Biomedical subjects

Wei Zhu

Publications and source records attributed to Wei Zhu.

At least 19 recordsLinked to original sources

PubMed2026

Induced pluripotent stem cell reprogramming: methodological evolution and challenges in clinical translation.

Cell reprogramming can transform somatic cells into induced pluripotent stem cells providing a platform for patient-specific disease modeling, drug screening and regenerative medicine research. Since the advent of OKSM-mediated reprogramming, the system of technical approaches has evolved continuously - from integrated viral vectors to non-integrated episomal systems and, more recently, chemical reprogramming and CRISPR approaches. The simultaneous advances in single-cell multi-omics, biomaterials engineering, and artificial intelligence have further refined the controllability and precision of the reprogramming process. Despite these innovations, problems persist that hinder clinical translation: incomplete epigenetic resetting, ongoing clonal heterogeneity, genomic instability in long-term culture, and the lack of standardized Good Manufacturing Practice protocols for large-scale manufacturing. This review summarizes the trajectory of iPSC reprogramming technologies, with special emphasis on the translational applicability of each modality. We evaluated viral and nonviral delivery systems, chemical reprogramming, strategies that aid gene editing, and emerging engineering platforms, including microfluidics, smart biomaterials, and artificial-intelligence-driven process optimization. We further identify the core "translational triltrilas", namely, the inherent tradeoffs between security, homogeneity, and scalability, and propose a comprehensive strategy to overcome these bottlenecks. By linking basic mechanistic understandings with industrial and regulatory considerations, this review aims to provide a route for transitioning iPSC technology from a laboratory tool to a clinically viable manufacturing platform.

clinical translation↗

PubMed2026

Retrograde intrarenal surgery with flexible and navigable suction access sheaths vs mini-percutaneous nephrolithotomy for large upper urinary tract stones: a systematic review and meta-analysis.

OBJECTIVE: To conduct a meta-analysis comparing the efficacy and perioperative outcomes of contemporary flexible and navigable suction access sheath-assisted retrograde intrarenal surgery (FANS-RIRS) against percutaneous nephrolithotomy (PCNL) for the management of large upper urinary tract stones, as despite technological advances in RIRS such as high-powered lasers and FANS that have substantially enhanced its performance, current guidelines continue to recommend PCNL as first-line treatment for renal stones >2cm. METHODS: MEDLINE, Embase, and the Cochrane Library were searched for studies performing direct comparisons of FANS-RIRS against PCNL in adult patients until September 2025. Primary outcomes included stone-free rates (SFRs) and need for ancillary procedures. Secondary outcomes included operative time, length of postoperative hospitalisation, and postoperative complications. RESULTS: A total of 10 studies (three randomised control trials, seven retrospective cohort studies) comprising 2347 patients were included; preoperative stone sizes were predominantly 2-3 cm. All PCNL procedures in the studies included were performed as mini-PCNL. The SFRs for FANS-RIRS were comparable with mini-PCNL across all stone sizes (odds ratio [OR] 0.90, 95% confidence interval [CI] 0.70-1.17) and stones ≥2 cm (OR 0.80, 95% CI 0.60-1.08), with low heterogeneity. Ancillary procedures rates were similar (OR 1.22, 95% CI 0.61-2.44). FANS-RIRS was associated with significantly fewer overall complications, specifically smaller haemoglobin decline, need for transfusion, and shorter hospital stay. However, mini-PCNL demonstrated shorter operative times for stones ≥2 cm. Urosepsis rates were low and similar between both groups. Limitations include predominance of Asian studies, variability of practice, and inclusion of non-randomised studies. CONCLUSIONS: Contemporary FANS-RIRS achieves SFRs comparable to mini-PCNL even for 2-3 cm stones, while offering superior safety profiles and shorter hospitalisation; this supports FANS-RIRS as a viable primary treatment in selected patients.

Humans↗

PubMed2026

Tanshinone IIA impairs platelet function and thrombus formation.

BACKGROUND: Tanshinone IIA (T-IIA) is a fat-soluble active ingredient derived from the traditional Chinese medicine Danshen and possesses cardioprotective property. However, its exact role in platelet function is unknown. OBJECTIVES: This study investigated T-IIA's role in platelet aggregation, granules release, spreading, clot retraction, as well as in vivo hemostasis and thrombus formation. METHODS: Human platelets were treated with different doses of T-IIA (10, 50, and 100 μM) to measure platelet function and activation. In addition, T-IIA was administrated into wild-type mice to evaluate hemostasis and thrombus formation. RESULTS: T-IIA significantly impaired platelet aggregation, adenosine triphosphate secretion, P-selectin expression, and spreading and clot retraction dose dependently without affecting the expression profiles of αIIbβ3 and glycoprotein VI or Ibα. Administration of T-IIA significantly prolonged mice tail bleeding time and inhibited arterial and venous thrombosis. Further analysis showed that T-IIA dose dependently reduced platelet reactive oxygen species generation. Quantitative proteomic and phosphoproteimic assays analyzing T-IIA-treated vs vehicle-treated platelets after stimulation identified dysregulated phosphorylation of several proteins, which were enriched in platelet activation. Among the downregulated phosphoproteins, Rho-associated protein kinase (ROCK)1, integrin β3, and talin1 exhibited the lower fold change of phosphorylation in T-IIA-treated platelets compared with those in vehicle-treated platelets. Consistently, T-IIA treatment inhibited the phosphorylation of ROCK1, p47phox, integrin β3, and talin1 in activated platelets. CONCLUSION: T-IIA impairs platelet function and thrombosis via inhibition of several signaling pathways including ROCK1/p47phox, β3, and talin1, implying that T-IIA may represent a promising therapeutic candidate for treating thrombotic diseases.

