Biology subjects

Ren, X.

Publications and source records attributed to Ren, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

A Semi-Automated MEA Spike sorting (SAMS) method for high throughput assessment of cultured neurons

Neurons derived from human pluripotent stem cells (hPSCs) are valuable models for studying brain development and developing therapies for brain disorders. Evaluating human-derived neurons requires assessing their electrical activity, which can be achieved using multi-electrode arrays (MEAs) for extracellular recordings. Because each electrode channel generally detects activity from multiple neurons, resolving the activity of single neurons requires a process called spike sorting. However, currently available spike sorting methods are not optimized for the analysis of hPSC-derived neurons, and require complex workflows and time-consuming manual intervention. Here, we introduce a Semi-Automated MEA Spike sorting software (SAMS) designed specifically for low-density MEA recordings of cultured neurons. SAMS outperforms commercially available automated spike sorting algorithms in terms of accuracy and greatly reduces computational and human processing time. By providing an accessible, efficient, and integrated platform for spike sorting, SAMS enhances the resolution and utility of MEA in disease modeling and drug development using human-derived neurons. HighlightsO_LISAMS is designed and optimized for high throughput analysis of hPSC-derived neurons. C_LIO_LISAMS is more efficient and accurate compared to recommended spike-sorting software. C_LIO_LISAMS resolves phenotypic differences previously not observed without spike sorting. C_LIO_LISAMS is an open-source software. C_LI

neuroscience↗

bioRxiv2025

Single-cell transcriptomics-guided development of flow cytometric tests predicting chronic myeloid leukemia blast crisis transformation at chronic phase diagnosis

Clinical risk scores in chronic myeloid leukemia (CML) are inadequate for identifying chronic phase (CP) patients at high-risk of blast crisis (BC) progression. The lack of accurate predictive tests hamper timely interventions, including stem cell transplants, that are more effective in early disease. By interrogating a single cell atlas of primary imatinib resistance for a BC-like gene expression signature, we identify aberrant CD42A+ megakaryocytic and CD10+CD19+ lymphoid progenitor expansion, as well as STAT1- and IFN{gamma}-related inflammatory programs, as consistent features in the bone marrow and peripheral blood of CP patients at high-risk of BC transformation. We develop multi-color flow cytometry-based tests (MFC) to detect these features in CP patients at the time of diagnosis. Validating our MFC panels on a combined Australia-Singapore cohort comprising 28 CP patients, including 14 who underwent transformation, we demonstrate their ability to detect 100% of CP patients who transform with no false positives. Our findings highlight small populations of inflamed hematopoietic stem and progenitor cells, present at CP diagnosis, as powerful harbingers of future BC transformation. The ability of MFC panels to detect these cells at diagnosis support their inclusion as accurate risk-assessment tools to improve management of high-risk patients.

cancer biology↗

bioRxiv2025

The Interplay Between Cell-cell Signaling and Negative Feedback Reduces Population Noise While Enhancing Single-cell Variability

Negative feedback is a well-known mechanism for attenuating noise and enhancing robustness in biological systems. When coupled with cell-cell signaling, it provides a strategy for achieving population-level control in multicellular systems. While cell-cell signaling alone tends to reduce cell-to-cell variability by averaging fluctuations across cells, its interplay with negative feedback can produce contrasting effects on noise regulation at single-cell and population levels. Therefore, to design population-level controllers that achieve robust behaviors with attenuated noise, a systematically understanding of how different noise sources impact cell gene expressions at these levels become a critical challenge. Here, we investigate noise regulation in a quorum sensing-based negative feedback system, focusing on two extrinsic noise sources: process noise from target gene dynamics and measurement noise from quorum sensing dynamics. Our results reveal that signal-based negative feedback significantly reduces process noise at the population level, especially for dynamic noise. However, at the single-cell level, it enhances variability, with increased noise levels under faster signal diffusion and higher population density. In contrast, measurement noise is consistently attenuated at both single-cell and population levels through the coupled cell-cell signaling and negative feedback, under conditions of faster diffusion and higher density.

