Biology subjects

Deng, C.

Publications and source records attributed to Deng, C..

At least 19 recordsLinked to original sources

bioRxiv2026

The periplasmic substrate-binding protein ThuE is required for sucrose uptake and multiplication of Pseudomonas syringae pv. tomato DC3000 in tomato leaves

Phytopathogenic bacteria depend on host-derived carbon for successful colonization of plant tissue. While sucrose is among the most abundant sugars in the leaf apoplast, the steps that limit its acquisition by Pseudomonas syringae are not known. In this study, we used base editing to generate mutants of six candidate sucrose utilization genes in P. syringae pv. tomato DC3000 (Pto). Loss of either the sucrose hydrolase ScrB or both levansucrases had no detectable effect, whereas the growth defect in the loss of the outer membrane porin mutant scry was overcome by raising external sucrose. Loss of the periplasmic substrate-binding protein ThuE impaired growth both in vitro and in planta, reducing bacterial populations to approximately two orders of magnitude lower in tomato leaves. Sucrose import through a single non-redundant inner membrane ABC transporter is therefore required for Pto multiplication in planta and serves as a potential target for controlling bacterial speck disease.

plant biology↗

bioRxiv2026

Stress-recovery dynamics reveal a separatrix in transcriptomic landscapes across organs and aging

Aging is often characterized statically as molecular profiles, but how these profiles may affect the capacity of systems to respond to the external environment remains elusive. We perturbed young and aged mice via transient sleep deprivation and profiled transcriptomes from six organs immediately after stress and following recovery. The same perturbation induced complex temporal dynamics for each gene in an organ- and age- dependent manner. A shape parameter distinguished genes that recovered toward control expression from those that continued to drift away during recovery. Transcriptomic vector fields were inferred from these transitions using neural ordinary differential equations, revealing distinct stability regimes across organ systems. Interestingly, that of testis from the young mice contained a separatrix bounding the region within which perturbed state can return toward control. These findings establish transient perturbation and recovery as a framework for probing age-dependent transcriptomic stability and identifying boundaries that determine whether a perturbed system can return.

systems biology↗

bioRxiv2026

Gradual evolution of multiplexed spatial coding within a conserved hippocampal scaffold

The hippocampus constructs spatial maps for navigation, yet their format differs markedly across species. Whether divergences reflect ecological adaptation, phylogenetic architecture, or flexible coding strategy within a conserved circuit has been difficult to disentangle. We recorded CA1 in rats and tree shrews (Tupaia belangeri chinensis), a mammal phylogenetically and ecologically between rodents and primates, using identical tasks and analyses. Unlike the position-dominant code of rats, tree shrew CA1 exhibited a hybrid representation: weaker position selectivity, stronger non-positional tuning, and prevalent multiplexing approaching primate characteristics. Multiplexed populations decoded location as accurately as rat position populations while using fewer neurons, suggesting computational advantages of high-dimensional coding. Despite this representational shift, proximo-distal gradient, pattern completion, and global remapping persisted. Representational format can be tuned without altering the underlying circuit. Tree shrews occupy an evolutionary intermediate in which ancestral network dynamics are repurposed for efficient multiplexed coding, tracing a transition toward primate-like spatial representations.

neuroscience↗

bioRxiv2026

Functional profiling of ESKAPE viromes uncovers resistance-limiting phage-host dynamics

