Biology subjects

Dong, C.

Publications and source records attributed to Dong, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Hepatic Arterial Flow-Induced Portal Tract Fibrosis in Portal Hypertension: The Role of VCAM-1 and Osteopontin-Expressing Macrophages

BackgroundThe liver undergoes significant hemodynamic changes during surgery, transplantation, or cirrhosis with portal hypertension(PH). The hepatic artery buffer response(HABR), which compensates for reduced portal venous flow by increasing hepatic artery(HA) flow, is hypothesized to induce pathological portal tract remodeling. This study investigates the molecular mechanisms underlying this process. MethodsPH was induced in Sprague-Dawley rats via partial portal vein ligation(PPVL). Structural evaluation(microCT), immune cell profiling, hemodynamic measurements, and transcriptomic analysis in macrophages(M{phi}) from sham or PPVL rats were conducted. ResultsMicroCT revealed decreased portal vein flow and increased HA flow correlated with portal pressure(r=0.799, p<0.01). A 2-fold increase in portal tract fibrosis(p<0.001) was observed with increased -SMA+ myofibroblasts in PPVL rats. CD68+ M{phi} peaked at 10 days post-PPVL, and their depletion significantly reduced fibrosis(p<0.001), indicating critical roles of M{phi} in portal tract remodeling. VCAM-1 was elevated in HA endothelium and portal fibroblasts (PFs); VCAM-1 neutralization reduced collagen accumulation(p<0.05), CD68+ M{phi}(46.3%, p<0.01), and CD3+ T cells(18%, p<0.05). M{phi}-conditioned medium increased VCAM-1 in PFs(8-fold, p<0.001) and enhanced PF migration, while VCAM-1 knockdown reduced this effect (p<0.01). Single-cell RNA sequencing data(GSE171904) and RNA-FISH revealed increased interactions between osteopontin (Spp1)+ M{phi} and PFs, with Spp1+ M{phi} driving fibrosis. Spp1 knockdown in M{phi} co-culture reduced PF fibrogenic markers, while recombinant Spp1 upregulated Col1a1, Fn1, and Acta2 expression in PFs. ConclusionIncreased VCAM-1 in arterial endothelial cells and PFs facilitates the recruitment of Spp1+ M{phi}, which drive HA flow-mediated vascular remodeling and portal tract fibrosis. These findings highlight arterial flow-induced fibrosis as a key mechanism in PH, potentially contributing to disease progression and decompensation. SynopsisLiver hemodynamic changes in portal hypertension drive extracellular matrix accumulation and portal tract remodeling via Spp1+ macrophages. This study highlights how altered blood flow induces fibrosis, and its potential role in decompensation, and identifies therapeutic targets for advanced liver disease.

pathology↗

bioRxiv2025

TransBrain: A computational framework for translating brain-wide phenotypes between humans and mice

Despite remarkable advances in whole-brain imaging technologies, the lack of quantitative approaches to bridge rodent preclinical and human studies remains a critical challenge. Here we present TransBrain, a computational framework enabling bidirectional translation of brain-wide phenotypes between humans and mice. TransBrain improves human-mouse homology mapping accuracy through: (1) a novel detached region-specific deep neural network trained on integrated multi-modal human transcriptomics to improve cortical correspondence (89.5% improvement over the original transcriptome), which revealed two evolutionarily conserved gradients explaining >50% of cortical organizational variance, and (2) random walk-based graph representation learning to construct a unified cross-species latent space incorporating anatomical hierarchies and structural connectivity. We demonstrated TransBrains utility through three cross-species applications: quantitative assessment of resting-state brain organizational features, inferring human cognitive functions from mouse optogenetic circuits, and translating molecular insights from mouse models to individual-level mechanisms in autism. TransBrain enables quantitative cross-species comparison and mechanistic investigation of both normal and pathological brain functions.

