Biology subjects

Jing, W.

Publications and source records attributed to Jing, W..

15 recordsLinked to original sources

bioRxiv2026

Daikenchuto modulates gut microbial metabolism to mitigate irinotecan-induced enterotoxicity

Gut microbiota metabolic remodeling is a pivotal determinant in irinotecan-induced enterotoxicity and epithelial damage, although the underlying mechanisms remain unclear. Herein, we discovered that Daikenchuto (DKT), a traditional Chinese prescription for intestinal disorders, alleviated irinotecan-induced enterotoxicity without compromising its anti-tumor efficacy by improving weight loss, diarrhea, intestinal inflammation, and barrier damage, and these effects were partially dependent on gut microbiota. DKT significantly restored microbial tryptophan metabolism in irinotecan-treated rats, which was characterized by the enrichment of Limosilactobacillus reuteri, and elevated levels of indole-3-ethanol (IE) and indole-3-propionic acid (IPA). Multi-omics analysis further revealed a positive correlation between L. reuteri and IE and IPA. Consistent with this, DKT promoted L. reuteri proliferation, leading to the conversion of tryptophan to IE and IPA, which improved epithelial barrier damage in the irinotecan-treated Caco-2 cells. In addition, DKT suppressed the growth of Loop 1 {beta}-glucuronidase ({beta}-GUS)-producing bacteria, such as Escherichia coli. Furthermore, the main constituents of DKT selectively inhibited Loop 1 {beta}-GUS activity independent of the gut microbiota, which reduced the intra-luminal level of 7-ethyl-10-hydroxycamptothecin, the toxic metabolite of irinotecan. Taken together, this study reveals a dual gut microbiota-driven mechanism by which DKT mitigates irinotecan-induced enterotoxicity, which provides a promising strategy for managing chemotherapy-related enterotoxicity.

pharmacology and toxicology↗

bioRxiv2025

ODFormer: a Virtual Organoid for Predicting Personalized Therapeutic Responses in Pancreatic Cancer

Pancreatic cancer (PC) patient-derived organoids (PDOs) faithfully recapitulate therapeutic responses but face clinical translation barriers, including high costs and technical complexity. To address these problems and the lack of frameworks for PDO-based drug-response assays, we developed ODFormer, a computational framework that simulates PC PDOs to predict clinically actionable, patient-specific drug responses by integrating transcriptomic and mutational profiles. ODFormer first employed two encoders, pretrained on 30,000 pan-cancer bulk transcriptomics and 1 million PC single-cell profiles respectively, to distil tissue-and organoid-specific representations. Then, trained on our curated 14,000 PDO drug-response assay (across 183 PDOs and 98 drugs) using a transformer-augmented hybrid contrastive network, ODFormer significantly outperformed state-of-the-art methods, notably achieving a PCC >0.9 in predicting standardized drug response. Multi-cohort retrospective analyses further demonstrated that ODFormer-guided personalized therapy significantly improves clinical outcomes, without requiring physical organoid assays. Furthermore, ODFormer identified novel clinico-biological PC subtypes and revealed therapy resistance biomarkers by stratifying predicted responders and non-responders. These were validated using independent datasets including TCGA-PDAC. Notably, ODFormer-guided treatment efficacy showed high concordance with prospective clinical responses by CA19-9.

bioinformatics↗

bioRxiv2025

INHBA promotes the progression of gastric cancer by activating MAPK signaling pathway via targeting ITGA6

Gastric cancer (GC) is one of the most common malignancies, ranking as the fifth most common cancer and the fourth leading cause among cancer related deaths worldwide. Upregulated INHBA expression in gastric cancer tissues compared to adjacent non-cancerous tissues was confirmed by immunohistochemistry and qRT-PCR analysis. This increased expression of INHBA was found to be significantly associated with the incidence of tumor lesion, lymph node metastasis and the progression to more advanced TNM stages in patients. Functional experiments showed that INHBA could promote the proliferation of GC cells, enhance migration and invasion in vitro, while simultaneously facilitating the inhibition of apoptosis. To test whether INHBA regulated the tumor growth in vivo, the animal studies were performed. The indicated that INHBA over-expression promoted the tumor growth, including weight and volume. Moreover, this study demonstrated through a series of experiments including RNA-seq, Co-IP, Co-IF, Western blot, and Rescue studies that INHBA promotes the progression of GC by targeting ITGA6 to regulate the MAPK signaling pathway. In summary, understanding the role of INHBA/ITGA6/MAPK in tumourigenesis could provide new insights into gastric cancer therapy and targeted inhibition of INHBA might be a potential therapeutic approach for GC treatment.

