Biology subjects

Shu, Q.

Publications and source records attributed to Shu, Q..

14 recordsLinked to original sources

bioRxiv2026

Matrix stiffness shapes immunometabolic states and response to PD-1 blockade in gastric cancer

The extracellular matrix of solid tumors exhibits spatially heterogeneous stiffness, yet how matrix stiffness shapes antitumor immunity in gastric cancer (GC) remains unclear. Here, we integrated anti-PD-1 clinical cohorts, GC specimens, single-cell and spatial transcriptomic analyses, a syngeneic mouse model, and tunable-stiffness hydrogels to clarify the immunological consequences of matrix stiffness. High matrix stiffness was associated with collagen accumulation and immune exclusion, while higher stiffness-associated transcriptional scores were related to poorer response to PD-1 blockade. Matrix softening markedly reshaped the immune microenvironment and enhanced the efficacy of PD-1 blockade. Mechanistically, stiff matrices promoted F-actin remodeling and YAP nuclear enrichment, driving LDHA-dependent glycolytic reprogramming in GC cells that further impaired the effector function of CD8 T cells. Intriguingly, matrix softening was accompanied by enhanced IFN-{gamma}-responsive PD-L1 expression in GC cells, consistent with adaptive immune resistance that may contribute to the limited antitumor effects of matrix softening alone. These findings suggest that matrix remodeling alleviates spatial and metabolic constraints on antitumor immunity, providing a preclinical rationale for combining matrix softening with PD-1 blockade in GC.

cancer biology↗

bioRxiv2026

Xenon improves autism-like behaviors in mice through potentiation of PVT-CeA glutamatergic neurotransmission

Autism spectrum disorder (ASD) is a common neurodevelopmental disease with no currently effective treatments. In this study, Xenon (Xe), a noble gas used clinically as an anesthetic and a neuroprotectant, has been investigated for its potential therapeutic effects in ASD. Two genetic ASD mouse models (Mef2c mutant and Shank3-/- mice) were exposed to a low concentration of xenon (25%) mixed with oxygen (30%) and balanced with nitrogen for a single exposure of 30 min or for 10 min per day for 10 days. These Xe exposure paradigms rescued ASD-like behaviors in both male and female mice. The behavioral improvements persisted for up to 10 days following termination of the 10-day exposure paradigm. Mechanistically, Xe reduced glutamic acid decarboxylase expression in the inhibitory neurons (verified with RNAseq) of the paraventricular thalamic nucleus (PVT) and decreased GABA release during social interaction. Targeted infusion of the GABAA receptor agonist muscimol into the PVT abolished the Xe-mediated behavioral improvements. Reduced GABAergic transmission following Xe exposure increased PVT glutamatergic neuronal activity. Chemogenetic inhibition of these neurons eliminated the therapeutic effects of Xe, whereas chemogenetic activation mimicked the Xe-induced behavioral improvements. Furthermore, opto-inhibition of PVT glutamatergic projections to the central amygdala (CeA) blocked Xe-mediated behavioral improvement. Opto-activation of the PVT-CeA glutamatergic circuit reversed ASD-like behaviors. These findings demonstrate that Xe ameliorates ASD-like phenotypes in mouse models by modulating the PVT Glu-CeA circuit, supporting Xe as a novel potential therapy for ASD.

animal behavior and cognition↗

bioRxiv2026

Prenatal 3i-0777 treatment attenuates left ventricular hypertrabeculation and dysfunction in a retinoic acid-induced mouse model

