Biology subjects

Deng, X.

Publications and source records attributed to Deng, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Brucella proline racemase protein A targets Tpl2 to promote IL-10 secretion for establishment of chronic infection

IL-10, an anti-inflammatory cytokine, plays a crucial role in limiting immune responses to pathogens, preventing host damage. However, the mechanisms underlying Brucella-mediated IL- 10 production remain incompletely understood. In this study, we demonstrate that the proline racemase protein A (PrpA) of Brucella melitensis M5-90 induces macrophages to secrete IL-10 by activating the Tpl2-ERK signaling pathway, thereby promoting chronic infection. Moreover, Tpl2 deletion impairs macrophage bactericidal ability, accompanied by reduced TNF- and IL-1{beta} but unaffected IL-10 levels. Additionally, Trp309, Glu103, and Glu129 of PrpA participate in interaction with Tpl2, but these residues do not influence PrpA-mediated IL-10 production in macrophages. PrpA deletion enhances IFN-{gamma} levels, specific anti-Brucella IgG, and CD4+ and CD8+ T cell numbers in mice. Furthermore, the Brucella melitensis M5-90 prpA mutant provides higher protection than the parental strain against virulent Brucella melitensis M28 infection in mice. Our findings suggest that Brucella PrpA promotes IL-10 secretion by macrophages through Tpl2 activation for bacterial survival and persistent infection, making the Brucella melitensis M5-90 prpA mutant a promising vaccine for enhanced protection. Author SummaryIL-10, an anti-inflammatory cytokine, is exploited by Brucella for survival. We identified Brucella PrpA as a potent IL-10 inducer, activating the Tpl2-ERK signaling pathway. Tpl2 deletion increased Brucella survival in macrophages, accompanied by reduced TNF- and IL-1{beta} but unaffected IL-10 secretion. Residues (Trp309, Glu103, and Glu129) of PrpA were crucial for interaction with Tpl2, yet did not impact PrpA-mediated IL-10 production. The B. melitensis M5-90 prpA mutant induced higher anti-Brucella IgG, IFN-{gamma}, and CD4+ and CD8+ T cell numbers in mice, providing better protection than B. melitensis M5-90. These findings unveil PrpAs role in IL-10 production and highlight the potential of the B. melitensis M5-90 prpA mutant as a promising vaccine for further evaluation.

microbiology↗

bioRxiv2025

Enhanced Detection of RNA Modifications in Escherichia coli Utilizing Nanopore RNA004 Technology

RNA modifications are critical regulators of diverse cellular processes, yet their roles in prokaryotic mRNAs remain poorly understood. Recent advances in Oxford Nanopore sequencing--especially the RNA004 kit--have enabled higher yields, reduced signal-to-noise ratio, and improved read accuracy, making them promising tools for investigating bacterial epitranscriptomes. Here, we presented a comprehensive walkthrough for Escherichia coli RNA modification analysis based on RNA004. Using both native (WT) and in vitro-transcribed (IVT) RNA samples, we first evaluated the Dorado modification detection models ({Psi}, mA, mC, and A-to-I). While each model successfully identified known rRNA modification sites, it also generated many false positives, emphasizing the need for careful data interpretation. To address these limitations, we introduced nanoSundial (https://github.com/lrslab/nanoSundial), a new comparative method that leveraged raw current features from WT and IVT samples to detect multiple types of RNA modifications in prokaryotes. We optimized nanoSundial on well-studied rRNA sites and validated its effectiveness with tRNA modifications. Through technical and biological replicate analyses, nanoSundial demonstrated reproducibility exceeding 95% in tRNA, rRNA, and ncRNA regions, albeit with lower reproducibility ([~]61%) in mRNA. We further found enrichment of mRNA modifications at the start or end of coding sequences. In total, 190 stably modified CDS regions were identified in E. coli, many of which cluster near the end of highly expressed transcriptional units (TUs) in each operon. Overall, this study highlighted the strengths and limitations of current nanopore-based modification detection methods on bacterial RNA, introduced a robust new comparative tool, and elucidated previously uncharacterized mRNA modification landscapes. Our findings open new avenues for understanding the functional impacts of bacterial RNA modifications and advancing epitranscriptomic research in prokaryotes.