cancer biology↗

bioRxiv2025

Amoebicidal Action of Licorice-Derived Compounds: Mechanisms and Effects Against Acanthamoeba castellanii

BackgroundAcanthamoeba is a widely distributed unicellular eukaryotic organism, causing Acanthamoeba keratitis, granulomatous amoebic encephalitis and chronic infectious ulcers. At present, there are no effective drugs available for treating Acanthamoeba infections, highlighting the urgent need for the development of novel anti-Acanthamoeba therapies. PurposeThis study aims to investigate the inhibitory effect of licorice on A. castellanii trophozoites growth and elucidate its molecular mechanisms. MethodsThe effect of licorice on trophozoite viability was assessed employing the CellTiter-Glo assay, while the viability of cells was evaluated via CCK-8 assay. Apoptotic cells were identified through Hoechst 33,342/PI double staining and caspase-3 detection. ROS level was measured via flow cytometry utilising DCFH-DA. Mitochondrial dysfunction was analysed with JC-1 and mtSOX Deep Red staining. RNA sequencing and RT-qPCR analysis were conducted to investigate the potential anti-Acanthamoeba mechanism. ResultsOur results showed that isoliquiritigenin (ISL) and glabridin (GLA) effectively inhibited A. castellaniitrophozoite growth in vitro dose-and time-dependently. ISL and GLA induced several apoptosis features, including Hoechst/PI-positive staining and increased caspase-3 expression. ISL and GLA increased intracellular ROS production, decreased SOD expression and mitochondrial membrane potential and enhanced mitochondrial ROS generation. ISL and GLA effectively prevent host cells from A. castellanii trophozoites invasion. RNA sequencing indicated that ISL may modulate the NAD+ metabolic process, while GLA may influence the sterol metabolic process. ISL reduced the NAD+/NADH ratio, while GLA lowered the levels of 7-dehydrocholesterol in A. castellanii trophozoites. ConclusionThese findings suggest that ISL and GLA may serve as the active components of licorice for treating A. castellanii trophozoites. Our findings suggest that ISL suppresses trophozoites by regulating NAD+ metabolism, while GLA inhibits trophozoites through the regulation of sterol metabolism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/638758v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e3ec1borg.highwire.dtl.DTLVardef@a212d2org.highwire.dtl.DTLVardef@81b710org.highwire.dtl.DTLVardef@19b003_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Systematic Investigation of Double Emulsion Dewetting Dynamics for the Droplet Microfluidic Production of Giant Unilamellar Vesicles (GUVs) under Biocompatible Conditions

Giant unilamellar vesicles (GUVs) embody biomimetic membranes with compartmentalization that serve not only as simplified models to better understand complex biochemical and biophysical processes, but also as a chassis for the bottom-up assembly of synthetic cells. Recently, double emulsion droplet microfluidics has proven to be a promising platform for their production, offering greater throughput, control, and reproducibility over traditional methods. However, the interplay of parameters--particularly under biocompatible conditions--that influence the complex multiphase fluid dynamics of the dewetting process underlying GUV production has not been thoroughly studied, limiting the democratization of the approach. In this study, we systematically investigate how lipid composition and concentration, aqueous phase conditions, droplet confinement, and fluid dynamics effects promote or impede the dewetting process. We show that the prevalent use of high concentrations of glycerol and P188 are unnecessary, and the altered dewetting dynamics with restricted surfactant usage can be tuned by adjusting chip dimensions and multi-phase compositions. Guided by these findings, we achieved robust, high throughput production of monodisperse GUVs using 0.1% P188 and no glycerol with salts. Our results improve the reliability and accessibility of droplet-microfluidics GUV platforms to catalyze advances in biophysics, synthetic biology, and drug discovery.

synthetic biology↗

bioRxiv2024

Neurodevelopmental deviations in schizophrenia: Evidences from multimodal connectome-based brain ages

