previously unidentified SARS-CoV-2 strains.

immunology↗

bioRxiv2023

Adenosine triggers astrocyte reactivity to drive the pathogenesis of sepsis-associated encephalopathy

Molecular pathways mediating systemic inflammation entering the brain parenchyma to induce sepsis-associated encephalopathy (SAE) remain elusive. Here, we report that in mice during the first 6 hours of peripheral lipopolysaccharide (LPS)-evoked systemic inflammation (6 hpi), the plasma level of adenosine quickly increased and enhanced the tone of central extracellular adenosine which then provoked neuroinflammation by triggering early astrocyte reactivity. Specific ablation of astrocytic A1 adenosine receptors (A1ARs) prevented this early reactivity and reduced the levels of inflammatory factors (e.g., CCL2, CCL5, and CXCL1) in astrocytes, thereby alleviating microglial activation, ameliorating blood-brain barrier disruption, neuronal dysfunction, and depression-like behaviour in the mice. Chemogenetic stimulation of Gi signaling in A1AR-deficent astrocytes at 2 and 4 hpi of LPS injection could restore neuroinflammation and depression-like behaviour, highlighting astrocytes rather than microglia as early drivers of neuroinflammation. Our results identify early astrocyte reactivity towards peripheral and central levels of adenosine as a novel pathway driving SAE.

neuroscience↗

bioRxiv2023

SMARTdb: an integrated database for exploring single-cell multi-omics data of reproductive medicine

Single-cell multi-omics sequencing has greatly accelerated reproductive research in recent years, and the data are continually growing. However, utilizing these data resources is challenging for wet-lab researchers. A comprehensive platform for exploring single-cell multi-omics data related to reproduction is urgently needed. Here we introduce SMARTdb (single-cell multi-omics atlas of reproduction), which is an integrative and user-friendly platform for exploring molecular dynamics of reproductive development, aging, and disease, covering multi-omics, multi-species, and multi-stage data. We have curated and analyzed single-cell transcriptome and epigenome data of over 2.0 million cells from 6 species across whole lifespan. A series of powerful functionalities are provided, such as "Query gene expression", "DIY expression plot", "DNA methylation plot", and "Epigenome browser". With SMARTdb, we found that the male germ-cell-specific expression pattern of RPL39L and RPL10L is conserved between human and other model animals. Moreover, DNA hypomethylation and open chromatin may regulate the specific expression pattern of RPL39L collectively in both male and female germ cells. In summary, SMARTdb is a powerful platform for convenient data mining and gaining novel insights into reproductive development, aging, and disease. SMARTdb is publicly available at https://smart-db.cn.

genomics↗

bioRxiv2023

Identifying latent genetic interactions in genome-wide association studies using multiple traits

Genome-wide association studies of complex traits frequently find that SNP-based estimates of heritability are considerably smaller than estimates from classic family-based studies. This missing heritability may be partly explained by genetic variants interacting with other genes or environments that are difficult to specify, observe, and detect. To circumvent these challenges, we propose a new method to detect genetic interactions that leverages pleiotropy from multiple related traits without requiring the interacting variable to be specified or observed. Our approach, Latent Interaction Testing (LIT), uses the observation that correlated traits with shared latent genetic interactions have trait variance and covariance patterns that differ by genotype. LIT examines the relationship between trait variance/covariance patterns and genotype using a flexible kernel-based framework that is computationally scalable for biobank-sized datasets with a large number of traits. We first use simulated data to demonstrate that LIT substantially increases power to detect latent genetic interactions compared to a trait-by-trait univariate method. We then apply LIT to four obesity-related traits in the UK Biobank and detect genetic variants with interactive effects near known obesity-related genes. Overall, we show that LIT, implemented in the R package lit, uses shared information across traits to improve detection of latent genetic interactions compared to standard approaches.

genetics↗

bioRxiv2023

NUCLEOPORIN1 mediates proteasome-based degradation of ABI5 to regulate Arabidopsis seed germination

NUCLEOPORIN1 (NUP1), a member of the Nuclear Pore Complex (NPC), is located on the inner side of the nuclear membrane. It is highly expressed in seeds; however, its role in seeds including germination has not been explored yet. Here, we identified an abscisic acid (ABA) hypersensitive phenotype of nup1 during germination. ABA treatment drastically changes the expression pattern of thousands of genes in nup1, including the major transcription factors (TFs) involved in germination, ABI3, ABI4, and ABI5. Double mutant analysis of NUP1 and these ABA-related genes showed that mutations in ABI5 can rescue the phenotype of nup1, suggesting that NUP1 acts upstream of ABI5 to regulate seed germination. ABI5, a key negative regulator of germination, is abundant in dry seeds and rapidly degrades during germination. However, its spatiotemporal regulation and interaction with other molecular players during degradation remained to be fully elucidated. We found that NUP1 is physically associated with ABI5 and the 26S proteasome. Mutation in NUP1 delayed ABI5 degradation through its post-translational retention in nucleolus under abiotic stress. Taken together, our findings suggest that NUP1 anchors the proteasome to NPC and modulates seed germination through proteasome-mediated degradation of ABI5 in the vicinity of NPC in the nucleoplasm.