Excessive left ventricular trabeculation and thinning of the compacted myocardium arise during cardiac development and may be accompanied by myocardial dysfunction. Gestational exposure to all-trans retinoic acid (ATRA) induces a comparable phenotype in mice, providing a model for evaluating prenatal pharmacological intervention. We examined whether 3i-0777, a small-molecule enhancer of GATA4-NKX2-5 transcriptional synergy, could attenuate these structural and functional abnormalities. Pregnant C57BL/6NCrl dams were randomly assigned to untreated control, vehicle control, ATRA, or ATRA plus 3i-0777 groups (12 independent litters per group). Both ATRA-exposed groups received ATRA (50 mg/kg) on embryonic day (E)12.5. In the ATRA plus 3i-0777 group, 3i-0777 (15 mg/kg) was administered as a separate injection concurrently with ATRA at E12.5, followed by 5 mg/kg every 8 h (three doses per day) on E13.5-E15.5. At postnatal day 1, one pup was randomly selected from each litter for echocardiography and subsequent histomorphometry. The echocardiographic and histomorphometric ratios of non-compacted to compacted myocardial layer thickness (N/C ratios) were higher, and the absolute magnitude of global longitudinal strain (|GLS|) was lower, in the ATRA group than in either control group (all adjusted P < 0.001). Compared with the ATRA group, the ATRA plus 3i-0777 group had lower echocardiographic and histomorphometric N/C ratios (0.58 {+/-} 0.19 vs 2.19 {+/-} 0.18 and 0.90 {+/-} 0.33 vs 2.46 {+/-} 0.48, respectively), higher |GLS| (25.9 {+/-} 2.5% vs 15.3 {+/-} 2.7%), and a smaller left ventricular internal diameter at end-diastole (1.15 {+/-} 0.06 vs 1.42 {+/-} 0.10 mm; all adjusted P < 0.001). These findings provide proof of concept that ATRA-induced left ventricular hypertrabeculation and dysfunction can be pharmacologically attenuated in utero.

developmental biology↗

bioRxiv2026

Persistent Post-Inflammatory Matrix Stiffening Defines a Premalignant Mechanical Niche in Ulcerative Colitis-Associated Neoplasia

Patients with long-standing ulcerative colitis (UC) remain at risk for colorectal neoplasia even after overt inflammatory activity improves, suggesting that repaired mucosa may retain residual tissue-level abnormalities. Whether extracellular matrix remodeling leaves a persistent mechanical cue that contributes to early neoplastic remodeling is unknown. Here we identify post-inflammatory matrix stiffening as a premalignant mechanical niche in UC-associated neoplasia. In human colonic biopsies, collagen remodeling and atomic-force-microscopy-based mucosal stiffness increased from non-UC controls to UC and UC-associated dysplasia. A stiffness-associated transcriptional program was also enriched in histologically non-dysplastic mucosa from patients with UC-associated neoplasia. In mouse models, colonic stiffness increased along the colitis-to-tumorigenesis axis and remained elevated during apparent recovery, when epithelial permeability, junctional protein loss, crypt proliferation and nuclear {beta}-catenin accumulation persisted despite reduced disease activity. Stiffness-controlled intestinal epithelial cultures showed that stiff substrates were sufficient to disrupt ZO-1 organization and enhance {beta}-catenin redistribution, particularly under TNF- stimulation. Pharmacological matrix normalization with {beta}-aminopropionitrile partially restored barrier organization and attenuated early epithelial remodeling in vivo. Single-cell profiling identified a stiffness-associated MMP7-positive/YAP-active epithelial state that was enriched in collagen-rich regions and reduced after matrix softening. Inhibition of YAP or MMP7 attenuated stiffness-associated junctional disruption and {beta}-catenin redistribution. These findings suggest that inflammatory recovery and mechanical recovery can be uncoupled, and that persistent mucosal stiffening provides a tissue-level mechanism by which chronically injured UC mucosa may remain biologically vulnerable to premalignant epithelial remodeling.

Cancer Biology↗

bioRxiv2025

The Pulmonary Microbial Signatures of Early Stages of Severe Infection in Children

The respiratory tract related diseases are the main causes of death in children. Child pulmonary severe infection is the most important inducement for Respiratory tract related diseases. Therefore, it is necessary to understand the composition of the microbial community and the species correlation in children with severe pulmonary infection. In this study, the bronchoalveolar lavage fluid (BALF), blood and cerebrospinal fluid (CSF) samples of 782 children with severe infection in the early stage were systematically analyzed by amplicon-sequencing technology to reveal the distribution of microbial community and its clinical correlation. Results reveal significantly higher bacterial abundance in BALF than in blood/cerebrospinal fluid, with community structures shaped by tissue microenvironments, geographical disparities, age, and clinical symptoms. Neonatal BALF harbors simplified microbiota dominated by probiotics, while diversity increases with age, showing marked differences between 1-3 and 6-12-year-olds. Sepsis samples exhibit reduced microbial diversity, with Staphylococcus and Moraxella enrichments in the CST-4 cluster. Respiratory symptom progression correlates with microbiota succession from oral colonizers to respiratory pathogens. Third-generation sequencing-derived co-occurrence networks illustrate synergistic interactions among opportunistic pathogens, providing a basis for ecological targeted therapy. This study provides a key basis for breaking through the limitations of traditional diagnosis, establishing a precise diagnosis and treatment system based on third-generation sequencing, and developing ecological targeted treatment strategies.