neuroscience↗

bioRxiv2025

Collagen Hydrogel Tube Microbioreactors for Cell and Tissue Manufacturing

The production of mammalian cells in large quantities is essential for various applications. However, scaling up cell culture using existing bioreactors poses significant technical challenges and high costs. To address this, we previously developed an innovative 3D culture system, known as the AlgTube cell culture system, for high-density cell cultivation. This system involves processing cells into microscale alginate hydrogel tubes, which are suspended in the culture medium within a vessel. These hydrogel tubes shield cells from hydrodynamic stress and maintain the cell mass below 400 {micro}m in diameter, facilitating efficient mass transport and creating a favorable microenvironment for cell growth. Under optimized conditions, AlgTubes supported long-term culture with high cell viability, rapid expansion (1000-fold increase over 9 days per passage), and high yield (5x10 cells/mL), offering significant advantages over conventional methods. Despite these benefits, AlgTubes have critical drawbacks. They are mechanically fragile, with frequent breakage during culture leading to cell leakage and production failures. Additionally, many cell types exhibit poor growth due to the inability to adhere to the alginate surface, making alginate hydrogel microtubes unsuitable for industrial-scale cell production. To overcome these challenges, we developed a novel collagen hydrogel tube-based microbioreactor system in this work. This system provides enhanced robustness and adhesion, enabling scalable, cost-effective, and efficient cell production for a wide range of applications.

bioengineering↗

bioRxiv2025

Dissection of the Global Responses of Mandarin Fish Pyloric Caecum to An Acute Ranavirus (MRV) Infection Reveals the Formation of Serositis and Then Ascites

Mandarin fish ranavirus (MRV), a variant of largemouth bass virus (LMBV), is a distinct member of the genus Ranavirus within the family Iridoviridae. Acute MRV infection predominantly affects the pyloric caecum, a critical visceral organ in mandarin fish, and is hypothesized to drive the characteristic external clinical sign of severe ascites. In this study, we reveal that acute MRV infection initially targets the serosal layer of the pyloric caecum of mandarin fish, leading to rapid progression into fibrinous serositis characterized by serosal hypertrophy, fibrosis, hyperemia, edema, and tissue adhesions. Using single-cell RNA sequencing, we dissect the cellular composition of epithelial, immune, and stromal populations, identifying significant enrichment of macrophages and granulocytes, alongside T and natural killer cells, as key mediators of acute cytokine and inflammatory responses. Then, robust experimental evidence demonstrates that MRV attacks specific immune cell subsets of T and B cells and stromal cells of fibroblasts, myofibroblasts, endothelial cells, and pericytes, resulting in upregulation of genes and pathways associated with extracellular matrix (ECM) formation, collagen biosynthesis, and vascular remodeling in the hyperplastic serosal zone. Additionally, both host-derived type V collagens and MRV-encoded collagens are implicated in ECM formation in the hypertrophic serosa. Collectively, this study provides a comprehensive single-cell resolution analysis of the pyloric caecums response to acute MRV infection and highlights virus- driven serositis as the underlying cause of severe ascites in mandarin fish. ImportanceThe pyloric caecum is a vital digestive and immune organ in many bony fish species, including the mandarin fish, a carnivorous species with an exceptionally developed pyloric caecum comprising 207-326 caeca per individual. While MRV/LMBV infects various fish species, severe ascites is uniquely observed in infected mandarin fish. This study demonstrates that acute MRV infection induces fibrinous serositis in the pyloric caecum, characterized by hyperemia, edema, and hyperplasia, ultimately resulting in ascites and mortality. Leveraging single-cell RNA sequencing, we provide a detailed landscape of the cell types affected or involved in the inflammatory response, revealing their roles in the pathogenesis of serositis. These findings advance our understanding of MRV-induced pathology and its species-specific manifestations.

microbiology↗

bioRxiv2024

TCPGdb: A comprehensive T cell perturbation genomics database for identification of critical T cell regulators