bioinformatics↗

bioRxiv2025

VZV gE Promotes STING Degradation via Midnolin-Proteasome Pathway to Inhibit cGAS-STING Signaling

Varicella-zoster virus (VZV) infects 85 million individuals annually and it is known for its intricate interplay with host cellular mechanisms, significantly impacting antiviral immune responses. Previous studies have highlighted the critical role of VZV glycoprotein E (gE) in virus-host interactions, but the precise mechanisms remain to be elucidated. Our results demonstrate that VZV gE interacts with STING, specifically through the gE (350-480aa) and STING (151-160aa) regions. This interaction predominantly involves incompletely glycosylated gE. Functional assays revealed that gE inhibits the cGAS-STING signaling pathway. gE enhances VZV proliferation and promotes STING degradation via the proteasome pathway, without affecting STING ubiquitination. We identified Midnolin as a mediator in this degradation process, with gE facilitating the interaction between STING and Midnolin. In vivo, gE expression in mice led to diminished antiviral responses upon HSV-1 infection, highlighting gEs role in modulating immune signaling. Our findings provide significant insights into VZVs evasion of host immune responses. By promoting STING degradation through an unconventional Midnolin-proteasome pathway, VZV gE effectively suppresses antiviral signaling, facilitating enhanced viral proliferation. The findings contribute significantly to the understanding of VZV pathogenesis and provide new therapeutic strategies against VZV.

microbiology↗

bioRxiv2025

Exosomal miR-145-5p promotes apoptosis of renal tubule epithelial cells through the JNK signalling pathway

Acute kidney injury (AKI) is the most prevalent extrapulmonary organ failure observed in patients with acute respiratory distress syndrome (ARDS). However, the underlying mechanisms leading to AKI in ARDS remain unclear. Exosomes facilitate intercellular and inter-organ communication via exosomal microRNAs (miRNAs), which potentially contribute to the crosstalk between the lung and kidney in ARDS. Therefore, the purposes of our study were to investigate the involvement of exosomal miRNAs in the development of AKI in ARDS. In current study, Sprague-Dawley rats were induced to develop ARDS via hydrochloric acid aspiration. Nanoparticle tracking analysis, Transmission electron microscopy and western blotting were conducted to analyse the exosomes. Quantitative reverse transcription-polymerase chain reaction and in situ hybridisation showed elevated expression level of miR-145-5p in the circulating exosomes and lung tissue of ARDS rats. Overexpression of miR-145-5p disrupted the proteomic profile of renal proximal tubule epithelial cells, leading to impacts on proteins associated with various biological processes, including apoptosis. We further demonstrate that miR-145-5p overexpression enhanced JNK phosphorylation by directly repressing RBM3 expression and promoted cell apoptosis. In vivo, administration of agomiR-145-5p injection via intravenous route, which subsequently induced renal tubular cell apoptosis. These findings have revealed that miR-145-5p may serve as a novel mediator for the apoptosis of renal cell in the context of ARDS.

cell biology↗

bioRxiv2025

Biochemical Profiling and Structural Basis of ADAR1-Mediated RNA Editing

ADAR1 is a pivotal regulator in RNA-induced immune responses by catalyzing the conversion of adenosine to inosine on double-stranded RNA. Mutations on ADAR1 are associated with human autoimmune disease, and targeting ADAR1 has been proposed for cancer immunotherapy. However, the molecular mechanisms governing ADAR1-mediated RNA editing remain enigmatic. Here, we provide detailed biochemical and structural characterizations of human ADAR1. Our biochemical profiling reveals that ADAR1 editing is both sequence and RNA duplex length-dependent, but can well tolerate mismatches near the editing site. Moreover, our high-resolution structures of ADAR1-RNA complexes, coupled with mutagenesis studies, revealed the molecular basis for RNA binding, substrate selection, dimerization, and the crucial role of the RNA-binding domain 3 for ADAR1 editing. The ADAR1 structures also help explain the potential defects of disease-associated mutations, where biochemical and RNA-sequencing analysis further indicate some of the mutations preferentially impact the editing of RNAs with short duplex. Our findings illustrate the molecular mechanism of ADAR1 editing and provide clues for deciphering its role in immune regulation and drug targeting. HIGHLIGHTSO_LIBiochemical profiling of ADAR1 RNA substrate preference C_LIO_LIAtomic resolution structures of ADAR1 with two physiological RNA substrates C_LIO_LIDisease-related mutations of ADAR1 preferentially impact RNA editing with short dsRNA. C_LIO_LIRNA-binding domain 3 is essential for ADAR1 RNA capture and editing C_LI

biochemistry↗

bioRxiv2024

AMPK acts to remove immune barriers to CD8+ T cell-mediated immunity against hepatocellular carcinoma

