Biology subjects

Shao, K.

Publications and source records attributed to Shao, K..

14 recordsLinked to original sources

bioRxiv2026

Targeting Cardiac Fibrosis with Chimeric Antigen Receptor Neutrophils Derived from Human Pluripotent Stem Cells

Heart failure remains a leading cause of global morbidity and mortality, with cardiac fibrosis contributing to disease progression. Following myocardial injury, activated cardiac fibroblasts orchestrate adverse extracellular matrix (ECM) remodeling, which leads to tissue stiffening and compromised contractility. Despite the clinical importance of cardiac fibrosis, current pharmacological interventions modulate disease progression without directly eliminating activated fibrogenic cells. To target these cells directly, we engineered human pluripotent stem cell (hPSC)-derived neutrophils expressing a chimeric antigen receptor (CAR) directed against fibroblast activation protein (FAP). In vitro, FAP CAR neutrophils exhibited increased reactive oxygen species-associated fluorescence during fibroblast co-culture and dose-dependent cytotoxicity in 2D cultures, while reducing fibroblast-associated fluorescence in 3D cardiac organoids without a significant reduction in cardiomyocyte-associated cardiac troponin T staining. FAP CAR neutrophils also showed increased iNOS and decreased Arginase-1 expression compared with unmodified neutrophils, consistent with a shift toward an N1-associated polarization profile. Analysis of public cardiac single-cell and single-nucleus RNA-sequencing datasets identified temporal patterns of immune-associated expression and fibroblast activation that informed treatment timing. In a murine myocardial infarction (MI) model, mice treated systemically with FAP CAR neutrophils showed higher day 7 left ventricular ejection fraction than PBS-treated mice in an exploratory comparison. Together, these findings support further evaluation of hPSC-derived FAP CAR neutrophils as an immunotherapeutic approach to cardiac fibrosis.

bioengineering↗

bioRxiv2026

Elucidating the JNK Signaling Pathway in Neonatal Muscle Growth and Neuromuscular Contractures

Neuromuscular contractures arising from neonatal brachial plexus injuries (NBPI) are highly disabling and currently incurable. We previously showed that contractures involve impaired longitudinal growth of denervated muscles, a defect mediated through myostatin (MSTN) signaling, a potent negative regulator of muscle size. However, MSTN-mediated contractures occur independent of canonical signaling pathways, including SMAD 2/3 and AKT/mTOR. Through a mouse model of NBPI, our present study extended these findings by revealing pharmacologic inhibition of JNK signaling, a noncanonical pathway downstream of MSTN, partially rescues contractures without restoring muscle length. Rather, JNK activation upregulates myofiber expression of the target gene Lmna, which encodes the nuclear envelope proteins Lamin A and Lamin C that are vital for nuclear stability, resulting in pervasive myonuclear displacement. These results suggest that other factors contribute to contracture pathology beyond deficits in longitudinal muscle growth. Further, while JNK inhibition does not restore length of denervated muscles, it impedes size and mass of normally innervated neonatal muscles, suggesting a requirement of JNK signaling for neonatal muscle growth. Our collective findings thereby establish new mechanistic insights into the molecular basis of aberrant muscle growth and neuromuscular contracture formation, potentially leading to novel targets for muscle restorative strategies and medical contracture prevention.

developmental biology↗

bioRxiv2026

GALILEO: Embodied AI scientist for autonomous therapeutic discovery in dynamic membrane systems

Generalizable Agentic Laboratory Intelligence for Learning, Experimentation, and Optimization (GALILEO) closes the prediction-to-intervention gap in therapeutic peptide discovery. Unlike prior AI-scientist systems, GALILEO couples an Observation-Thought-Action-Summary (OTAS) reasoning loop with robotic peptide synthesis and multimodal phenotyping. Candidate peptides are retrieved from a clinically informed peptide prior (CPP) and locally edited through auditable operations. GALILEO autonomously prioritized LRRC8C and SLC25A1 branches and used wet-lab feedback to update target beliefs, sequence policies, assay choices, and mechanism hypotheses. Peptides generated under this framework blocked LRRC8C currents, perturbed osmolyte/redox homeostasis, and promoted tumor-dependent T-cell activation, while SLC25A1 peptides disrupted citrate-export metabolism, reduced extracellular acidosis, and enhanced CD8+ T-cell function. These results establish retrieval-and-editing-based physical learning as a route for auditable, experimentally grounded interventions and transferable membrane-blocker rules.