BackgroundPathologic schizophrenia process originate early in brain development, leading to detectable brain alterations via structural and functional magnetic resonance imaging (MRI). Recent MRI studies have sought to characterize disease effects from a brain age perspective, but developmental deviations from the typical brain age trajectory in youths with schizophrenia remain unestablished. AimThis study investigated brain development deviations in early-onset schizophrenia (EOS) patients by applying machine learning algorithms to structural and functional MRI data. MethodsMultimodal MRI data, including T1-weighted MRI (T1w-MRI), diffusion MRI, and resting-state functional MRI (rs-fMRI) data, were collected from 80 antipsychotic-naive first-episode EOS patients and 91 typically developing (TD) controls. The morphometric similarity connectome (MSC), structural connectome (SC), and functional connectome (FC) were separately constructed by using these three modalities. According to these connectivity features, eight brain age estimation models were first trained with the TD group, the best of which was then used to predict brain ages in patients. Individual brain age gaps (BAGs) were assessed as brain ages minus chronological ages. ResultsBoth the SC and MSC features performed well in brain age estimation, whereas the FC features did not. Compared with the TD controls, the EOS patients presented widened structural BAGs, with opposite trends between childhood and adolescence. These increased absolute BAG scores for EOS patients were positively correlated with the severity of their clinical symptoms. ConclusionThese findings from a multimodal brain age perspective suggest that advanced BAGs exist early in youths with schizophrenia.

neuroscience↗

bioRxiv2024

Nitroxoline evidence Amoebicidal Activity against Acanthamoeba castellanii through DNA damage and the stress response pathways

Acanthamoeba castellanii is a widespread unicellular eukaryote found in diverse environments, including tap water, soil, and swimming pools. It is responsible for severe infections, such as Acanthamoeba keratitis and granulomatous amebic encephalitis, particularly in individuals with immunocompromisation. The ability of protozoans to form dormant cysts complicates treatment, as current therapies are ineffective against cyst stages and suffer from poor specificity and side effects. Nitroxoline, a quinoline derivative with well-established antibacterial, antifungal, and antiviral properties, is a promising therapeutic candidate. This study aimed to elucidate cellular signalling events that counteract the effects of nitroxoline. In this study, nitroxoline significantly reduced the viability of A. castellanii trophozoites in a dose- and time-dependent manner, inducing morphological changes and apoptosis. Transcriptomic analysis revealed substantial alterations in gene expression, including enrichment of metabolic pathways, DNA damage responses, and iron ion binding. Nitroxoline treatment upregulated genes involved in DNA repair and oxidative stress response while regulating genes in the methionine and cysteine cycles. It also decreased the mitochondrial membrane potential, H2S production, and total iron amount in A. castellanii. Bioinformatics analyses and molecular docking studies suggest direct interactions between nitroxoline and A. castellanii proteins. Our research provides a comprehensive molecular map of the response of A. castellanii to nitroxoline, revealing significant changes in gene expression related to the stress response and metabolic pathways. These findings underscore the potential of nitroxoline as a potent anti-Acanthamoeba agent, offering new insights into its mechanism of action and paving the way for effective therapeutic strategies.

microbiology↗

bioRxiv2024

Drop-by-drop Addition of Reagents to a Double Emulsion

Developments in droplet microfluidic assays have facilitated an era of high-throughput, sensitive single-cell, or single-molecule measurements capable of tackling the heterogeneity present in biological systems. Relying on single emulsion (SE) compartments, droplet assays achieve absolute quantification of nucleic acids, massively parallel single-cell profiling, identification of rare variants, and more. Double emulsions (DEs) have seen new interest in recent years for their potential to enable new droplet assays and build upon SE techniques. DEs are compatible with flow cytometry enabling high-throughput multi-parameter drop screening and eliminate content mixing due to coalescence during lengthy workflows, addressing inherent limitations of SEs. Despite these strengths, DEs lack important technical functions that exist in SEs such as picoinjection or any other method for adding reagents to droplets on demand. Consequently, DEs cannot be used for multistep workflows which has limited their adoption in assay development. Here, we report a simple device achieving picoinjection of DEs. We developed strategies to enable active manipulations on DEs by converting DE inputs to SEs on chip. The released aqueous cores of the DE can be manipulated using existing SE techniques, such as reagent addition, before reforming a DE at the outlet. We identified device designs and operation conditions achieving drop-by-drop reagent addition to DEs and used it as part of a muti-step aptamer screening assay performed entirely in DE drops. This work enables the further development of multistep DE droplet assays.