CAR-T therapies utilizing T cells engineered with chimeric antigen receptors (CARs) have revolutionized the treatment of hematologic and immune-related malignancies. However, the anti-tumor capability of engineered CAR-T cells are often not persistent, which greatly dampen its clinical efficacy. To address this limitation, massive parallel genetic screens were widely used to identified novel targets and regulators that enhance T cell anti-tumor capability and persistence in tumor microenvironment. We hypothesized that by combining the pooled screen data from multiple independent genetic screens we could provide a systematic, comprehensive, and robust analysis of the effect of gene perturbation on T-cell based immunotherapies. After collecting data from previously published T cell screens, including CRISPR-based and ORF-based screens, through Gene Expression Omnibus (GEO), we reprocessed the gene hits summary and conducting a pathway enrichment analysis. A T cell screen perturbation score (TPS) was employed to quantifies the impact of the gene on T cell function. Additionally, gene expression data (both bulk RNA level and single-cell RNA level) from autoimmune disease and T cell-derived cancers were analyzed to pick up gene perturbations that potentially augment T cell proliferation. We integrated all data and analysis on 27 T-cells screens into our state-of-the-art T cell perturbation genomics database (TCPGdb), which is made easily accessible through our webserver and allows users to interactively explore the impact of query genes on T cell function based on prior screen data and our TPS scoring module. TCPGdb is publicly accessible at http://tcpgdb.sidichenlab.org/.

bioinformatics↗

bioRxiv2024

A contextual fear conditioning paradigm in head-fixed mice exploring virtual reality.

Contextual fear conditioning is a classical laboratory task that tests associative memory formation and recall. Techniques such as multi-photon microscopy and holographic stimulation offer tremendous opportunities to understand the neural underpinnings of these memories. However, these techniques generally require animals to be head-fixed. There are few paradigms that test contextual fear conditioning in head-fixed mice, and none where the behavioral outcome following fear conditioning is freezing, the most common measure of fear in freely moving animals. To address this gap, we developed a contextual fear conditioning paradigm in head-fixed mice using virtual reality (VR) environments. We designed an apparatus to deliver tail shocks (unconditioned stimulus, US) while mice navigated a VR environment (conditioned stimulus, CS). The acquisition of contextual fear was tested when the mice were reintroduced to the shock-paired VR environment the following day. We tested three different versions of this paradigm and, in all of them, observed an increased conditioned fear response characterized by increased freezing behavior. This was especially prominent during the first trial in the shock-paired VR environment, compared to a neutral environment where the mice received no shocks. Our results demonstrate that head-fixed mice can be fear conditioned in VR, discriminate between a feared and neutral VR context, and display freezing as a conditioned response, similar to freely behaving animals. Furthermore, using a two-photon microscope, we imaged from large populations of hippocampal CA1 neurons before, during, and following contextual fear conditioning. Our findings reconfirmed those from the literature on freely moving animals, showing that CA1 place cells undergo remapping and show narrower place fields following fear conditioning. Our approach offers new opportunities to study the neural mechanisms underlying the formation, recall, and extinction of contextual fear memories. As the head-fixed preparation is compatible with multi-photon microscopy and holographic stimulation, it enables long-term tracking and manipulation of cells throughout distinct memory stages and provides subcellular resolution for investigating axonal, dendritic, and synaptic dynamics in real-time.

animal behavior and cognition↗

bioRxiv2024

Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for simultaneous co- sequencing of spatial transcriptome and guide RNAs (gRNAs) on the same tissue section for in vivo CRISPR screen with genome-scale gRNA libraries, offering a comprehensive understanding of how genetic modifications affect cellular behavior and tissue architecture. This platform supports a variety of delivery vectors, gRNA library sizes, and tissue preparations, along with two distinct gRNA capture methods, making it adaptable to a wide range of experimental setups. In applying Perturb-DBiT, we conducted un-biased knockouts of tens of genes or at genome-wide scale across three cancer models. We mapped all gRNAs in individual colonies and corresponding transcriptomes in a human cancer metastatic colonization model, revealing clonal dynamics and cooperation. We also examined the effect of genetic perturbation on the tumor immune microenvironment in an immune-competent syngeneic model, uncovering differential and synergistic perturbations in promoting immune infiltration or suppression in tumors. Perturb-DBiT allows for simultaneously evaluating the impact of each knockout on tumor initiation, development, metastasis, histopathology, and immune landscape. Ultimately, it not only broadens the scope of genetic inquiry, but also lays the groundwork for developing targeted therapeutic strategies.

genomics↗

bioRxiv2024

FB5P-seq-mAbs: monoclonal antibody production from FB5P-seq libraries for integrative single-cell analysis of B cells