ESKAPE pathogens drive clinical antibiotic resistance and intractable infections, severely compromising antimicrobial therapies. Bacteriophages are promising alternatives to antibiotics, yet their diversity, function and ecological impacts in ESKAPE pathogens remain poorly defined, hindering phage therapy translation. Here, we integrated 11,947 high-quality ESKAPE genomes with global metagenomic viral data to construct a comprehensive non-redundant virome of 14,496 ESKAPE-associated viruses, including four unreported viral clades. We found pervasive competition among mobile genetic elements (MGEs) in the ESKAPE mobilome, where nested MGE architectures empower low-mobility antibiotic resistance genes (ARGs) with horizontal transfer ability to fuel resistance dissemination. Unlike ARG-rich MGEs, ESKAPE phages carry minimal ARGs and antagonize plasmids to constrain ARG propagation, confirming their biosafety for therapy. We further revealed distinct phage-host arms races, typically virulent phages enrich anti-defense genes to evade bacterial immunity, and novel viruses hijack host methyltransferases targeted by CRISPR-Cas systems. This study establishes a systematic ESKAPE virome resource, demonstrates phages dual roles in targeting resistant pathogens and curbing resistance spread, and provides mechanistic support for phage therapy clinical application.

microbiology↗

bioRxiv2026

A genetic switch involving EGR1 and EZH2 links aging and development across human tissues

Aging is often regarded as the last chapter of development. There is growing evidence that aging and development are mechanistically linked. Here we describe a genetic switch involving EZH2 and EGR1 as opposing regulatory nodes that appears to connect aging and development across human tissues. We show that this switch defines two distinct states in fibroblasts: a proliferative (EZH2-high/EGR1-low) state and a non-proliferative and extracellular matrix-expressing (EGR1-high/EZH2-low) state. During replicative aging, cells shift from the proliferative state to the non-proliferative state and targeting either regulatory node--by overexpressing EZH2 or suppressing EGR1--rejuvenates aged fibroblasts. We provide evidence that this switch is involved in the transition from neural progenitor cells to matured neurons during brain development and becomes destabilized during aging, partially reversing the gene expression program established during development. We observed that this same switch becomes blurred and biased towards EGR1-high/EZH2-low state during the aging of muscle stem cells and hematopoietic stem cells. Since genetic switches are widely used in development to establish and reinforce cellular identity, we propose that attenuation of developmental switches may underlie aging across diverse organs and tissues, and partially accounts for the erosion of the epigenetic landscape and the loss of cellular identity.

systems biology↗

bioRxiv2026

Massively parallel characterization and predictive modelling of neuronal regulatory variation

Disease-associated variants reside frequently in noncoding cis-regulatory elements (CREs), yet their functional consequences remain poorly understood. We performed a large-scale lentiMPRA in human excitatory neurons, quantifying the impact of >46,000 naturally occurring variants across >27,000 candidate CREs near 524 disease-associated genes. These data improved regulatory variant effect predictions beyond state-of-the-art models. Significant allelic effects occurred at comparable rates across common, rare, and singleton variants, demonstrating that, within MPRA-measurable effects, population frequency carries limited information about per-variant regulatory impact. Variant effect detectability and magnitude were governed primarily by baseline activity of the enclosing regulatory element and local sequence context. Regulatory effects were distributed across numerous transcription factors rather than concentrated in master regulators, consistent with a combinatorial enhancer architecture. We establish a large-scale functional variant catalog and provide a complementary benchmark and resource for developing and evaluating models of noncoding regulatory variation.

genetics↗

bioRxiv2026

Fluorescently-labeled split-QF hemidrivers: simplifying and enhancing methods enabling intersectional targeting of discrete cell types

Single cell transcriptomics data predict greater cell type diversity than previously appreciated, defined by combinatorial gene expression "codes". These codes can enable intersectional targeting strategies for selectively labeling and manipulating predicted cell types, thereby facilitating functional tests to resolve cell-specific roles and refine cell-type definitions. One such approach cleaves driver components of binary expression systems (e.g., Gal4/UAS and QF/QUAS) into two co-dependent halves, an Activation Domain (AD) and a DNA Binding Domain (DBD). The transcriptional activity of these "split-drivers" (aka, hemidrivers) is only reconstituted in cells that co-express them. While widely used in invertebrates, these systems have yet to be systematically deployed in vertebrates. Here, we developed a series of fluorescently labeled split-QF and QF2 hemidrivers via direct reporter fusions or the 2A viral peptide co-expression system. Fluorescent labeling serves to 1) simplify hemidriver transgenic line creation and maintenance, 2) allow AD and DBD intersects to be visualized directly, and 3) enable robust quality control assessments of on-target efficacy and off-target activity. These resources can enhance transgenic targeting specificity, enabling functional dissections of cell types revealed by single cell transcriptomics. SUMMARYWe engineered fluorescently labeled split-QF and -QF2 hemidrivers in zebrafish to simplify intersectional targeting tool generation and enable robust quality control assessments of split-driver function.