pathology↗

bioRxiv2024

The Biochemical Effects of Carotenoids in Orange Carrots on the Colonic Proteome in a Mouse Model of Diet-induced Obesity

Carotenoids are naturally occurring pigments in plants and are responsible for the orange, yellow, and red color of fruits and vegetables. Carrots are one of the primary dietary sources of carotenoids. The biological activities of carotenoids in higher organisms are well documented in most tissues but not the large intestine. The gastrointestinal barrier acts as a line of defense against the systemic invasion of pathogenic bacteria, especially at the colonic level. Proteins involved in tight junction assembly between epithelial cells and mucus secretion from goblet cells are essential for maintaining intestinal barrier homeostasis. A high-fat diet can cause gut impairment by inducing barrier permeability, leading to low-grade chronic inflammation via metabolic endotoxemia. Our hypothesis for this study is that the dietary intake of carotenoid-rich foods can alleviate obesity-associated gut inflammation and strengthen the intestinal barrier function. Male C57BL/6J mice were randomized to one of four experimental diets for 20 weeks (n = 20 animals/group): Low-fat diet (LFD, 10% calories from fat), high-fat diet (HFD, 45% calories from fat), HFD with white carrot powder (HFD + WC), or HFD with orange carrot powder (HFD + OC). Colon tissues were harvested to analyze the biochemical effects of carotenoids in carrots. The distal sections were subjected to isobaric labeling-based quantitative proteomics in which tryptic peptides were labeled with tandem mass tags, followed by fractionation and LC-MS/MS analysis in an Orbitrap Eclipse Tribrid instrument. High-performance liquid chromatography results revealed that the HFD+WC pellets were carotenoid-deficient, and the HFD+OC pellets contained high concentrations of provitamin A carotenoids, specifically -carotene and {beta}-carotene. As a result of the quantitative proteomics, a total of 4410 differentially expressed proteins were identified. Intestinal barrier-associated proteins were highly upregulated in the HFD+OC group, particularly mucin-2 (MUC-2). Upon closer investigation into mucosal activity, other proteins related to MUC-2 functionality and tight junction management were upregulated by the HFD+OC dietary intervention. Collectively, our findings suggest that carotenoid-rich foods can prevent high-fat diet-induced intestinal barrier disruption by promoting colonic mucus synthesis and secretion in mammalian organisms. Data are available via ProteomeXchange with identifier PXD054150.

biochemistry↗

bioRxiv2024

A human forebrain organoid model reveals the essential function of GTF2IRD1-TTR-ERK axis for the neurodevelopmental deficits of Williams Syndrome

Williams Syndrome (WS; OMIM#194050) is a rare disorder, which is caused by the microdeletion of one copy of 25-27 genes, and WS patients display diverse neuronal deficits. Although remarkable progresses have been achieved, the mechanisms for these distinct deficits are still largely unknown. Here, we have shown that neural progenitor cells (NPCs) in WS forebrain organoids display abnormal proliferation and differentiation capabilities, and synapse formation. Genes with altered expression are related to neuronal development and neurogenesis. Single cell RNA-seq (scRNA-seq) data analysis revealed 13 clusters in healthy control and WS organoids. WS organoids show an aberrant generation of excitatory neurons. Mechanistically, the expression of transthyretin (TTR) are remarkably decreased in WS forebrain organoids. We have found that GTF2IRD1 encoded by one WS associated gene GTF2IRD1 binds to TTR promoter regions and regulates the expression of TTR. In addition, exogenous TTR can activate ERK signaling and rescue neurogenic deficits of WS forebrain organoids. Gtf2ird1 deficient mice display similar neurodevelopmental deficits as observed in WS organoids. Collectively, our study reveals critical function of GTF2IRD1 in regulating neurodevelopment of WS forebrain organoids and mice through regulating TTR-ERK pathway.