Parallel analysis of phenotype, transcriptome and antigen receptor sequence in single B cells is a useful method for tracking B cell activation and maturation during immune responses. However, in most cases, the specificity and affinity of the B cell antigen receptor cannot be inferred from its sequence. Antibody cloning and expression from single B cells is then required for functional assays. Here we propose a method that integrates FACS-based 5-end single-cell RNA sequencing (FB5P-seq) and monoclonal antibody cloning for integrative analysis of single B cells. Starting from a cell suspension, single B cells are FACS-sorted into 96-well plates for reverse transcription, cDNA barcoding and amplification. A fraction of the single-cell cDNA is used for preparing 5-end RNA-seq libraries that are sequenced for retrieving transcriptome-wide gene expression and paired BCR sequences. The archived cDNA of selected cells of interest is used as input for cloning heavy and light chain variable regions into antibody expression plasmid vectors. The corresponding monoclonal antibodies are produced by transient transfection of a eukaryotic producing cell line and purified for functional assays. We provide detailed step-by-step instructions and describe results obtained on ovalbumin-specific murine germinal center B cells after immunization. Our method is robust, flexible, cost-effective, and applicable to different B cell types and species. We anticipate it will be useful for mapping antigen specificity and affinity of rare B cell subsets characterized by defined gene expression and/or antigen receptor sequence.

immunology↗

bioRxiv2024

Polyacrylamide-based Antimicrobial Copolymers Immune to Typical Resistance Mechanisms to Replace or Rescue Antibiotics

Antibiotics save countless lives each year and have dramatically improved human health outcomes since their introduction in the 20th century. Unfortunately, bacteria are now developing resistance to antibiotics at an alarming rate, with many new strains of "superbugs" showing simultaneous resistance to multiple classes of antibiotics. To mitigate the global burden of antimicrobial resistance, we must develop new antibiotics that are broadly effective, safe, and highly stable for the purpose of global access. In this manuscript, we report the development of polyacrylamide-based copolymers as a novel class of broad-spectrum antibiotics with efficacy against several critical pathogens. We demonstrate that these copolymer drugs are selective for bacteria over mammalian cells, indicating a favorable safety profile. We show that they kill bacteria through a membrane disruption mechanism, which allows them to overcome traditional mechanisms of antimicrobial resistance. Finally, we demonstrate their ability to rehabilitate an existing small-molecule antibiotic that is highly subject to resistance development by improving its potency and eliminating the development of resistance in a combination treatment. This work represents a significant step towards combatting antimicrobial resistance.

bioengineering↗

bioRxiv2024

Glassy Surfactants Enable Ultra-High Concentration Biologic Therapeutics

Protein therapeutics, like peptides and antibodies, have become critical to healthcare. Despite their exceptional potency and specificity, biopharmaceuticals are prone to aggregation, often necessitating low formulation concentrations as well as cold storage and distribution to maintain stability. Yet, high doses are required to treat many diseases. To achieve these doses, most approved protein drug products are administered intravenously, imposing excessive burdens on patients and the healthcare system. New approaches are needed to formulate proteins at high concentrations to enable less burdensome subcutaneous injection, preferably in an autoinjector format. To address this challenge, we report a subcutaneously injectable biotherapeutic delivery platform composed of spray-dried protein microparticles suspended in a non-solvent liquid carrier. These microparticles contain only active biopharmaceutical agent and a high glass transition temperature polyacrylamide-derived copolymer excipient affording several key benefits over traditional excipients, including: (i) improved stabilization of biopharmaceuticals through the spray drying process, and (ii) improved morphology and properties of the spray-dried particles, enhancing suspension injectability. Experiments with albumin and antibodies demonstrate that this technology enables ultra-high-concentration protein formulations (exceeding 500 mg/mL) that are injectable through standard needles with clinically relevant injection forces. Additionally, experiments in mice with two clinically relevant antibody drugs show these ultra-high- concentration formulations reduce required injection volumes without altering pharmacokinetics or efficacy. This approach could nearly triple the number of commercial protein drugs amenable to subcutaneous administration, dramatically reducing burden and improving access to these critical biopharmaceuticals. One Sentence SummaryHere we leverage a unique copolymer excipient to enable ultra-high concentration protein formulations with improved stability and amenable to subcutaneous injection that can reduce patient burden, lower costs, and improve access to critical drugs.

bioengineering↗

bioRxiv2024

GageTracker: a tool for dating gene age by micro- and macro-synteny with high speed and accuracy