bioengineering↗

bioRxiv2023

Rice potassium transporter OsHAK18 mediates phloem K+ loading and redistribution

High-Affinity K+ transporters/K+ Uptake Permeases/K+ Transporters (HAK/KUP/KT) are important pathways mediating K+ transport across cell membrane, which function in maintaining K+ homeostasis during plant growth and stress response. An increasing number of studies have shown that HAK/KUP/KT transporters play important roles in potassium uptake and root-to-shoot translocation. However, whether some HAK/KUP/KT transporters mediate K+ redistribution in phloem remains unknown. In this study, we revealed that a phloem-localized HAK/KUP/KT transporter, OsHAK18 operated as a typical KUP/HAK/KT transporter mediating cell K+ uptake when expressed in yeast, E. coli and Arabidopsis. It was localized at plasma membrane. Disruption of OsHAK18 rendered rice seedlings insensitive to low-K+ stress. Compared with WT, the oshak18 mutants accumulated more K+ in shoots but less K+ in roots, leading to a higher shoot/root ratio of K+ per plant. Although disruption of OsHAK18 doesnt affect root K+ uptake and K+ level in xylem sap, it significantly decreases phloem K+ concentration and inhibits root-to-shoot-to-root K+ translocation in split-root assay. These results reveal that OsHAK18 mediates phloem K+ loading and redistribution, whose disruption is favor of shoot K+ retention under low-K+ stress. Our findings not only reveal a unique function of rice HAK/KUP/KT family member, but also provide a promising strategy to improve rice tolerance under K+ deficiency.

plant biology↗

bioRxiv2022

Changes of urinary proteome in an ApoE-/- mouse model of atherosclerosis

Cardiovascular disease is currently the leading cause of death worldwide. Atherosclerosis is an important pathological basis of cardiovascular disease, and its early diagnosis is of great significance. Urine is more conducive in the accumulation and response of changes in the physiological state of the body and is not regulated by homeostasis mechanisms, so it is a good source of biomarkers in the early stage of disease. In this study, ApoE-/- mice were fed with a high-fat diet for 5 months. Urine samples from the experimental group and control group, which were C57BL/6 mice fed a normal diet, were collected at seven time points. Proteomic analysis was used for internalcontrol and intergroup control. Internal control results showed a significant difference in the urinary proteome before and after a 1-week high-fat diet, and several differential proteins have been reported to be associated with atherosclerosis or for use as candidate biomarkers. The results of the intergroup control indicated that the biological process enriched by the GO analysis of the differential proteins corresponded to the progression of atherosclerosis. Differences in chemical modifications of urinary proteins have also been reported to be associated with the disease. This study demonstrates that urinary proteomics has the potential to monitor changes in the body sensitively and provides the possibility of identifying early biomarkers of atherosclerosis.

biochemistry↗

bioRxiv2021

Three-dimensional tracking of tethered particles for probing nanometer-scale single-molecule dynamics using plasmonic microscope

Three-dimensional (3D) tracking of surface-tethered single-particle reveals the dynamics of the molecular tether. However, most 3D tracking techniques lack precision, especially in axial direction, for measuring the dynamics of biomolecules with spatial scale of several nanometers. Here we present a plasmonic imaging technique that can track the motion of [~]100 tethered particles in 3D simultaneously with sub-nanometer axial precision at millisecond time resolution. By tracking the 3D coordinates of tethered particle with high spatial resolution, we are able to determine the dynamics of single short DNA and study its interaction with enzyme. We further show that the particle motion pattern can be used to identify specific and non-specific interactions in immunoassays. We anticipate that our 3D tracking technique can contribute to the understanding of molecular dynamics and interactions at the single-molecule level.

biophysics↗

bioRxiv2020

Induction of core symptoms of autism spectrum disorders by in vivo CRISPR/Cas9-based gene editing in the brain of adolescent rhesus monkeys

Although CRISPR/Cas9 mediated gene editing is widely applied to mimic human disorders, whether acute manipulation of disease causing genes in the brain leads to behavioral abnormalities in non human primates remains to be determined. Here we induced genetic mutations in MECP2, a critical gene linked to Rett syndrome (RTT) and autism spectrum disorders (ASDs), in the hippocampus (DG and CA1~4) of adolescent rhesus monkeys (Macaca mulatta) in vivo via adeno associated virus (AAV) delivered Staphylococcus aureus Cas9 with sgRNAs targeting MECP2. In comparison to monkeys injected with AAV-SaCas9 alone (n = 4), numerous autistic-like behavioral abnormalities were identified in the AAV~SaCas9~sgMECP2 injected monkeys (n = 7), including social interaction deficits, abnormal sleep patterns, insensitivity to aversive stimuli, abnormal hand motions and defective social reward behaviors. Furthermore, some aspects of ASDs and RTT, such as stereotypic behaviors, did not appear in the MECP2 gene-edited monkeys, suggesting that different brain areas likely contribute to distinct ASD symptoms. This study showed that acute manipulation of disease-causing genes via in vivo gene editing directly led to behavioral changes in adolescent primates, paving the way for the rapid generation of genetically engineered non-human primate models for neurobiological studies and therapeutic development.