Animals↗

PubMed2026

TriosCompass: a snakemake workflow for integrated detection of SNVs, indels, STRs, and structural de novo variants in parent-child trios.

MOTIVATION: The accurate and sensitive identification of de novo variants, which are unique to an individual and not found in the parents' germlines, is critical for understanding the genetic basis of rare diseases, developmental disorders, and evolutionary processes. Existing de novo variant detection pipelines often lack the flexibility to handle multiple variant types, struggle with speed and reproducibility across computational environments, demand extensive manual configuration, or require bioinformatics expertise for downstream curation and analysis, limiting their scalability and usability for large genomic studies. Accordingly, there is a pressing need to better address these challenges. RESULTS: We introduce TriosCompass, an open-source Snakemake workflow that addresses these challenges by providing a modular, accelerated, and environmentally-configurable end-to-end solution for comprehensive de novo variant discovery. It integrates state-of-the-art tools into a reproducible framework, empowering researchers to discover novel genetic insights with greater efficiency and reliability. AVAILABILITY: TriosCompass is implemented as a Snakemake workflow and is freely available at https://github.com/NCI-CGR/TriosCompass_v2 or on Zenodo (10.5281/zenodo.17981062). SUPPLEMENTARY INFORMATION: Supplementary data is available on GitHub at https://github.com/NCI-CGR/TriosCompass_v2/tree/manuscript/report_dashboards. Supplementary methods on DeepTrio benchmark runs can be viewed at: https://github.com/NCI-CGR/TriosCompass_v2/blob/manuscript/TriosCompass_Supp_Methods_deeptrio_benchmark.md.

Software↗

PubMed2025

Untargeted metabolomics in a prospective cross-sectional observational study reveals differences in plasma and cerebrospinal fluid between asymptomatic neurosyphilis and serofast syphilis.

Asymptomatic neurosyphilis (ANS), a diagnostically elusive complication of Treponema pallidum infection, necessitates invasive cerebrospinal fluid (CSF) analysis for detection. This study investigated metabolic differences between patients with ANS and those with serofast syphilis. Using untargeted metabolomics, we analyzed plasma and CSF from 15 patients with ANS, 15 patients with serofast syphilis, and 16 healthy controls via liquid chromatography-mass spectrometry. Univariate statistical analyses identified differential metabolites, followed by pathway enrichment through Kyoto encyclopedia of genes and genomes enrichment analysis and biomarker evaluation. Plasma analysis identified dysregulated tryptophan metabolism as a central feature in ANS, with key alterations in 4-(2-aminophenyl)-2,4-dioxobutanoic acid and 2-formylaminobezaldehyde. Comparative analysis further distinguished ANS through perturbations in inositol phosphate metabolism in both plasma and CSF. Spearman correlation analysis identified positive associations of the plasma biomarkers 1D-myo-inositol-1,3,4,6-tetrakisphosphate, inositol-1,3-bisphosphate, 4-(2-aminophenyl)-2,4-dioxobutanoic acid, and 2-formylaminobezaldehyde with CSF total protein. Our findings suggest that dysregulation in tryptophan and inositol phosphate metabolism may play an important role in ANS pathogenesis, warranting further confirmatory studies.

Humans↗

PubMed2025

Individualized patient tumor organoids faithfully preserve human brain tumor ecosystems and predict patient response to therapy.

Tumor organoids are important tools for cancer research, but current models have drawbacks that limit their applications for predicting response to therapy. Here, we developed a fast, efficient, and complex culture system (IPTO, individualized patient tumor organoid) that accurately recapitulates the cellular and molecular pathology of human brain tumors. Patient-derived tumor explants were cultured in induced pluripotent stem cell (iPSC)-derived cerebral organoids, thus enabling culture of a wide range of human tumors in the central nervous system (CNS), including adult, pediatric, and metastatic brain cancers. Histopathological, genomic, epigenomic, and single-cell RNA sequencing (scRNA-seq) analyses demonstrated that the IPTO model recapitulates cellular heterogeneity and molecular features of original tumors. Crucially, we showed that the IPTO model predicts patient-specific drug responses, including resistance mechanisms, in a prospective patient cohort. Collectively, the IPTO model represents a major breakthrough in preclinical modeling of human cancers, which provides a path toward personalized cancer therapy.

Humans↗

PubMed2025

Sensitive and Visualized Detection of Hantavirus Using CRISPR/Cas12a Based on AutoCORDSv2 Design.