Molecular Biology↗

bioRxiv2026

Photo-click Decellularized Matrix Hydrogels for Generating Pancreatic Ductal Organoids

Pancreatic ductal organoids (PDOs) generated from human induced pluripotent stem cells (iPSCs) can be used to model pancreatic diseases and to conduct drug screening/testing. However, current protocols for generating PDOs rely heavily on tumor-derived Matrigel, which has been shown to upregulate oncogenes. Furthermore, Matrigel has undefined composition and weak mechanical properties that hamper mechanistic studies of cell-material interactions. In this study, we explore photo-clickable decellularized small intestine submucosa-norbornene (dSIS-NB) hydrogels as a Matrigel replacement for generating human iPSC-derived PDOs. To achieve this, pancreatic progenitors (PP) were first differentiated in conventional two-dimensional (2D) culture, aggregated into spheroids, then encapsulated and differentiated within dSIS-NB hydrogels with tunable stiffness. The differentiated organoids were analyzed by morphology, expression of key pancreatic ductal markers, and single-cell RNA sequencing (scRNA-seq). Post-differentiation, PDOs generated in stiffer photo-clickable dSIS-NB hydrogels (shear moduli [~]2.5 kPa) maintained ductal epithelial phenotype and exhibited pronounced forskolin-induced swelling. In contrast, differentiation of PP spheroids in softer dSIS-NB gels (shear moduli [~]0.9 kPa) and Matrigel resulted in a persistent mesenchymal phenotype and failed to generate functional PDOs. Finally, scRNA-seq results revealed that stiffer dSIS-NB hydrogels strongly biased ductal cell differentiation, yielding greater than 97% ductal progeny.

bioengineering↗

bioRxiv2025

MouseGPT: A Large-scale Vision-Language Model for Mouse Behavior Analysis

Analyzing animal behavior is crucial in advancing neuroscience, yet quantifying and deciphering its intricate dynamics remains a significant challenge. Traditional machine vision approaches, despite their ability to detect spontaneous behaviors, fall short due to limited interpretability and reliance on manual labeling, which restricts the exploration of the full behavioral spectrum. Here, we introduce MouseGPT, a Vision-Language Model (VLM) that integrates visual cues with natural language to revolutionize mouse behavior analysis. Built upon our first-of-its-kind dataset--incorporating pose dynamics and open-vocabulary behavioral annotations across over 42 million frames of diverse psychiatric conditions--MouseGPT provides a novel, context-rich method for comprehensive behavior interpretation. Our holistic analysis framework enables detailed behavior profiling, clustering, and novel behavior discovery, offering deep insights without the need for labor-intensive manual annotation. Evaluations reveal that MouseGPT surpasses existing models in precision, adaptability, and descriptive richness, positioning it as a transformative tool for ethology and for unraveling complex behavioral dynamics in animal models.

animal behavior and cognition↗

bioRxiv2025

Inwardly rectifying potassium channels regulate membrane potential polarization and direction sensing during neutrophil chemotaxis

Potassium channels regulate membrane potential and diverse physiological processes, including cell migration. However, the specific function of the inwardly rectifying potassium channels in immune cell chemotaxis is unknown. Here, we identified that the inwardly rectifying potassium channel Kir7.1 (KCNJ13) maintains the resting membrane potential and is required for directional sensing during neutrophil chemotaxis. Pharmacological or genetic inhibition of Kir7.1 in neutrophils impaired direction sensing toward various chemoattractants without affecting cell polarization in multiple neutrophil models. Using genetically encoded voltage indicators, we observed oscillating depolarization of the membrane potential in protrusions in zebrafish neutrophils, and Kir7.1 is required for polarized depolarization towards the chemokine source. Focal depolarization with optogenetic tools biases pseudopod selection and induces de novo protrusions. Global hyperpolarizing neutrophils stalled cell migration. Furthermore, Kir7.1 regulates GPCR signaling activation. This work adds membrane potential to the intricate feedforward mechanism, coupling the adaptive and excitable network required to steer immune cells in complex tissue environments.

cell biology↗

bioRxiv2024

scChat: A Large Language Model-Powered Co-Pilot for Contextualized Single-Cell RNA Sequencing Analysis