neuroscience↗

bioRxiv2020

Dynamic Configuration of Coactive Micropatterns in the Default Mode Network during Wakefulness and Sleep

The default mode network (DMN) is a prominent intrinsic network that is observable in many mammalian brains. However, few studies have investigated the temporal dynamics of this network based on direct physiological recordings. Herein, we addressed this issue by characterizing the dynamics of local field potentials (LFPs) from the rat DMN during wakefulness and sleep with an exploratory analysis. We constructed a novel coactive micropattern (CAMP) algorithm to evaluate the configurations of rat DMN dynamics and further revealed the relationship between DMN dynamics with different wakefulness and alertness levels. From the gamma activity (40-80 Hz) in the DMN across wakefulness and sleep, three spatially stable CAMPs were detected: a common low-activity level micropattern (cDMN), an anterior high-activity level micropattern (aDMN) and a posterior high-activity level micropattern (pDMN). A dynamic balance across CAMPs emerged during wakefulness and was disrupted in sleep stages. In the slow-wave sleep (SWS) stage, cDMN became the primary activity pattern, whereas aDMN and pDMN were the major activity patterns in the rapid eye movement sleep (REM) stage. Additionally, further investigation revealed phasic relationships between CAMPs and the up-down states of the slow DMN activity in the SWS stage. Our study revealed that the dynamic configurations of CAMPs were highly associated with different stages of wakefulness and provided a potential three-state model to describe the DMN dynamics for wakefulness and alertness. Impact StatementIn the current study, a novel coactive micropattern method (CAMP) was developed to elucidate fast DMN dynamics during wakefulness and sleep. Our findings demonstrated that the dynamic configurations of DMN activity are specific to different wakefulness stages and provided a three-state DMN CAMP model to depict wakefulness levels, thus revealing a potentially new neurophysiological representation of alertness levels. This work could elucidate the DMN dynamics underlying different stages of wakefulness and have important implications for the theoretical understanding of the neural mechanism of wakefulness and alertness.

bioinformatics↗

bioRxiv2019

Moxifloxacin efficacy against Mycobacterium abscessus in vivo using zebrafish model

Moxifloxacin (MFX) showed good activity in vitro against Mycobacterium abscessus (M. abscessus) and was suggested as one of the antibiotic regimens for adults with M. abscessus disease. However, some other studies showed that MFX showed less or none activity against M. abscessus. In our study we aim to evaluate MFX activity against M. abscessus using zebrafish (ZF) model in vivo. MIC of each drugs were determined by broth microdilution method. M. abscessus labeled by CM-DiI, were micro-injected into ZF. Survival curves were determined by recording dead ZF every day. After 4 days of incubation ZF were lysed. Colony-forming unit (CFU) were enumerated and results are expressed as mean log10 CFU per ZF. Bacteria dissemination and fluorescence intensity in ZF were observed and analyzed. Inhibition rate was also calculated. In our study MFX showed good activity in vitro. But in vivo MFX showed limited restriction to M. abscessus. The association between increased survival and high dose of MFX is not significant. Same results were observed in bacterial fluorescence intensity and inhibition rates, with no significant difference when compared with no drug group (P > 0.05). However, significant difference was observed in azithromycin (AZM) group. MFX showed limited efficacy on Mycobacterium abscessus in vivo using ZF model. MFXs activity in vivo need to be confirmed.

microbiology↗

bioRxiv2018

Time-resolved digital immunoassay for rapid and sensitive quantitation of procalcitonin with plasmonic imaging

Timely diagnosis of acute diseases improves treatment outcomes and saves lives, but it requires fast and precision quantification of biomarkers. Here we report a time-resolved digital immunoassay based on plasmonic imaging of binding of single nanoparticles to biomarkers captured on a sensor surface. The real-time and high contrast of plasmonic imaging lead to fast and precise counting of the individual biomarkers over a wide dynamic range. We demonstrated the detection principle, evaluated the performance of the method using procalcitonin (PCT) as an example, and achieved a limit of detection of ~ 3 pg/mL, dynamic range of 4-12500 pg/mL, for a total detection time of ~ 25 mins.

bioengineering↗