synthetic biology↗

bioRxiv2024

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes

Three-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive. To address this, we propose a computational approach to predict SV impacts on genome folding, which can help prioritize causal hypotheses for functional testing. We developed a weighted scoring method that measures chromatin contact changes specifically affecting regions of interest, such as regulatory elements or promoters, and implemented it in the SuPreMo-Akita software (Gjoni and Pollard 2024). With this tool, we ranked hundreds of de novo SVs (dnSVs) from autism spectrum disorder (ASD) individuals and their unaffected siblings based on predicted disruptions to nearby neuronal regulatory interactions. This revealed that putative cisregulatory element interactions (CREints) are more disrupted by dnSVs from ASD probands versus unaffected siblings. We prioritized candidate variants that disrupt ASD CREints and validated our top-ranked locus using isogenic excitatory neurons with and without the dnSV, confirming accurate predictions of disrupted chromatin contacts. This study establishes disrupted genome folding as a potential genetic mechanism in ASD and provides a general strategy for prioritizing variants predicted to disrupt regulatory interactions across tissues.

bioinformatics↗

bioRxiv2024

Amino acid competition shapes Acinetobacter baumannii gut carriage

Antimicrobial resistance is an urgent threat to human health. Asymptomatic colonization is often critical for persistence of antimicrobial-resistant pathogens. Gut colonization by the antimicrobial-resistant priority pathogen Acinetobacter baumannii is associated with increased risk of clinical infection. Ecological factors shaping A. baumannii gut colonization remain unclear. Here we show that A. baumannii and other pathogenic Acinetobacter evolved to utilize the amino acid ornithine, a non- preferred carbon source. A. baumannii utilizes ornithine to compete with the resident microbiota and persist in the gut in mice. Supplemental dietary ornithine promotes long-term fecal shedding of A. baumannii. By contrast, supplementation of a preferred carbon source--monosodium glutamate (MSG)-- abolishes the requirement for A. baumannii ornithine catabolism. Additionally, we report evidence for diet promoting A. baumannii gut carriage in humans. Together, these results highlight that evolution of ornithine catabolism allows A. baumannii to compete with the microbiota in the gut, a reservoir for pathogen spread.

microbiology↗

bioRxiv2024

Manipulation of the brown glume and internode 1 gene leads to alterations in lignified tissue coloration, lignification, and pathogen resistance in wheat

Lignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defense. In this study, we identified an ethyl methanesulfonate (EMS)-derived Aegilops tauschii mutant named brown glume and internode 1 (bgi1), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes, and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identified AET6Gv20438400 (BGI1) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon in BGI1. We validated the function of BGI1 using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues. BGI1 knockout mutants exhibited reduced lignin content and shearing force relative to wild type, while BGI1 overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot and Fusarium crown rot. We confirmed that BGI1 exhibits CAD activity both in vitro and in vivo, playing an important role in lignin biosynthesis. BGI1 was highly expressed in the stem and spike and localized in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated with BGI1. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signaling pathway. The identification and functional characterization of BGI1 significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defense against pathogen infection in wheat.

plant biology↗

bioRxiv2024

CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription

Precise transcriptional regulation is critical for cellular function and development, yet the mechanism of this process remains poorly understood for many genes. To gain a deeper understanding of the regulation of neuropsychiatric disease risk genes, we identified a total of 39 functional enhancers for four dosage-sensitive genes, APP, FMR1, MECP2, and SIN3A, using CRISPR tiling deletion screening in human induced pluripotent stem cell (iPSC)-induced excitatory neurons. We found that enhancer annotation provides potential pathological insights into disease-associated copy number variants. More importantly, we discovered that allelic enhancer deletions at SIN3A could be compensated by increased transcriptional activities from the other intact allele. Such allelic compensation effects (ACE) on transcription is stably maintained during differentiation and, once established, cannot be reversed by ectopic SIN3A expression. Further, ACE at SIN3A occurs through dosage sensing by the promoter. Together, our findings unravel a regulatory compensation mechanism that ensures stable and precise transcriptional output for SIN3A, and potentially other dosage-sensitive genes.

genetics↗

bioRxiv2024

Efficacy and Safety of a novel virulent phage against acute pulmonary infection of Acinetobacter baumanniii in mice