Single-cell RNA sequencing (scRNA-seq) has transformed biomedical research by enabling transcriptomic analysis at single-cell resolution. Yet, existing computational approaches remain primarily data-driven and lack the ability to integrate research context, limiting their interpretability and impact on hypothesis generation or experimental planning. We present scChat, a large language model (LLM)-powered co-pilot for contextualized scRNA-seq analysis. Unlike conventional pipelines restricted to tasks such as cell type annotation or enrichment analysis, scChat has an interactive, reasoning-based framework. It combines quantitative algorithms with retrieval-augmented generation and a multi-agent architecture to support hypothesis validation, mechanistic interpretation, and next-step experimental design. Through showcase and benchmarking studies, we demonstrate that scChat not only achieves high accuracy in cell type annotation but also provides biologically grounded explanations and contextual insights.

bioinformatics↗

bioRxiv2022

A comprehensive single cell data analysis of in lymphoblastoid cells reveals the role of Super-enhancers in maintaining EBV latency

We probed the lifecycle of EBV on a cell-by-cell basis using single cell RNA sequencing (scRNA-seq) data from nine publicly available lymphoblastoid cell lines (LCL). While the majority of LCLs comprised cells containing EBV in the latent phase, two other clusters of cells were clearly evident and were distinguished by distinct expression of host and viral genes. Notably, both were high expressors of EBV LMP1/BNLF2 and BZLF1 compared to another cluster that expressed neither gene. The two novel clusters differed from each other in their expression of EBV lytic genes, including glycoprotein gene GP350. The first cluster, comprising GP350-LMP1hi cells, expressed high levels of HIF1A and was transcriptionally regulated by HIF1-. Treatment of LCLs with Pevonedistat, a drug that enhances HIF1- signaling, markedly induced this cluster. The second cluster, containing GP350+LMP1hi cells, expressed EBV lytic genes. Host genes that are controlled by super-enhancers (SEs), such as transcription factors MYC and IRF4, had the lowest expression in this cluster. Functionally, the expression of genes regulated by MYC and IRF4 in GP350+LMP1hi cells were lower compared to other cells. Indeed, induction of EBV lytic reactivation in EBV+ AKATA reduced the expression of these SE-regulated genes. Furthermore, CRISPR-mediated perturbation of the MYC or IRF4 SEs in LCLs induced the lytic EBV gene expression, suggesting that host SEs and/or SE target genes are required for maintenance of EBV latency. Collectively, our study revealed EBV associated heterogeneity among LCLs that may have functional consequence on host and viral biology. ImportanceEpstein-Barr virus (EBV) establishes a life-long latency program within host cells. As such, EBV immortalized lymphoblastoid cells (LCLs) often carry the latent EBV genome and only a small percentage of LCLs containing lytic EBV. However, the cellular programs that distinguish latent from lytic cells and the heterogeneity of cells in latent or lytic phases remains poorly explored. To explore these unknowns, we reanalyzed publicly available single cell RNA-seq data from nine LCLs. This approach permitted the simultaneous study of cells in both latent and lytic phases. We identified three cell populations with distinct lytic/latent activity and further characterized the transcriptomes of these cells. We also identified a new role of super-enhancers in regulating EBV lytic replication. Collectively, our studies revealed EBV associated heterogeneity among LCLs that contribute to EBV life cycle and biology.

microbiology↗

bioRxiv2022

Incorporating Prior Genomic Dose-Response Data to Support the Benchmark Dose Estimation of Toxicogenomics

Chemical risk assessment is an important tool to evaluate the toxicity of chemicals in the environment, and high throughput toxicogenomics plays an increasingly important role in risk assessment. In toxicogenomics, dose-response analysis for each gene is a data-limited situation, and thus parameter and benchmark dose (BMD) estimations typically have large uncertainty. To solve this problem, an informative prior by synthesizing toxicological information is integrated into the Bayesian benchmark dose modeling system (BBMD), a leading web-based toxicogenomics analysis application. We analyzed 276,126 toxicogenomics dose-response datasets and obtained plausible estimation of informative priors for seven commonly used continuous dose-response models. The effects of informative priors are investigated at the individual probe and pathway levels. Simulation studies based on six "true" models generated from typical genomic dose-response shapes show a significant decrease in uncertainty and an increase in accuracy of BMD estimates for most scenarios with informative priors than the counterpart with uninformative priors. The case study on the pathway analysis indicates that informative priors slightly improve the correlation between the pathway-based point of departure and apical point of departure. Overall, our study provides a practical strategy to incorporate existing toxicogenomic information as priors to improve the quality of chemical risk assessment. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/500899v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1cca1c3org.highwire.dtl.DTLVardef@1903430org.highwire.dtl.DTLVardef@524b80org.highwire.dtl.DTLVardef@dadb56_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2022