With the advent of the Earth Genome Project, an increasing number of species' genomes presents exciting opportunities for exploring genetic and phenotypic diversity in organisms. Determining the origin time of genes facilitates the elucidation of crucial genetic mechanisms underlying significant biological evolutionary questions such as the transition from aquatic to terrestrial life, the emergence of mammals, the origin of humans, as well as the development of species- or lineage-specific traits. However, accurately determining the origin time of these genes in species separated by long evolutionary distances remains a major challenge in bioinformatics as these genes often undergo significant changes in their genome sequences, making it difficult to trace them back to their origin. Here, we proposed a new approach for dating gene age based on the micro- and macro-synteny algorithms. This approach employs the parallel computation of orthologous genome alignments across multiple species. Our method was integrated into the GageTracker (Gene Age Tracker) software, providing a fast and accurate way to trace gene age with minimal user input, available at https://github.com/RiversDong/GageTracker. Benchmarked against the simMammals dataset (Alignathon), GageTracker achieved the same high-quality genome alignments as the optimized LastZ aligner, but improved operation speed by 1.4-7 times. In a separate analysis of 12 Drosophila genomes, GageTracker efficiently assessed the ages of 23,720 genes (including ~13,965 protein-coding genes) in just ~22 hours with default parameters. When comparing with the GenTree database (recognized as the most comprehensive and accurate tool for evaluating gene age), GageTracker achieved an impressive ~94.4% accuracy and ~99% macro consistency in assessing the age of protein-coding genes. Moreover, for the ~5.6% conflicting genes, GageTracker displayed slightly higher support rates than GenTree, as evidenced by data from OrthoDB, FlyBase, and Ensembl ortholog databases. Notably, younger genes identified by GageTracker exhibited a preferential expression pattern in the testis, further reinforcing the reliability of GageTracker in accurately tracing gene age.

bioinformatics↗

bioRxiv2024

Dynorphin modulates motivation through a pallido-amygdala cholinergic circuit

The endogenous opioid peptide dynorphin and its receptor {kappa}-opioid receptor (KOR) have been implicated in divergent behaviors, but the underlying mechanisms remain elusive. Here we show that dynorphin released from nucleus accumbens dynorphinergic neurons exerts powerful modulation over a ventral pallidum (VP) disinhibitory circuit, thereby controlling cholinergic transmission to the amygdala and motivational drive in mice. On one hand, dynorphin acts postsynaptically via KORs on local GABAergic neurons in the VP to promote disinhibition of cholinergic neurons, which release acetylcholine into the amygdala to invigorate reward-seeking behaviors. On the other hand, dynorphin also acts presynaptically via KORs on dynorphinergic terminals to limit its own release. Such autoinhibition keeps cholinergic neurons from prolonged activation and release of acetylcholine, and prevents perseverant reward seeking. Our study reveals how dynorphin exquisitely modulate motivation through cholinergic system, and provides an explanation for why these neuromodulators are involved in motivational disorders, including depression and addiction.

neuroscience↗

bioRxiv2024

Specific pre-plasma cell states and local proliferation at the dark zone - medulla interface characterize germinal center-derived plasma cell differentiation in lymph node

High affinity antibody-producing plasma cells (PC) generated in germinal centers (GC) are crucial for durable immunity after vaccination or infection. The selection of high affinity B cells in the GC light zone instructs PC differentiation in a subset of cells, but the cellular transitions and spatial organization of GC to PC differentiation remain poorly understood. Here, we have used a mouse model to track GC-derived B cells with integrative single-cell and spatial analyses in draining lymph node after immunization or infection. We first identified putative PrePC cells in scRNA-seq datasets, then enriched those cells through their specific surface phenotype for further analysis of their gene expression trajectories and BCR repertoire. We found a continuum of actively proliferating transitional states bridging selected LZ GC B cells and recently exported PCs, with gradually increasing levels of endoplasmic reticulum stress-associated genes and Ig transcripts. Spatial analyses revealed that recently differentiated PC continued their maturation and affinity-restricted proliferation at a previously uncharacterized interface between the DZ and extensions of the lymph node medulla. Our findings provide insights into the intermediate stages and microenvironmental factors involved in the differentiation of GC B cells into PC, with implications for vaccine development and understanding antibody responses.