Acinetobacter baumannii (A.baumannii) is a notable opportunistic pathogen responsible for severe hospital-acquired infections, with multidrug-resistant strains posing significant treatment challenges. Phage therapy, which employs bacteriophages as natural bacterial antagonists, has gained renewed attention as a promising solution to combat antibiotic-resistant infections. In this study, we isolated and characterized a novel virulent phage, vB_AbaS_qsb1, which specifically lyses A.baumannii. Phylogenetic and genomic analyses indicate that vB_AbaS_qsb1 is the founding member of a previously unreported genus, which we have named as Acinibactriovirus, with Acinibactriovirus lysinus as the type species. vB_AbaS_qsb1 demonstrated robust stability across diverse temperature and pH ranges, a short latent period, and no known virulence or antibiotic resistance genes within its 54,713 bp dsDNA genome. Safety assessments showed that high-dose vB_AbaS_qsb1 induced no adverse effects in mice, with histopathology confirming its safety profile. Therapeutic experiments further indicated that vB_AbaS_qsb1 provided at least 50% protection against A.baumannii-induced pneumonia, significantly reducing bacterial loads and inflammation markers, while maintaining high phage titers in lung tissue.This study introduces vB_AbaS_qsb1 as a promising candidate for phage therapy against A.baumannii, offering both innovative insights and a valuable framework for future isolation, genomic characterization, and efficacy evaluation of phages targeting antibiotic-resistant bacteria. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/617119v3_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@17bf4cdorg.highwire.dtl.DTLVardef@104c49eorg.highwire.dtl.DTLVardef@89e1dorg.highwire.dtl.DTLVardef@1c4b018_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

scDrugAtlas: an integrative single-cell drug response atlas for unraveling tumor heterogeneity in therapeutic efficacy

Tumor heterogeneity often leads to substantial differences in responses to same drug treatment. The presence of pre-existing or acquired drug-resistant cell sub-populations within a tumor survive and proliferate, ultimately resulting in tumor relapse and metastasis. The drug resistance is the leading cause of failure in clinical tumor therapy. Therefore, accurate identification of drug-resistant tumor cell subpopulations could greatly facilitate the precision medicine and novel drug development. However, the scarcity of single-cell drug response data significantly hinders the exploration of tumor cell resistance mechanisms and the development of computational predictive methods. In this paper, we propose scDrugAtlas, a comprehensive database devoted to integrating the drug response data at single-cell level. We manually compiled more than 100 datasets containing single-cell drug responses from various public resources. The current version comprises large-scale single-cell transcriptional profiles and drug response labels from 1,023 samples (cell line, mouse, PDX models, patients and bacterium), across 78 unique drugs and 24 major cancer types. Particularly, we assigned a confidence level to each response label based on the tissue source (primary or relapse/metastasis), drug exposure time and drug-induced cell phenotype. We believe scDrugAtlas could greatly facilitate the Bioinformatics community for developing computational models and biologists for identifying drug-resistant tumor cells and underlying molecular mechanism. The scDrugAtlas database is available at: http://drug.hliulab.tech/scDrugAtlas/.

bioinformatics↗

bioRxiv2024

Reconstitution of BNIP3/NIX-mediated autophagy reveals two pathways and hierarchical flexibility of the initiation machinery

Selective autophagy is a lysosomal degradation pathway that is critical for maintaining cellular homeostasis by disposing of harmful cellular material. While the mechanisms by which soluble cargo receptors recruit the autophagy machinery are becoming increasingly clear, the principles governing how organelle-localized transmembrane cargo receptors initiate selective autophagy remain poorly understood. Here, we demonstrate that transmembrane cargo receptors can initiate autophagosome biogenesis not only by recruiting the upstream FIP200/ULK1 complex but also via a WIPI-ATG13 complex. This latter pathway is employed by the BNIP3/NIX receptors to trigger mitophagy. Additionally, other transmembrane mitophagy receptors, including FUNDC1 and BCL2L13, exclusively use the FIP200/ULK1 complex, while FKBP8 and the ER-phagy receptor TEX264 are capable of utilizing both pathways to initiate autophagy. Our study defines the molecular rules for initiation by transmembrane cargo receptors, revealing remarkable flexibility in the assembly and activation of the autophagy machinery, with significant implications for therapeutic interventions.

cell biology↗

bioRxiv2024

Compressed higher-order structures facilitate human knowledge network learning

Humans naturally seek knowledge, yet integrating vast, fragmented information remains challenging. Traditionally, knowledge acquisition has relied on random walks within network--an unguided and inefficient process. We introduce compressive learning, a framework that embeds higher-order structural features--specifically node-degree inhomogeneity--into pre-learning trajectories to scaffold more efficient learning. Across two large-scale experiments, we demonstrate that scale-free networks--due to their pronounced node-degree inhomogeneity--are more compressible and learnable than other network types, and confirm the efficacy of the compressive learning approach. Magnetoencephalography (MEG) recordings reveal that compressive pre-learning enhances structured neural representations in the dorsal anterior cingulate cortex (ACC). A hypergraph-based two-stage model further reveals that compressive learning constructs a network skeleton of hyperedge-defined substructures that more effectively accommodate new inputs. Together, our results highlight the central role of higher-order network structure in human learning and offer a strategic approach to effectively "connect the dots."