neuroscience↗

bioRxiv2024

Mechano-regulation of GLP-1 production by Piezo1 in intestinal L cells

Glucagon-like peptide 1 (GLP-1) is a gut-derived hormone secreted by intestinal L cells and vital for postprandial glycemic control. As open-type enteroendocrine cells, whether L cells can sense mechanical stimuli caused by chyme and thus regulate GLP-1 synthesis and secretion is unexplored. Our study showed expression of Piezo1 in intestinal L cells. Its level varied in different energy status and correlates with blood glucose and GLP-1 levels. Mice with L cell-specific loss of Piezo1 (IntL-Piezo1-/-) exhibited impaired glucose tolerance, increased body weight, reduced GLP-1 production and decreased CaMKK{beta}/CaMKIV-mTORC1 signaling pathway under normal chow diet or high fed diet. Activation of the intestinal Piezo1 by its agonist Yoda1 or intestinal bead implantation increased the synthesis and secretion of GLP-1, thus alleviated glucose intolerance in diet-induced-diabetic mice. Overexpression of Piezo1, Yoda1 treatment or stretching stimulated GLP-1 production and CaMKK{beta}/CaMKIV-mTORC1 signaling pathway, which could be abolished by knockdown or blockage of Piezo1 in primary cultured mouse L cells and STC-1 cells. These findings suggest a previously undiscovered mechano-regulation of GLP-1 production in L cells, which may shed new light on the treatments of diabetes.

physiology↗

bioRxiv2023

Predicting resprouting of Platanus x hispanica following branch pruning by means of machine learning

O_LIResprouting is a crucial survival strategy following the loss of branches, being it by natural events or artificially by pruning. The prediction of resprouting patterns on a physiological basis is a highly complex approach. However, trained gardeners try to predict a trees resprouting after pruning purely based on their empirical knowledge and a visual check of the trees geometry. In this study, we explore in how far such predictions can also be made by algorithms, especially using machine learning. C_LIO_LITable-topped annually pruned Platanus x hispanica trees at a nursery were documented with terrestrial LiDAR scanners in two consecutive years. Topological structures for these trees were abstracted from point clouds by cylinder fitting. Then, new shoots and trimmed branches were labelled on corresponding cylinders. Binary and multiclass classification models were tested for predicting the location and number of new sprouts. C_LIO_LIThe accuracy for predicting whether having or not new shoots on each cylinder reaches 90.8% with the LGBMClassifier, the balanced accuracy is 80.3%. The accuracy for predicting the exact numbers of new shoots with GaussianNB model is 82.1% but its balanced accuracy is reduced to 42.9%. C_LIO_LIThe results were validated with a separate evaluation dataset. It proves a feasibility in predicting resprouting patterns after pruning using this approach. Different tree species, tree forms, and other variables should be addressed in further research. C_LI

plant biology↗

bioRxiv2023

Identification of bioactive constituents for colitis from traditional Chinese medicine prescription via deep neural network

Colitis is a commonly encountered inflammatory disease in colon tissue, which can be triggered by various causes. Although traditional Chinese medicine (TCM) has been utilized for the treatment of colitis, it is still a great challenge to identify the major bioactive constituents and their modes of action among thousands of ingredients in TCM prescriptions. Inspired by the success of artificial intelligence and deep learning methods, we proposed a deep neural network (DNN) for TCM prescription recommendation. We constructed a graph-based DNN with 9,845 nodes and 161,950 edges, which integrated microscopic information including bioactive molecules, protein targets, and extracted features of prescriptions through feature embedding. A novel and efficient data augmentation strategy was implemented to expand the sample size based on 378 collected TCM prescriptions. Network pharmacology study revealed that the 10 most frequent ingredients in generated prescriptions were associated with multiple inflammatory signaling pathways. To verify the bioactive constituents in the generated prescriptions, 5 selected constituents were administrated to BALB/c mice with colitis. Suppressive effects of disease progression and pro-inflammatory factors comparable to sulfasalazin were observed with these compounds, revealing the effectiveness of our artificial intelligence strategy on idetification of bioactive constituents from TCM prescriptions.

bioinformatics↗

bioRxiv2022

AHR agonist ITE boosted PD1 antibodys effects by inhibiting myeloid-derived cells suppressive cells in an orthotopic mouse glioma model