genetics↗

bioRxiv2026

Bright Probes, Blurred Metabolism: Navigating Fluorescent Protein Cross-Excitation in NADH FLIM

Fluorescence lifetime imaging microscopy (FLIM) of endogenous NAD(P)H enables the label-free assessment of cellular metabolic state. Although metabolic imaging is increasingly combined with fluorescent protein (FP) reporters to enhance biological specificity, the potential cross-talk between the intrinsic and extrinsic labels remain ill-defined. Here, we systematically evaluate cross-talk from FPs in metabolic FLIM using phasor analysis of two-photon fluorescence microscopy. The results clearly show that many widely used fluorescent proteins are excited under the conditions used for NADH imaging; they emit blue-shifted, short-lifetime fluorescence that can interfere with imaging NADH metabolic signatures. This overlap persists across excitation wavelengths and FP classes, posing a significant challenge for multiplexed metabolic imaging. This cautionary tale argues against unvalidated multiplexing strategies in metabolic FLIM studies. Our study aims to identify acceptable imaging partners, offer a pipeline for assaying potential cross-talk, and provide practical guidance for experimental design. SignificanceFluorescence lifetime imaging of NADH autofluorescence is a powerful, label-free approach to map cellular metabolism in living tissues. A growing number of studies combine NADH imaging with fluorescent protein (FP) reporters to simultaneously identify specific cell types or subcellular compartments. This study reveals that many FPs, spanning the visible spectrum, are unexpectedly excited under NADH conditions. Commonly used green, yellow, and red variants produce short-lifetime, blue-shifted fluorescence that directly overlaps with metabolic NADH signals. This cross-excitation can be falsely interpreted as a shift in cellular metabolic state, posing a significant risk for multiplexed metabolic imaging studies. Our studies establish a pipeline to assess and manage this risk. We identify StayGoldE138D and mNeonGreen as the most compatible FPs for co-imaging with NADH, and provide a practical framework to guide experimental design and control strategies for multiplexed metabolic FLIM.

biophysics↗

bioRxiv2026

RNA-binding proteins activate transcription through defined molecular grammars

Transcription factors (TFs) regulate gene expression through interactions with DNA, RNA, and proteins. RNA-binding proteins (RBPs) also assemble near regulatory elements and mediate RNA processing, yet their perturbation causes transcriptional defects. Here, we find select RBPs activate transcription through latent activation domains akin to TFs. RBP activators regulate distinct genes and interact with transcriptional condensates. Their activation domains are enriched in aromatic and polar residues but depleted of basic residues - essential features that are conserved and partially mimic TF activation domains. We validated additional RBP activators across the human proteome based on this molecular grammar, including the C-terminal domain (CTD) of RPB1, the catalytic subunit of RNA polymerase II. RPB1-CTD activates transcription by recruiting coactivators, demonstrating a non-enzymatic function in transcriptional regulation. These findings position RBPs and RPB1 as transcriptional regulators, explain coupling between transcription and RNA processing, and reveal RNA-RBP regulatory networks that parallel DNA-TF networks.