immunology↗

bioRxiv2024

Longevity or Well-being? A Dual-Dimension Structure of Neuroticism

The development of personality traits is often viewed as evolutionarily adaptive. Current neuroticism research, however, predominantly highlights its negative health impacts, neglecting its potential evolutionary advantages. We propose that neuroticisms inter-individual variability can be structured into two distinct geometric dimensions. One, named the Emotional Reactivity-Instability/Distress Spectrum (ERIS), correlates strongly with longevity and is associated with chronic diseases and risk-averse lifestyle. This dimension is underpinned by evolutionarily conserved subcortical brain regions and genes. The other, resembling the overall neuroticism score, is primarily linked to mental and stress-related disorders, as well as life satisfaction. It involves higher-order emotional brain regions and is genetically enriched in human-accelerated regions. Collectively, these dimensions represent a dual-strategy personality framework that optimizes survival and well-being, with the former being evolutionarily conservative and the latter potentially a unique human adaptation.

neuroscience↗

bioRxiv2024

Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs

Emerging immunotherapies such as immune checkpoint blockade (ICB) and chimeric antigen receptor T-cell (CAR-T) therapy have revolutionized cancer treatment and have improved the survival of patients with multiple cancer types. Despite this success many patients are unresponsive to these treatments or relapse following treatment. CRISPR activation and knockout (KO) screens have been used to identify novel single gene targets that can enhance effector T cell function and promote immune cell targeting and eradication of tumors. However, cancer cells often employ multiple genes to promote an immunosuppressive pathway and thus modulating individual genes often has a limited effect. Paralogs are genes that originate from common ancestors and retain similar functions. They often have complex effects on a particular phenotype depending on factors like gene family similarity, each individual genes expression and the physiological or pathological context. Some paralogs exhibit synthetic lethal interactions in cancer cell survival; however, a thorough investigation of paralog pairs that could enhance the efficacy of cancer immunotherapy is lacking. Here we introduce a sensitive computational approach that uses sgRNA sets enrichment analysis to identify cancer-intrinsic paralog pairs which have the potential to synergistically enhance T cell-mediated tumor destruction. We have further developed an ensemble learning model that uses an XGBoost classifier and incorporates features such as gene characteristics, sequence and structural similarities, protein-protein interaction (PPI) networks, and gene coevolution data to predict paralog pairs that are likely to enhance immunotherapy efficacy. We experimentally validated the functional significance of these predicted paralog pairs using double knockout (DKO) of identified paralog gene pairs as compared to single gene knockouts (SKOs). These data and analyses collectively provide a sensitive approach to identify previously undetected paralog pairs that can enhance cancer immunotherapy even when individual genes within the pair has a limited effect.

bioinformatics↗

bioRxiv2024

Endogenous opioid dynamics in the dorsal striatum sculpt neural activity to control goal-directed action

Endogenous neuropeptides are uniquely poised to regulate neuronal activity and behavior across multiple timescales. Traditional studies ascribing neuropeptide contributions to behavior lack spatiotemporal precision. The endogenous opioid dynorphin is highly enriched in the dorsal striatum, known to be critical for regulating goal-directed behavior. However, the locus, the precise timescale, or functional role of endogenous dyn-KOR signaling on goal-directed behavior is unknown. Here, we report that local, time-locked dynorphin release from the dorsomedial striatum is necessary and sufficient for goal-directed behavior using a suite of high resolution modern approaches including in vivo two-photon imaging, neuropeptide biosensor detection, conditional deletions and time-locked optogenetic manipulations. We discovered that glutamatergic axon terminals from the basolateral amygdala evoke striatal dynorphin release, resulting in retrograde presynaptic GPCR inhibition during behavior. Collectively, our findings isolate a causal role for endogenous neuropeptide release at rapid timescales, and subsequent GPCR activity for tuning and promoting fundamental goal-directed behaviors.

neuroscience↗

bioRxiv2024

Construction of a breast cancer predictive nomogram based on diverse cell death methods and reveal tumor microenvironment characterization