Mice lacking dopamine production in neurotensin receptor 1 neurons voluntarily undergo time-restricted feeding of high fat diet and resist obesity

The introduction of processed foods high in fat and sugars has caused a dramatic increase in obesity in humans. Diet-induced obesity (DIO) can be modeled in laboratory mice by increasing the fat content of their diet. Previously, it was determined that mice lacking dopamine receptor 1 (Drd1) are completely resistant to DIO and do not eat as much food during the day as control mice. Surprisingly, when Drd1 is restored to the suprachiasmatic nucleus (SCN), which is the central regulator of circadian rhythms, these mice increase day-eating and become obese. The source of dopamine in the SCN is the ventral tegmental area (VTA), but the genetic identity of the dopamine neurons is unknown. Here we create conditional deletion mutants for tyrosine hydroxylase (TH) using neurotensin receptor 1 (Ntsr1) Cre and other Cre drivers and measure feeding and body weight homeostasis on standard and high fat diets. Control mice were susceptible to DIO and overate during the day whereas Ntsr1-Cre conditional knockouts for TH mice did not increase day-eating, nor did they gain much weight on HFD. We used an adeno-associated virus to selectively restore TH to the VTA Ntsr1 neurons and observed an increase in body weight and increased day-eating of HFD. These results implicate VTA Ntsr1 dopamine neurons as promoting out-of-phase feeding behavior on a high fat diet that could be an important contributor to diet-induced obesity.

neuroscience↗

bioRxiv2021

A model of Ponto-Geniculo-Occipital waves supports bidirectional control of cortical plasticity across sleep-stages

During sleep, cortical network connectivity likely undergoes both synaptic potentiation and depression through system consolidation and homeostatic processes. However, how these modifications are coordinated across sleep stages remains largely unknown. Candidate mechanisms are Ponto-Geniculo-Occipital (PGO) waves, propagating across several structures during Rapid Eye Movement (REM) sleep and the transitional stage from non-REM sleep to REM sleep (pre-REM), and exhibiting sleep stage-specific dynamic patterns. To understand their impact on cortical plasticity, we built an acetylcholine-modulated neural mass model of PGO wave propagation through pons, thalamus and cortex, reproducing a broad range of electrophysiological characteristics across sleep stages. Using a population model of Spike-Time-Dependent Plasticity, we show that cortical circuits undergo different transient regimes depending on the sleep stage, with different impacts on plasticity. Specifically, PGO-induced recurrent cortical activities lead to the potentiation of cortico-cortical synapses during pre-REM, and to their depression during REM sleep. Overall, these results shed light on how the dynamical properties of sleep events propagating to cortical circuits can favor different types of local plastic changes. The variety of events occurring across sleep stages may thus be instrumental in controlling the reorganization of cortical networks from one day to the next. Significance statementConsiderable evidence supports rescaling of cortical synaptic connec-tions during sleep, requiring both long term potentiation to consolidate newly acquired memories, and long-term depression to maintain homeostatic levels of brain activity. However, which aspects of sleep activity contribute to this bidirectional control of plasticity remains unclear. This computational modeling study suggests that widespread transient phenomena called Ponto-geniculo-occipital (PGO) waves, have a sleep-stage dependent effect on plasticity. The alternation between sleep stages can thus be exploited in combination with spontaneously occurring transients, to trigger both up- and down-regulating effects on cortical connectivity, and may explain why the basic structure of sleep-cycles is a well-preserved property across mammalian species.

neuroscience↗

bioRxiv2019

Geographic Patterns of Bacterioplankton among Lakes of the Middle and Lower Reaches of the Yangtze River Basin, China