Dysregulated metabolism in tumor tissues, and para-tumor tissues alike, can lead to immunosuppression, which may underlie cancer development. However, metabolic intervention as a therapeutic strategy has been of no avail. In this study, we explored the anti-cancer therapeutic effect of aldometanib that specifically targets lysosome-associated aldolase to mimic glucose starvation and thereby activates the lysosomal AMP-activated protein kinase (AMPK), a master regulator of metabolic homeostasis. We show that aldometanib inhibits the growth of HCC in an AMPK-dependent manner, allowing hepatoma-bearing mice to survive to mature ages, although aldometanib does not possess cytotoxicity towards HCC or normal cells. Intriguingly, aldometanib exerts anti-cancer effects only in immune-competent host mice, but not in immune-defective mice. We have further found that the HCC tissues in aldometanib-treated mice are massively infiltrated with CD8+ T cells, which is not seen in mice with liver-specific knockout of AMPK. Our findings thus suggest that the metabolic regulator AMPK rebalances the tumor microenvironment to allow the cytotoxic immune cells inside the body to eliminate cancer cells and effectively contain the tumor tissues. The finding that metabolic intervention can make cancer a life-long manageable disease, may potentially usher in a new era of cancer therapy.

immunology↗

bioRxiv2024

Microbial Partner (MiPner) Analysis

Although a few bacteria have been studied in great depth, relatively little is known about the characteristics of microbe-microbe interactions that occur within ecosystems on a daily basis. A simple, robust technique was developed to set up the foundation for investigating pairwise bacterial-bacterial interactions, using cell-cell binding as a self-selective mechanism to identify interesting bacterial species pairs. Using a Serratia marcescens strain (SMC43) isolated from Georgia soil as a "bait", specific bacteria were purified by their specificity in binding SMC43 bacteria that were themselves attached to a wooden applicator stick. The isolated Microbial Partners (MiPners) were greatly enriched for members of the genera Sphingobium and Caulobacter. Two out of 24 streaked MiPners were unable to be separated from, and grow on the plate type tested without, SMC43. This suggests that the MiPner technology will be one strategy for purifying bacteria that were previously recalcitrant to culturing.

microbiology↗

bioRxiv2024

Slit regulates compartment-specific targeting of dendrites and axons in the Drosophila brain

Proper nervous system functioning requires axons or dendrites targeting to specific subcellular domains of target neurons to form precise connections. Using mushroom body output neurons (MBONs) and dopaminergic neurons (DAN) in the Drosophila mushroom body as a model, we demonstrate that subcellular-specific targeting of MBON dendrites and DAN axons is regulated by repulsion between their dendrites/axons in neighboring subcellular domains. We further show that Slit mediates such repulsion by binding to distinct Robo receptors in different neurons. Loss of Slit-mediated repulsion leads to expansion of MBON dendrites and DAN axons into neighboring compartments, formation of ectopic synapses, and altered learning and memory. Our findings reveal a critical role of Slit-mediated repulsion between neighboring compartments in regulating subcellular-specific dendrite and axon targeting.

neuroscience↗

bioRxiv2024

Ephrin-mediated dendrite-dendrite repulsion regulates compartment- specific targeting of dendrites in the central nervous system

Neurons often forms synaptic contacts at specific subcellular domains to differentially regulate the activity of target neurons. However, how dendrites are targeted to specific subcellular domains of axons is rarely studied. Here we use Drosophila mushroom body out neurons (MBONs) and local dopaminergic neurons (DANs) as a model system to study how dendrites and axons are targeted to specific subcellular domains (compartments) of mushroom body axonal lobes to form synaptic contacts. We found that Ephrin-mediated dendrite-dendrite repulsion between neighboring compartments restricts the projection of MBON dendrites to their specific compartments and prevents the formation of ectopic synaptic connections with DAN axons in neighboring compartments. Meanwhile, DAN neurons in a subset of compartments may also depend on their partner MBONs for projecting their axons to a specific compartment and cover the same territory as their partner MBON dendrites. Our work reveals that compartment-specific targeting of MBON dendrites and DAN axons is regulated in part by a combination of dendrite-dendrite repulsion between neighboring compartments and dendrite-axon interactions within the same compartment.