ObjectiveTo develop a robust predictive model and nomogram for breast cancer (BC) linked to genes associated with diverse cell death methods. MethodsThe prognostic model was constructed using the LASSO Cox method. Model performance was assessed using K-M analysis, ROC curves, and independent prognostic analysis. Subsequently, we constructed a nomogram and analyzed differences in tumor microenvironment and drug sensitivity between different subgroups. The enrichment of differentially expressed genes between different subgroups was assessed. Additionally, we overexpressed CD24 in BC cell lines to assess its impact on cellular proliferation using CCK8 assays, migration through scratch and transwell assays, and apoptosis via flow cytometry. ResultsA prognostic model comprising twelve genes (CREB3L1, SFRP1, SHARPIN, AIFM1, IL-18, CD24, EDA2R, CRIP1, XBP1, BCL2A1, NKX3-1, and NME5) was constructed. BC patients were categorized into different subgroups, with the low-risk subgroup demonstrating superior survival. Additionally, we constructed a nomogram. The nomogram was validated as a reliable independent predictor of outcome. The enrichment analyses imply a connection between patient risk and immune response. The low-risk subgroup had a higher TME score. Patients in the high-risk group had improved responses to lapatinib, BI-2536, OSI-027, and SB505124, while those in the low-risk subgroup showed improved sensitivity to axitinib, epirubicin, fulvestrant, and olaparib. Furthermore, CD24 overexpression was found to promote proliferation and migration, while inhibiting apoptosis. ConclusionThese findings contribute to the individualization of treatment and aid in uncovering the tumor microenvironment characterization for BC patients.

cancer biology↗

bioRxiv2024

Peripheral B Lymphocyte Serves as A Reservoir for The Persistently Covert Infection of Mandarinfish Siniperca chuatsi Ranavirus

Genus Ranavirus in family Iridoviridae is composed of large members with various genomic sizes and viral gene contents, infecting a variety of ectothermic vertebrates including reptile, amphibians and bony fish worldwide. Mandarinfish ranavirus (MRV) is a very distinctive member among genus Ranavirus. Persistently convert infection of MRV were previously observed in natural outbreak of MRV, but the underlying mechanism remains unclear. We here evidenced that mandarinfish peripheral B lymphocytes are implemented as viral reservoirs to maintain persistent and covert infection. When mandarinfish were infected with sublethal dosage of MRV under nonpermissive temperature (19 {o}C) and permissive temperature (26 {o}C), respectively, all fish in 19 {o}C group survived and entered persistent phase of infection characterized with very low viral load in white blood cell, whereas partial fish died of MRV infection in 26 {o}C group, and the survivals then initiated persistent status. Gradually raising temperature, vaccination and dexamethasone treatment can reactivate the quiescent MRV to replicate and result in partial mortality. The viral reservoir investigates showed that IgM+-labelled B lymphocytes but not CD3{Delta}+-labelled T lymphocytes and MRC-1+-labelled macrophages are target cells for the persistent infection of MRV. Moreover, the quiescent MRV could not be reactivated by heat-killed Escherichia coli, indicating a very different reactivation mechanism from that of other known rannaviral member. Collectively, we are the first to confirm the presence of B cell-dependent persistent and covert infection of ranavirus, and provide a new clue for better understanding the complex infection mechanism of vertebrate iridovirus, especially regarding ranavirus. IMPORTANCEViruses known as HIV, HBV and EBV etc. evade host immune clearance by establishing long-term even lifelong persistent or latent infection. In vertebrate iridovirus, FV3, the type species of genus Ranavirus was evidenced to establish persistent infection by using Xenopus peritoneal macrophages as reservoirs. MRV is a very distinctive ranavirus from FV3 with very different genomic content and host species. We here uncovered MRV establishes persistent and covert infection by using peripheral B lymphocytes as virus reservoirs. During persistent infection, very low copies of quiescent MRV were harbored in peripheral B lymphocytes. Water temperature stress, vaccination stimulation, and dexamethasone treatment can reactivate quiescent MRV to replicate in abundance via a non-TLR5-mediated manner, and results in recurrence of MRV disease. Our finding suggests the diversity and complexity of the pathogenic mechanisms among ranaviruses, and also has important scientific significance for in-depth understanding of the infection and immunity interaction of vertebrate iridoviruses.

microbiology↗