molecular biology↗

bioRxiv2026

MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes

Drugs induce coordinated phenotypic changes across multiple modalities, including transcriptional reprogramming and cellular morphological remodeling. Predicting these drug-induced modality changes is central to drug discovery, mechanism-of-action studies and precision therapeutics, however, prediction performance depends critically on how both drug compounds and cellular states are represented. Despite rapid advances in drug molecular and gene representation methods, a systematic evaluation of these methods remains lacking. Herein, we introduce MVCBench, a comprehensive benchmarking framework for evaluating drug molecular and gene representation methods in predicting drug-induced multimodal virtual cell (MVC) phenotypes. MVCBench leverages large-scale transcriptomic and high-content imaging data and systematically evaluates 24 representation methods (12 drug molecular and 12 gene representation methods) across nearly 1.1 million drug-induced profiles, under both in-distribution and out-of-distribution settings spanning unseen compounds, cell lines, assay plates and datasets. Our benchmarking reveals a pronounced modality-dependent asymmetry: advanced drug molecular representations substantially improve the prediction of drug-induced morphological phenotypes but provide only limited gains for gene expression prediction relative to classical fingerprints, whereas task-specific gene representations outperform general-purpose foundation models in predicting drug-induced transcriptomic responses. Predictive performance also deteriorates sharply under distribution shift, highlighting persistent challenges in cross-dataset and cross-platform generalization. We further show that integrating transcriptomic and morphological modalities consistently improves prediction accuracy, and derive practical design principles for MVC architectures, including modality-aware loss calibration and fusion strategies. Together, MVCBench provides a systematic foundation for evaluating representation methods and offers guidance for developing robust MVC models of drug-induced cellular responses.

bioinformatics↗

bioRxiv2026

Asymmetric Division in a Two-Cell-Like State Rejuvenates Embryonic Stem Cells

A fundamental question in biology is whether cellular aging is inevitable. Embryonic stem cells (ESCs) challenge this paradigm as rare normal cells capable of indefinite in vitro passage. However, the mechanisms underlying ESC lineage immortality remain unresolved. Using long-term live-cell imaging to follow fates of single ESCs, we show here that ESC lineage renewal is achieved through sporadic entry into a state characterized by the expression of two-cell embryo-specific markers. During this state, cells undergo asymmetric divisions, segregating accumulated DNA damage into one daughter lineage destined for elimination, while producing a second lineage that reverts to the pluripotent state. Importantly, the latter lineage exhibits signs of rejuvenation, including reduced DNA damage and enhanced chimeric efficiency. These findings underscore the crucial role of asymmetric cell division in maintaining the long-term health of the ESC lineage against mounting damage within individual cells, a potential model for studying cellular aging and rejuvenation in mammalian cells.

cell biology↗

bioRxiv2025

Integrative k-mer and Transcriptomic Analysis Reveals Putative Sex-Determining Genes in Spinacia turkestanica

Deciphering the regulation of sex-determining gene/s in dioecious crops is crucial for molecular breeding. However, the identification of sex-determining gene/s in Spinacia is challenging due to incomplete genome assemblies, high genomic similarity between males and females, and the limitations of transcriptome-only analyses, which may miss unannotated or novel genes in poorly assembled or absent genomic regions. To overcome these limitations, we employed a reference-genome-free k-mer approach to identify candidate sex-determining genes in Spinacia turkestanica, the closest evolutionary relative of cultivated spinach (S. oleracea). Male-specific reads were de novo assembled into contigs, revealing 21.5 Mb of the sex-determining region (SDR). Using the MAKER pipeline, which integrates transcriptomic and proteomic evidence, we predicted 226 protein-coding genes within the SDR, including nine previously unannotated. Transcriptomic profiling combined with weighted gene co-expression network analysis identified eight SDR DEGs, including two newly annotated genes, co-expressing during early male flower development. qPCR validation confirmed three SDR genes as candidate sex-determining factors, including TU_SDR00087 (bZIP domain), TU_SDR000168 (RNA-binding splicing factor domain), and TU_SDR000174 (MYB domain). Together, these findings provide a foundation for functional characterization of sex determination in Spinacia. HighlightA k-mer based analysis uncovered male-specific regions and candidate sex-determining genes in Spinacia turkestanica, advancing understanding of sex regulation and spinach breeding.

genetics↗

bioRxiv2025

Bioinformatic analysis and experimental validation of ursolic acid's effects on Staphylococcus aureus-induced osteomyelitis