neuroscience↗

bioRxiv2024

Global transcription factors analyses reveal hierarchy and synergism of regulatory networks and master virulence regulators in Pseudomonas aeruginosa

The transcription factor (TF) regulatory network in Pseudomonas aeruginosa is complex and involves multiple regulators that respond to various environmental signals and physiological cues by regulating gene expression. However, the biological functions of at least half of its 373 putative TFs remain uncharacterised. Herein, chromatin immunoprecipitation sequencing (ChIP-seq) was used to investigate the binding sites of 172 TFs in the P. aeruginosa PAO1 strain. The results revealed 81,009 significant binding peaks in the genome, more than half of which were located in the promoter regions. To further decode the diverse regulatory relationships among TFs, a hierarchical network was assembled into three levels: top, middle, and bottom. Thirteen ternary regulatory motifs revealed flexible relationships among TFs in small hubs, and a comprehensive co-association atlas was established, showing the enrichment of seven core associated clusters. Twenty-four TFs were identified as the master regulators of virulence-related pathways. The pan-genome analysis revealed the conservation and evolution of TFs in P. aeruginosa complex and other species. A Web-based database combining existing and new data from ChIP-seq and the high-throughput systematic evolution of ligands by exponential enrichment was established for searching TF-binding sites. This study provides important insights into the pathogenic mechanisms of P. aeruginosa and related bacteria and is expected to contribute to the development of effective therapies for infectious diseases caused by this pathogen.

microbiology↗

bioRxiv2024

ConoDL: A Deep Learning Framework for Rapid Generation and Prediction of Conotoxins

Conotoxins, being small disulfide-rich and bioactive peptides, manifest notable pharmacological potential and find extensive applications. However, the exploration of conotoxins vast molecular space using traditional methods is severely limited, necessitating the urgent need of developing novel approaches. Recently, deep learning (DL)-based methods have advanced to the molecular generation of proteins and peptides. Nevertheless, the limited data and the intricate structure of conotoxins constrain the application of deep learning models in the generation of conotoxins. We propose ConoDL, a framework for the generation and prediction of conotoxins, comprising the end-to-end conotoxin generation model (ConoGen) and the conotoxin prediction model (ConoPred). ConoGen employs transfer learning and a large language model (LLM) to tackle the challenges in conotoxin generation. Meanwhile, ConoPred filters artificial conotoxins generated by ConoGen, narrowing down the scope for subsequent research. A comprehensive evaluation of the peptide properties at both sequence and structure levels indicates that the artificial conotoxins generated by ConoDL exhibit a certain degree of similarity to natural conotoxins. Furthermore, ConoDL has generated artificial conotoxins with novel cysteine scaffolds. Therefore, ConoDL may uncover new cysteine scaffolds and conotoxin molecules, facilitating further exploration of the molecular space of conotoxins and the discovery of pharmacologically active variants. The code is available at https://github.com/xueww/ConoDL.The supplementary material and model are available at https://zenodo.org/records/10679280.

bioinformatics↗

bioRxiv2024

Target protein identification in live cells and organisms with a non-diffusive proximity tagging system

Identifying target proteins for bioactive molecules is essential for understanding their mechanisms, developing improved derivatives, and minimizing off-target effects. Despite advances in target identification (target-ID) technologies, significant challenges remain, impeding drug development. Most target-ID methods use cell lysates, but maintaining an intact cellular context is vital for capturing specific drug-protein interactions, such as those with transient protein complexes and membrane-associated proteins. To address these limitations, we developed POST-IT (Pup-On-target for Small molecule Target Identification Technology), a non-diffusive proximity tagging system for live cells, orthogonal to the eukaryotic system. POST-IT utilizes an engineered fusion of proteasomal accessory factor A (PafA) and HaloTag to transfer Pup to proximal proteins upon directly binding to the small molecule. After significant optimization to eliminate self-pupylation and polypupylation, minimize depupylation, and optimize chemical linkers, POST-IT successfully identified known targets and discovered a new binder, SEPHS2, for dasatinib, and VPS37C as a new target for hydroxychloroquine, enhancing our understanding these drugs mechanisms of action. Furthermore, we demonstrated the application of POST-IT in live zebrafish embryos, highlighting its potential for broad biological research and drug development.