Glioblastoma is a "cold" tumor lacking T cell infiltration and tryptophan metabolites such as kynurenine function as an immune suppressor by binding to aryl hydrocarbon receptor(AHR). Hence AHR antagonists have been developed and some shown to activate the immune response in IDO over-expressing cancer models. Paradoxically, AHR has been reported to block glioma cell invasion like a tumor suppressor, and how to target AHR in cancer remains an open question. We previously discovered that an AHR agonist ITE can effectively inhibit glioma invasion. Here we report that ITE combined with PD1 antibody significantly increased the infiltration of CD8+ T cells while reducing that of the myeloid-derived suppressive cells (MDSCs), extending mouse survival. To identify factors that possibly mediated ITEs effects, we analyzed RNA-seq data and discovered that ITE significantly down-regulated IL11, a known MDSC regulator. In contrast, kynurenine upregulated IL11, further supporting IL11 as an AHR target. Moreover, ITE inhibited IL11s induction of MDSC from mouse PBMC in vitro, supporting that IL11 might mediate ITEs MDSC regulation effects. The discovery of ITEs immune-activating effects highlighted the complexity of AHRs signaling in cancers. The unexpected increase in STAT3, downstream of IL11 provided clues for combination therapy development.

cancer biology↗

bioRxiv2021

Retro Drug Design: From Target Properties to Molecular Structures

To generate drug molecules of desired properties with computational methods is the holy grail in pharmaceutical research. Here we describe an AI strategy, retro drug design, or RDD, to generate novel small molecule drugs from scratch to meet predefined requirements, including but not limited to biological activity against a drug target, and optimal range of physicochemical and ADMET properties. Traditional predictive models were first trained over experimental data for the target properties, using an atom typing based molecular descriptor system, ATP. Monte Carlo sampling algorithm was then utilized to find the solutions in the ATP space defined by the target properties, and the deep learning model of Seq2Seq was employed to decode molecular structures from the solutions. To test feasibility of the algorithm, we challenged RDD to generate novel drugs that can activate opioid receptor (MOR) and penetrate blood brain barrier (BBB). Starting from vectors of random numbers, RDD generated 180,000 chemical structures, of which 78% were chemically valid. About 42,000 (31%) of the valid structures fell into the property space defined by MOR activity and BBB permeability. Out of the 42,000 structures, only 267 chemicals were commercially available, indicating a high extent of novelty of the AI-generated compounds. We purchased and assayed 96 compounds, and 25 of which were found to be MOR agonists. These compounds also have excellent BBB scores. The results presented in this paper illustrate that RDD has potential to revolutionize the current drug discovery process and create novel structures with multiple desired properties, including biological functions and ADMET properties. Availability of an AI-enabled fast track in drug discovery is essential to cope with emergent public health threat, such as pandemic of COVID-19.

bioinformatics↗

bioRxiv2020

IP-MS Analysis of ESX-5 and ESX-1 Substrates Enables Mycobacterial Species Identification

Pulmonary disease resulting from non-tuberculous mycobacteria (NTM) infection has emerged as an increasingly prevalent clinical entity in the past two to three decades, but there are no standardized, commercial assays available for the molecular diagnosis of NTM infections from clinical samples. Herein we discuss the development of an assay that employs immunoprecipitation coupled with mass spectrometry (IP-MS) to rapidly and accurately discriminate prevalent slow-growing mycobacterial species (i.e., M. avium and M. intracellulare, M. kansasii, M. gordonae, M. marinum and M. tuberculosis) during early growth in mycobacterial growth indicator tube (MGIT) cultures. This IP-MS assay employs antibodies specific for conserved tryptic peptides of M. tuberculosis EsxN (AQAASLEAEHQAIVR) and CFP-10 (TQIDQVESTAGSLQGQWR) to capture and identify specific mycobacterial species and allows species-specific mycobacterium identification at the first sign of MGIT culture positivity.

microbiology↗

bioRxiv2019

Endosomal explosion induced by hypertonicity enhances chitosan transfection

Transferring DNA into cells to regulate cell function is a novel research field in recent decades. Chitosan is a gene vector with the properties of low-cost and safe, but high efficient delivery has remained challenging. We developed a strategy termed EEIH for endosomal explosion induced by hypertonicity, in which short-time exposure to hypertonic solutions triggers endosomes destabilization like explosions. EEIH can force chitosan/DNA polyplexes to break through the endosomal barriers to approach the nucleus, which results in boosting the transfection efficiency of chitosan in several cell lines. We demonstrate that EEIH is a significant and practical strategy in chitosan transfection system without sophisticated modification of chitosan.

biophysics↗