In aquatic ecosystems, microbial biogeography research is critical for unveiling the mechanisms of microbial community succession. However, little is known about the microbial biogeography among interconnected lakes. To address this deficit, we used high-throughput sequencing to explore geographic patterns and the relative importance of ecological processes that shape these patterns in abundant and rare bacterial subcommunities from 25 lakes across the middle and lower reaches of Yangtze River basin (MLYB, located in southeast China), where most of the lakes are interconnected by river networks. We found that there were significant differences in both abundant and rare bacterial subcommunities between the two lake groups that were far from each other, while were no difference among the nearby lakes in each group. Both abundant and rare bacteria followed a strong distance-decay relationship, especially for rare bacteria. These findings suggest that although the interconnectivity between lakes breaks the geographical isolation of bacteria, the dispersal capability of bacterial taxa was still limited by geographic distance. We also found that although deterministic processes and stochastic processes together drive the bacterial subcommunities assembly, the stochastic processes (based on adjusted R2 in redundancy analysis) exhibited a greater influence on bacterial subcommunities. Our results implied that bacterial dispersal among interconnected lakes was more stochastically. ImportanceUnraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. In aquatic ecosystems, microbial communities often occur in spatially structured habitats, where connectivity directly affects dispersal and metacommunity processes. Recent theoretical work suggests that directional dispersal among connected habitats leads to higher variability in local diversity and among-community composition. However, the study of microbial biogeography among natural interconnected habitats is still lacking. The findings of this study revealed interesting phenomena of microbial biogeography among natural interconnected habitats, suggested that the high interconnectivity reduced the spatial heterogeneity of bacteria, and caused the dispersal of bacteria to be more stochastically. This study has provided a deeper understanding of the biogeographic patterns of rare and abundant bacterial taxa and their determined processes among interconnected aquatic habitats.

microbiology↗

bioRxiv2019

Gene Panel Sequencing in a Chinese High-risk Breast Cancer Cohort

Currently, over 20 genes have been defined that can confer susceptibility for high-risk breast cancer. Although research has proved the utility of multiple-gene sequencing in the assessment of breast cancer risk, there is little data from China patients. Here, we use a multiple-gene sequencing panel to identify the variant spectrum in Chinese high-risk breast cancer subjects.\n\nA total of 829 Chinese high-risk breast cancer patients participated in the research. The coding regions of 115 hereditary cancer susceptibility genes were sequenced using a next generation sequencing platform. In total, 193 pathogenic variants were identified in 45 genes from 177 patients. The pathogenic variant carrier rate is 21.4%: with 10.5% patients carrying a BRCA1 or BRCA2 mutation only, 10.0% of patients carried non-BRCA gene mutations only, while 1.0% of patients carried both a BRCA1/2 and a non-BRCA gene mutation. Variants of uncertain significance (VUS) totaling 2632 were identified in 115 genes from 787 of 829 patients: 82.5% patients carried more than one VUS, and only 5.1% patients did not carry any VUS. Families carrying pathogenic variants were tracked and adenoma was founded in three of them. Our data provide a comprehensive analysis of potential susceptibility variations of high-risk for breast cancer in a Chinese population. This data will be useful for the comparison of the susceptibility variation spectrum between different populations and to discover potential pathogenic variants to improve the prevention and treatment of high-risk breast cancer.

cancer biology↗

bioRxiv2018

Integrated Analysis Revealed Hub Genes in Breast Cancer

The aim of this study was to identify the hub genes in breast cancer and provide further insight into the tumorigenesis and development of breast cancer. To explore the hub genes in breast cancer, we performed an integrated bioinformatics analysis. Two gene expression profiles were downloaded from the GEO database. The differentially expressed genes (DEGs) were identified by using the \"limma\" package. Then, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to explore the functional annotation and potential pathways of the DEGs. Next, protein-protein interaction (PPI) network analysis and weighted gene coexpression network analysis (WGCNA) were conducted to screen for hub genes. To confirm the reliability of the identified hub genes, we obtained TCGA-BRCA data by using WGCNA to screen for genes that were strongly related to breast cancer. By combining the results from the GEO and TCGA datasets, we finally identified 15 real hub genes in breast cancer. Finally, we performed an overall survival analysis to explore the connection between the expression of hub genes and the overall survival time of breast cancer patients. We found that for all hub genes, higher expression was associated with significantly shorter overall survival times among breast cancer patients.

bioinformatics↗