pharmacology and toxicology↗

bioRxiv2024

RNase III in Salmonella Enteritidis enhances bacterial virulence by reducing host immune responses

Salmonella is an important foodborne pathogen which comprises strains that exhibit varied virulence phenotypes and the capability of causing invasive human infection. In this study, the gene expression profile of foodborne and clinical Salmonella strains that exhibit high- and low-level virulence was investigated, with results showing that the expression level of a number of genes, including the rnc gene which encodes the RNase III ribonuclease, were exceptionally high in the high virulence strains. Investigation of the role of rnc in mediating expression of virulence phenotypes in Salmonella showed that the product of this gene could enhance expression of the superoxide dismutase SodA, which is an essential determinant of survival fitness of Salmonella under the oxidative stress elicited by the host immunity. On the other hand, we also discovered that the double-stranded RNA (dsRNA) released from Salmonella could trigger immune response of the host, and that the high-level expression of the rnc gene enabled Salmonella to evade the host immunity by reducing the amount of dsRNA accumulated in the bacterial cell. These findings provide insightful understanding of the regulation of Salmonella virulence and facilitate development of novel antimicrobial treatments through suppression of virulence expression and survival fitness of this important pathogen.

microbiology↗

bioRxiv2024

Blocking Toxin Function and Modulating the Gut Microbiota: Caffeic Acid and its Derivatives as Potential Treatments for Clostridioides difficile Infection

Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired diarrhea that seriously threatens public health. The disruption of normal gut microbiota by the use of broad-spectrum antimicrobial agents enables C. difficile to proliferate in the colon. The emergence and prevalence of hypervirulent C. difficile strains result in increased morbidity, mortality, and high recurrence rates of CDI, thus creating a pressing need for novel therapeutics. The multi-domain toxins TcdA and TcdB are the primary determinants of CDI pathogenesis, rendering them ideal drug targets in the anti-virulence paradigm. In this study, we identified caffeic acid and its derivatives from natural compounds library as active inhibitors of TcdB via a cell-based high-throughput phenotypic screening. Further mechanistic investigations revealed that caffeic acid phenethyl ester (CAPE) could directly bind to TcdB, thus suppressing InsP6-induced autoproteolysis and inhibiting glucosyltransferase activity. CAPE treatment remarkably reduces the pathology of CDI in a murine infection model in terms of alleviated diarrhea symptoms, decreased bacterial colonization, and relieved histopathological lesions. Moreover, CAPE treatment of C. difficile-challenged mice induces a remarkable increase in the diversity and composition of the gut microbiota and alterations of gut metabolites (e.g., adenosine, D-proline, and melatonin), which might partially contribute to the therapeutic outcomes of CAPE against CDI. Our results reveal the potential of CAPE as a therapeutic for the management of CDI, or CAPE might serve as a lead compound for the development of antivirulence drugs targeting TcdB.