Osteomyelitis (OM), particularly methicillin-resistant Staphylococcus aureus (MRSA)-induced OM, remains a serious clinical challenge due to complex pathogenesis and rising antibiotic resistance. This study aimed to elucidate the therapeutic mechanism of ursolic acid (UA) against MRSA- induced OM using integrated network pharmacology, bioinformatics, and experimental validation. Through target prediction and multi-database mining, we identified 57 common targets of UA and OM. ML algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO) and random forest, pinpointed three core genes: Neutrophil Elastase (ELANE), Lactoferrin (LTF), and S100A12. Enrichment analyses revealed significant involvement in neutrophil extracellular trap (NET) formation, inflammatory response, and immune regulation. Molecular docking and dynamics simulations confirmed stable binding between UA and ELANE. In vitro, UA exhibited antibacterial activity against clinical MRSA isolates (MIC = 16-64 g/mL) and showed synergistic effects with Penicillin (FICI = 0.125-0.5). These results demonstrate that UA combats OM through immunomodulation, anti-inflammatory actions, and direct antibacterial activity, providing a foundation for its use as an adjuvant therapy against MRSA-related OM.

microbiology↗

bioRxiv2025

Visible Light-Controllable Surgical Hemostatic Adhesives Enabled by Vitamin B12-Stabilized Poly(α-Lipoic Acid)

Water-resistant adhesives are indispensable for biomedical applications, from surgical wound closure to internal hemostasis. While poly(-lipoic acid)-based adhesives show promise for their strong underwater adhesion, their clinical utility has been limited by uncontrolled polymerization-depolymerization dynamics. Here we present a visible light-controllable adhesive system enabled by a simple mix of -lipoic acid (LA) and vitamin B12 (i.e., adenosylcobalamin or AdoB12)--a photolabile compound--without resorting to any chemical modification. Benign visible light irradiation facilitates the cleavage of the C-Co bond and the subsequent formation of B12-thiolate complexes that stabilize LA polymers against depolymerization. The photoresponsive LA-AdoB12 adhesive system has proven highly effective in a wide range of surgical applications, achieving (1) strong bonding in porcine skin models in vitro, (2) reliable sealing of punctured organs (lung, heart and stomach) ex vivo, and (3) immediate hemostasis in active bleeding models such as topical, esophageal, and intestinal wounds in vivo. This work highlights a simple yet powerful strategy for creating visible light-controllable bioglues well-suited for diverse surgical applications.

bioengineering↗

bioRxiv2025

Mid-zone hepatocytes trade proliferation for survival via Atf4-Chop axis in early acute liver injury

Hepatocytes undergo extensive proliferation to facilitate liver repair after injury, yet early adaptive changes prior to proliferation remain unclear. Here, we report that during early acetaminophen (APAP)-induced liver injury, hepatocytes exhibit transient proliferation suppression that is most pronounced in mid-zone hepatocytes, consistent with zonal APAP metabolism. While spatial transcriptomics (ST) provided robust evidence for this arrest in the mid-zone, support for a similar arrest in pericentral hepatocytes was limited. Integrating ST with immunohistochemistry and functional studies, we identified a unique mid-zone stress-response program centered on the Atf4-Chop axis, which suppresses proliferation via the cell cycle inhibitor Btg2. Together, our findings support a model in which mid-zone hepatocytes transiently prioritize stress adaptation over proliferation, thereby preserving regenerative capacity for subsequent liver repair.