neuroscience↗

bioRxiv2024

Wheat TaNADPO promotes spot blotch resistance

Bipolaris sorokiniana is a common soil-borne fungal pathogen that can infect various organs of wheat (Triticum aestivum L.), causing diseases such as spot blotch, common root rot, head blight, and black point. The genetic basis of wheat resistance to B. sorokiniana is not yet fully understood. In this study, a natural population of 1,302 global common wheat germplasms was established and inoculated with B. sorokiniana at the seedling stage in a greenhouse. Resistance to spot blotch was assessed, revealing that only about 3.8% of the germplasms exhibited moderate or higher resistance levels. A genome-wide association study (GWAS) using high-density 660K single nucleotide polymorphism (SNP) data identified a region on chromosome 1BL (621.2-674.0 Mb) with 9 SNPs significantly associated (p < 10e-4) with spot blotch resistance, designated as Qsb.hebau-1BL. RNA sequencing and qRT-PCR assays showed that the gene TraesCS1B02G410300, encoding nicotinamide-adenine dinucleotide phosphate-binding oxidoreductase (TaNADPO), was significantly induced by B. sorokiniana. Five SNP variations were found in the promoter region of TaNADPO in wheat lines with or without Qsb.hebau-1BL. Transient expression of TaNADPO in Nicotiana benthamiana leaves showed a cytoplasmic subcellular localization of the fusion protein with a green fluorescent protein (GFP) tag. Wheat transgenic lines overexpressing TaNADPO exhibited significantly enhanced resistance to spot blotch compared to wildtype plants, with higher accumulation of reactive oxygen species (ROS). The knockout EMS mutant of Triticum turgidum NADPO (tdnadpo-K2561, Gln125*) showed significantly reduced resistance to spot blotch and lower ROS accumulation compared to wildtype plants. In summary, TaNADPO has been identified as a crucial gene for resistance to B. sorokiniana, providing valuable insights for developing spot blotch-resistant wheat varieties through molecular breeding techniques.

genetics↗

bioRxiv2024

Visual analysis of spatial transcriptomics data with RedeViz

Spatial transcriptomics (ST) technologies are powerful tools to illustrate the spatial hierarchy and heterogeneity of tissues with the lens of multiplexed gene readouts. However, ST technologies generate sequence data rather than images, preventing intuitive examination of the cellular contexture of tissues. Moreover, the inherent sparsity of ST data caused by molecular crowdedness and sequencing dropouts poses great challenges to accurate and clear visualization. In this study, we introduce RedeViz, a toolkit crafted for enhancing and visualizing subcellular-resolution ST data. RedeViz applies a pixel-level enhancement strategy, visualizes ST data in automatic or customized manners, and can display the cellular and genic spatial patterns with effects akin to HE staining. Strict evaluations confirm that RedeViz fits a wide range of ST platforms, including Xenium, Visium HD, MERFISH, CosMx, Stereoseq, as well as spatial proteomic platforms like CODEX. The impressive performance of RedeViz across various scales from cell-, tissue-, organ-, to organism-levels brings us a universal "What You See Is What You Get" framework for visual analysis of ST data.

bioinformatics↗

bioRxiv2024

SARS-CoV-2 shedding dynamics in human respiratory tract

It is crucial to understand how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) sheds in human respiratory tract, but this question is still elusive to understand due to technical limitations. Here we integrated published human metagenomic data of SARS-CoV-2 and developed a novel algorithm named as RedeCoronaVS to systematically dissect SARS-CoV-2 shedding modes with single-cell data as reference. We identify that SARS-CoV-2 particles are the dominant mode of viral shedding in the very early infection phase ([≤]24 hours after hospitalization). Within the first week after hospitalization, SARS-CoV-2 replicons within host cells dominate SARS-CoV-2 shedding together with viral particles. One week later, viral fragments become the dominant mode in patients with mild or moderate symptoms, but viral replicons still dominate in some patients with severe symptoms. In addition to epithelial cells, SARS-CoV-2 replicons in neutrophils, macrophages, and plasma cells also show important roles and are associate with sampling time and disease severity.

bioinformatics↗

bioRxiv2024

Spatial Transcriptomics Prediction from Histology Images at Single-cell Resolution using RedeHist