plant biology↗

bioRxiv2023

Cryo-EM structures of Kv1.2 potassium channels, conducting and non-conducting

We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 [A], 2.5 [A], 3.2 [A], and 2.9[A]. These structures, all obtained at nominally zero membrane potential in detergent micelles, reveal distinct ion-occupancy patterns in the selectivity filter. The first two structures are very similar to those reported in the related Shaker channel and the much-studied Kv1.2-2.1 chimeric channel. On the other hand, two new structures show unexpected patterns of ion occupancy. First, the toxin -Dendrotoxin, like Charybdotoxin, is seen to attach to the negatively-charged channel outer mouth, and a lysine residue penetrates into the selectivity filter, with the terminal amine coordinated by carbonyls, partially disrupting the outermost ion-binding site. In the remainder of the filter two densities of bound ions are observed, rather than three as observed with other toxin-blocked Kv channels. Second, a structure of Kv1.2 in Na+ solution does not show collapse or destabilization of the selectivity filter, but instead shows an intact selectivity filter with ion density in each binding site. We also attempted to image the C-type inactivated Kv1.2 W366F channel in Na+ solution, but the protein conformation was seen to be highly variable and only a low-resolution structure could be obtained. These findings present new insights into the stability of the selectivity filter and the mechanism of toxin block of this intensively studied, voltage-gated potassium channel.

biophysics↗

bioRxiv2023

ImSpiRE: Image feature-aided spatial resolution enhancement method

The resolution of most spatially resolved transcriptomic technologies usually cannot attain the single-cell level, limiting their applications in biological discoveries. Here, we introduce ImSpiRE, an image feature-aided spatial resolution enhancement method for in situ capturing spatial transcriptome. Taking the information stored in histological images, ImSpiRE solves an optimal transport problem to redistribute the expression profiles of spots to construct new transcriptional profiles with enhanced resolution, together with imputing the gene expression profiles in unmeasured regions. Applications to multiple datasets confirm that ImSpiRE can enhance spatial resolution to the subspot level while contributing to the discovery of tissue domains, signaling communication patterns, and spatiotemporal characterization.

bioinformatics↗

bioRxiv2021

OsciDrop: A versatile on-demand droplet generator

Droplet microfluidics is a powerful tool in many biological and clinical applications. Microfluidic chips, such as flow-focusing droplet generators, have been extensively used to high-throughput encapsulate reactions with single-cell and single-molecular resolutions. However, microfabrication is expensive and precision-demanding, preventing it from widespread use in biomedical laboratories and clinical facilities. Herein, we present a versatile chip-free droplet generator, OsciDrop, for generating size-tunable droplets on demand, with high uniformity. OsciDrop segments the fluid flowing out of the orifice of a micropipette tip into droplets by oscillating the tip under the surface of a continuous oil phase. We investigated the factors influencing droplet generation by examining several control parameters. Results show that flow rate, oscillating amplitude, and frequency are key parameters to generate monodisperse droplets on demand. And OsciDrop is able to generate droplets in a flexible and repeatable manner. Importantly, using an optimal asymmetrical oscillation waveform, OsciDrop can controllably generate monodisperse droplets spanning a wide volume range (200 pL - 2 L). To demonstrate the ability of OsciDrop for chip-free droplet assays, a digital loop-mediated isothermal amplification (dLAMP) was performed to absolutely quantify African swine fever virus (ASFV). The OsciDrop method opens up a feasible and versatile avenue to perform droplet-based assays, exhibiting full accessibility for chip-free droplet microfluidics.

bioengineering↗

bioRxiv2020

Genetic structure, function and evolution of capsule biosynthesis loci in Vibrio parahaemolyticus

Capsule-forming extracellular polysaccharides are crucial to bacterial host colonization, invasion, immune evasion and ultimately pathogenicity. Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important food-borne enteropathogen implicated in acute gastroenteritis, wound infections, and septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. parahaemolyticus, while disclosure of genetic elements encoding 13 O-serogroups have allowed molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene cluster across different K-serogroups, and expanded its new right-border by identifying glpX as a key gene conserved across all serotypes. A total of 217 genes involved in CPS biosynthesis were annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, gene duplication and nonsense mutations are likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. It is the first time, to the best of our knowledge, that a large-scale of CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus, and provide a framework for developing diagnostically relevant serotyping methods. Author summaryDue to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important food-borne enteropathogen. However, the genetic structure of CPS loci for 71 K-serogroups V. parahaemolyticus have remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We expanded and identified its new right-border by identifying glpX as a key gene conserved across all serotypes. We proposed an evolution model of the CPS gene clusters of 40 K-serogroups. We also found horizontal gene transfer by recombination from other Vibrio species, gene duplication and nonsense mutations are likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. It is the first time, to the best of our knowledge, that a large-scale of CPS loci of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus, and provide a framework for developing diagnostically relevant serotyping methods.

microbiology↗

bioRxiv2017

Fused dorsal-ventral cerebral organoids model human cortical interneuron migration

Development of the forebrain involves the migration of GABAergic interneurons over long distances from ventral into dorsal regions. Although defects in interneuron migration are implicated in neuropsychiatric diseases such as Epilepsy, Autism, and Schizophrenia, model systems to study this process in humans are currently lacking. Here, we describe a method for analyzing human interneuron migration using 3D organoid culture. By fusing cerebral organoids specified toward dorsal and ventral forebrain, we generate a continuous dorsal-ventral axis. Using fluorescent reporters, we demonstrate robust directional GABAergic interneuron migration from ventral into dorsal forebrain. We describe methodology for time lapse imaging of human interneuron migration that is inhibited by the CXCR4 antagonist AMD3100. Our results demonstrate that cerebral organoid fusion cultures can model complex interactions between different brain regions. Combined with reprogramming technology, fusions offer a possibility to analyze complex neurodevelopmental defects using cells from neuropsychiatric disease patients, and to test potential therapeutic compounds.

neuroscience↗