microbiology↗

bioRxiv2024

Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in millions of deaths globally. Adults with immunosuppression (e.g., solid organ transplant recipients) and those undergoing active cancer treatments experience worse infections and more severe COVID-19. It is difficult to conduct clinical studies in these populations, resulting in a restricted amount of data that can be used to relate mechanisms of immune dysfunction to COVID-19 outcomes in these vulnerable groups. To study immune dynamics after infection with SARS-CoV-2 and to investigate drivers of COVID-19 severity in individuals with cancer and immunosuppression, we adapted our mathematical model of the immune response during COVID-19 and generated virtual patient cohorts of cancer and immunosuppressed patients. The cohorts of plausible patients recapitulated available longitudinal clinical data collected from patients in Montreal, Canada area hospitals. Our model predicted that both cancer and immunosuppressed virtual patients with severe COVID-19 had decreased CD8+ T cells, elevated interleukin-6 concentrations, and delayed type I interferon peaks compared to those with mild COVID-19 outcomes. Additionally, our results suggest that cancer patients experience higher viral loads (however, with no direct relation with severity), likely because of decreased initial neutrophil counts (i.e., neutropenia), a frequent toxic side effect of anti-cancer therapy. Furthermore, severe cancer and immunosuppressed virtual patients suffered a high degree of tissue damage associated with elevated neutrophils. Lastly, parameter values associated with monocyte recruitment by infected cells were found to be elevated in severe cancer and immunosuppressed patients with respect to the COVID-19 reference group. Together, our study highlights that dysfunction in type I interferon and CD8+ T cells are key drivers of immune dysregulation in COVID-19, particularly in cancer patients and immunosuppressed individuals.

immunology↗

bioRxiv2024

The big tau splice isoform resists Alzheimer's-related pathological changes

In Alzheimers disease (AD), the microtubule-binding protein tau becomes abnormally hyperphosphorylated and aggregated in selective brain regions such as the cortex and hippocampus1-3. However, other brain regions like the cerebellum and brain stem remain largely intact despite the universal expression of tau throughout the brain. Here, we found that an understudied splice isoform of tau termed "big tau" is significantly more abundant in the brain regions less vulnerable to tau pathology compared to tau pathology-vulnerable regions. We used various cellular and animal models to demonstrate that big tau possesses multiple properties that can resist AD-related pathological changes. Importantly, human AD patients show a higher expression level of pathology-resisting big tau in the cerebellum, the brain region spared from tau pathology. Our study examines the unique properties of big tau, expanding our current understanding of tau pathophysiology. Altogether, our data suggest that alternative splicing to favor big tau is a viable strategy to modulate tau pathology.

neuroscience↗

bioRxiv2024

Deficiency of m6A RNA methylation promotes ZBP1-mediated cell death

m6A RNA methylation suppresses the immunostimulatory potential of endogenous RNA. Deficiency of m6A provokes inflammatory responses and cell death, but the underlying mechanisms remain elusive. Here we showed that the noncoding RNA 7SK gains immunostimulatory potential upon m6A depletion and subsequently activates the RIG-I/MAVS axis to spark interferon (IFN) signaling cascades. Concomitant excess of IFN and m6A deficiency synergistically facilitate the formation of RNA G-quadruplexes (rG4) to promote ZBP1-mediated necroptotic cell death. Collectively, our findings delineate a hitherto uncharacterized mechanism that links m6A dysregulation with ZBP1 activity in triggering inflammatory cell death.

molecular biology↗

bioRxiv2024

Phosphoglycerate mutase regulates Treg differentiation through control of serine synthesis and one-carbon metabolism

The differentiation and suppressive functions of regulatory CD4 T cells (Tregs) are supported by a broad array of metabolic changes, providing potential therapeutic targets for immune modulation. In this study, we focused on the regulatory role of glycolytic enzymes in Tregs and identified phosphoglycerate mutase (PGAM) as being differentially overexpressed in Tregs and associated with a highly suppressive phenotype. Pharmacologic or genetic inhibition of PGAM reduced Treg differentiation and suppressive function while reciprocally inducing markers of a pro-inflammatory, T helper 17 (Th17)-like state. The regulatory role of PGAM was dependent on the contribution of 3-phosphoglycerate (3PG), the PGAM substrate, to de novo serine synthesis. Blocking de novo serine synthesis from 3PG reversed the effect of PGAM inhibition on Treg polarization, while exogenous serine directly inhibited Treg polarization. Additionally, altering serine levels in vivo with a serine/glycine-free diet increased peripheral Tregs and attenuated autoimmunity in a murine model of multiple sclerosis. Mechanistically, we found that serine limits Treg polarization by contributing to one-carbon metabolism and methylation of Treg-associated genes. Inhibiting one-carbon metabolism increased Treg polarization and suppressive function both in vitro and in vivo in a murine model of autoimmune colitis. Our study identifies a novel physiologic role for PGAM and highlights the metabolic interconnectivity between glycolysis, serine synthesis, one-carbon metabolism, and epigenetic regulation of Treg differentiation and suppressive function.

immunology↗