pharmacology and toxicology↗

bioRxiv2025

Differential Regulation of Hepatic Macrophage Fate by Chi3l1 in MASLD

Metabolic dysfunction-associated steatotic liver disease (MASLD) progression involves the replacement of protective embryo-derived Kupffer cells (KCs) by inflammatory monocyte-derived macrophages (MoMFs), yet the regulatory mechanisms remain unclear. Here, we identify chitinase 3-like 1 (Chi3l1/YKL-40) as a critical metabolic regulator of hepatic macrophage fate. We observed high expression of Chi3l1 in both KCs and MoMFs during MASLD development. Genetic deletion of Chi3l1 specifically in KCs significantly exacerbated MASLD severity and metabolic dysfunction, whereas MoMF-specific Chi3l1 deletion showed minimal metabolic effects. Mechanistic studies revealed that this cell type-specific regulation arises from differential metabolic requirements: KCs display elevated glucose metabolism compared to MoMFs. Chi3l1 directly interacts with glucose to inhibit its cellular uptake, thereby selectively protecting glucose-dependent KCs from metabolic stress-induced cell death while having negligible effects on less glucose-dependent MoMFs. These findings uncover a novel Chi3l1-mediated metabolic checkpoint that preferentially maintains KCs populations through glucose metabolism modulation, providing important new insights into the pathogenesis of MASLD and potential therapeutic strategies targeting macrophage-specific metabolic pathways.

molecular biology↗

bioRxiv2025

GABA produced by multiple bone marrow cell types regulates hematopoietic stem and progenitor cells

Hematopoietic stem and progenitor cells (HSPCs) maintain homeostasis of the blood system by balancing proliferation and differentiation. Many extrinsic signals in the bone marrow (BM) microenvironment that regulate this balance are still unknown. We report gamma aminobutyric acid (GABA) metabolite produced in the BM as a regulator of HSPCs. Deletion of the glutamate decarboxylase enzymes (Gad1/2) that produce GABA in either B lineages or endothelial cells (ECs) leads to a moderate reduction in BM GABA levels and HSPC number, suggesting both cell types are GABA sources. However, simultaneous blockade of GABA production from both hematopoietic cells and ECs resulted in a greater reduction of both GABA levels and HSPC numbers. Lower GABA levels in the BM altered the gene expression profile of HSPCs, with expression reduced for proliferation-associated genes and increased for B lineage genes. Our findings suggest GABA from multiple sources coordinates to regulate HSPC activity. HighlightsO_LIGABA is produced by B cells and endothelial cells in the bone marrow C_LIO_LILower GABA level in the bone marrow reduces HSPC proliferation C_LIO_LILower GABA level primes HSPCs to upregulate B cell differentiation programs C_LI eTOC blurbTamplin and colleagues functionally test production of GABA metabolite in the bone marrow microenvironment as a regulator of hematopoietic stem and progenitor cells. Conditional deletion of GAD enzymes in B cells and endothelial cells demonstrated both are sources of GABA. Lower GABA level primed HSPCs to reduce proliferation and upregulate B cell differentiation programs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/651482v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1db5c9forg.highwire.dtl.DTLVardef@9dfadcorg.highwire.dtl.DTLVardef@1c0b939org.highwire.dtl.DTLVardef@1c08a9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

SRSF3 is oncogenic in breast but tumor-suppressive in liver by differential regulation of gene expression

SRSF3 (SRp20) is an essential splicing factor. We discovered Srsf3 plays an oncogenic role in breast cancer and Srsf3 knockout (KO) in mammary glands delays the development of breast cancer in an Erbb2 mouse model. In contrast, Srsf3 is tumor-suppressive in mouse liver tissues. Srsf3 KO in hepatocytes enhances DEN-induced liver cancer and disrupts the sex disparity in DEN-induced liver cancer. Comparing to Srsf3 WT liver cancer, Srsf3 KO significantly increases Sox4, E2f1, Trpv4, Trim6, and Myc expression, but does not so in Erbb2 breast cancer. Srsf3 KO inhibits expression of Mfsd4a and Eif4a2 in breast cancer but enhances Mfsd4a and Eif4a2 expression in liver cancer. Moreover, Srsf3 KO suppresses the expression of ER and Foxa genes to reduce Lifr and Egfr but induce Myc expression and promote liver cancer in female mice. Together, our data highlight a new functional paradigm of SRSF3 at its physiological level in tissue context-dependent gene regulation.

cancer biology↗