Spatial transcriptomics (ST) offers substantial promise in elucidating the tissue architecture of biological systems. However, its utility is frequently hindered by constraints such as high costs, time-intensive procedures, and incomplete gene readout. Here we introduce RedeHist, a novel deep learning approach integrating scRNA-seq data to predict ST from histology images at single-cell resolution. Application of RedeHist to both sequencing-based and imaging-based ST data demonstrated its outperformance in high-resolution and accurate prediction, whole-transcriptome gene imputation, and fine-grained cell annotation compared with the state-of-the-art algorithms.

bioinformatics↗

bioRxiv2024

An immunoediting map of human cancers

Understanding how cancer immunoediting sculpts tumor microenvironments is essential to disentangling tumor immune evasion mechanisms and developing immunotherapies. Here, we construct a comprehensive immunoediting map of human cancers via single-cell deconvolution of 11057 tumor-derived samples across 33 cancer types from TCGA and comparison with 17382 healthy samples across 30 tissues from GTEx. The map covers >1000 different cell states across all the major immune cell types. Mast cells, megakaryocytes, macrophages, neutrophils, plasma cells and T cells are up-regulated across a wide range of tumor types while natural killer cells and platelets are down-regulated in most tumor types, suggesting common cancer immunoediting events. While tumor heterogeneity is higher than the normal corresponding tissues, significant immune homogeneity exists among different tumor types compared with the distinct immune composition among normal tissues and organs. Our study provides a new holistic perspective to understanding cancer immunoediting. Our findings may provide important hints for developing novel cancer immunotherapies, and the high-resolution immunoediting map may serve as a rich resource for further pan-cancer investigation.

immunology↗

bioRxiv2024

Fluid flow reconstruction around a free-swimming sperm in 3D

We investigate the dynamics and hydrodynamics of a human spermatozoa swimming freely in 3D. We simultaneously track the sperm flagellum and the sperm head orientation in the laboratory frame of reference via high-speed high-resolution 4D (3D+t) microscopy, and extract the flagellar waveform relative to the body frame of reference, as seen from a frame of reference that translates and rotates with the sperm in 3D. Numerical fluid flow reconstructions of sperm motility are performed utilizing the experimental 3D waveforms, with excellent accordance between predicted and observed 3D sperm kinematics. The reconstruction accuracy is validated by directly comparing the three linear and three angular sperm velocities with experimental measurements. Our microhydrodynamic analysis reveals a novel fluid flow pattern, characterized by a pair of vortices that circulate in opposition to each other along the sperm cell. Finally, we show that the observed sperm counter-vortices are not unique to the experimental beat, and can be reproduced by idealised waveform models, thus suggesting a fundamental flow structure for free-swimming sperm propelled by a 3D beating flagellum.

biophysics↗

bioRxiv2024

SASH1 impairs melanin synthesis and metastasis by down-regulating the TGF-β signaling pathway

Dyschromatosis universalis hereditaria (DUH) is a rare genetic dermatosis characterized by widespread hyperpigmentation and depigmentation. In our previous study, we identified SH3 domain-containing protein 1 (SASH1) mutations associated with the DUH phenotype in Chinese families and predict SASH1/THBS1/TGF-{beta}1 signaling to mediate melanin production and melanocyte transport. We detected SASH1/THBS1/TGF-{beta}1 pathway genes expression and evaluated cell phenotypes and melanin synthesis in A375 and PIG1 cell lines by regulating the expression of SASH1 and THBS1 respectively. Finally, we validated the results of the cellular experiments in nude mice. Results showed that SASH1 inhibited the proliferation, migration, invasion, EMT ability and melanin synthesis via TGF-{beta}1 signaling, and THBS1 reversed the elevation of TGF-{beta}1 caused by SASH1 knockdown. We demonstrated that SASH1 further inhibits TGF-{beta}1 through its regulatory effect on THBS1, thereby inhibiting melanin synthesis and metastasis, which may advance the utilization of TGF-{beta}1 for therapeutic purposes. Plain Language SummaryDyschromatosis universalis hereditaria(DUH) is a genetic disease showing uneven pigment pattern, which greatly affects the appearance. In our previous study, we had reported a SASH1 mutation in a Chinese DUH pedigree. In this study, we mainly focus on the effect of SASH1 gene on pigment synthesis and metabolism at the cell and animal level. The results show SASH1 inhibits the melanin synthesis of melanocytes, it can also hinder cell migration, invasion, and EMT. More than that, SASH1 reduced TGF-{beta}1 mRNA, protein expression and promoter activity, and THBS1 could discharge this effect. In mice, SASH1 inhibits the tumor growth via TGF-{beta}1 signaling. We detected a novel SASH1/THBS1/TGF-{beta}1 pathway in cell phenotypes and melanin synthesis.

cell biology↗