In recent years, detection technologies based on the CRISPR/Cas12a method have been extensively utilized in the fields of nucleic acid, enzyme, and macromolecule detection, thereby reinforcing their significant role in the detection landscape. Enhancing the simplicity of design, efficiency, and automation of the CRISPR/Cas12a detection system is essential for advancing its application in diagnostics. Recently, we developed an automated CRISPR/Cas12a design system named AutoCORDSv2. This system can process published genomic sequences of pathogenic bacteria in a high-throughput manner and automatically generate conserved and highly specific crRNA sequences, along with primer sequences for target amplification. This capability facilitates the specific and precise design of the CRISPR/Cas12a detection system. In this study, crRNAs targeting the Hantaan virus (HTNV) and Seoul virus (SEOV), as well as RT-PCR primers and RT-RPA primers, were designed using AutoCORDSv2. The experimental results demonstrated that the CRISPR/Cas12a system, automatically designed by AutoCORDSv2, was specific for the detection of both the HTNV and SEOV, with no cross-reactivity observed with other pathogens. The detection sensitivity reached 6 copies/μL (equivalent to 111 copies per amplification reaction), whether measured by a microplate reader or directly observed with the naked eye. The detection results for 50 samples were consistent with those obtained from commercial RT-qPCR kits, indicating high precision. Furthermore, the CRISPR/Cas12a system designed by AutoCORDSv2 can also be utilized for the development of a single-tube detection system with a sensitivity of 42 copies per reaction. This system combined with a 5-min extraction step and RT-RPA, further underscoring its potential for application.

CRISPR-Cas Systems↗

PubMed2007

Involvement of non-NMDA glutamate receptors in central amygdala in synaptic actions of ethanol and ethanol-induced reward behavior.

The central nucleus of the amygdala (CeA) plays a critical role in positive emotional responses that involve stimulus-reward learning and are induced by the reinforcing effects of many drugs of abuse, including alcohol. Behavioral studies have implicated CeA as a key brain structure in alcohol reward, but the underlying mechanisms are still poorly understood. Recent studies have demonstrated that both NMDA and non-NMDA receptors in CeA neurons are targets of acute and chronic alcohol in naive and alcohol-dependent animals. However, little is known about the role of CeA non-NMDA receptors in synaptic actions of alcohol and, particularly, in the behavior of alcohol reward. In the present study with both whole-cell voltage-clamp recordings in CeA slices in vitro and analysis of an animal model of conditioned place preference (CPP) in vivo, we investigated the synaptic mechanisms for actions of acute and chronic ethanol on CeA non-NMDA receptor functions and their contribution to ethanol-induced reward behavior. Acute ethanol significantly inhibited evoked and miniature synaptic currents mediated by non-NMDA receptors through inhibitions of both postsynaptic non-NMDA receptors and presynaptic glutamate release involving N-type Ca2+ channels. CeA neurons from rats exhibiting the ethanol-induced CPP behavior showed a significant increase in non-NMDA synaptic transmission. Blockade of this increased synaptic transmission through CeA microinjection abolished the CPP behavior. These results suggest that acute alcohol inhibits CeA non-NMDA synaptic transmission through both presynaptic and postsynaptic mechanisms, and chronic alcohol upregulates this synaptic activity, which is required for the alcohol-induced reward behavior.

Amygdala↗

PubMed2007

Proliferative status of tumor stem cells may be correlated with malignancy grade of human astrocytomas.

Tumor stem cells are implicated in tumor initiation and maintenance. Recent studies have shown that a subpopulation of cells isolated from brain tumors can form neurospheres in vitro, and have multiple characteristic properties observed in neural stem cells. In vivo implantation of these cells can induce tumors that phenocopy original tumors, suggesting that tumor stem cells are involved in brain carcinogenesis. We found that a population of cells in human glioblastoma multiforme expressed multiple protein markers of neural stem cells including nestin, TUC-4, doublecortin and beta III-tubulin. In contrast, these markers were not expressed in human capillary hemangioblastoma or meningioma. Double immunolabeling showed that a portion of doublecortin-, beta III-tubulin-, TUC-4- and nestin-positive cells express Ki67 antigen, a cell proliferation marker. To investigate further whether these properties of tumor stem cells are correlated with their biological behavior, immunohistochemistry was performed on brain sections from astrocytomas of different grades using antibodies against neural stem cell markers. The number of cells expressing Ki67 antigen and neural stem cell markers was increased in relation to worsening histological grade of astrocytomas, indicating that the capacity for tumor stem cell proliferation may be clinically relevant. Thus, tumor stem cells in astrocytomas may be involved in carcinogenesis.

Adolescent↗

PubMed2007

Unified structural equation modeling approach for the analysis of multisubject, multivariate functional MRI data.

The ultimate goal of brain connectivity studies is to propose, test, modify, and compare certain directional brain pathways. Path analysis or structural equation modeling (SEM) is an ideal statistical method for such studies. In this work, we propose a two-stage unified SEM plus GLM (General Linear Model) approach for the analysis of multisubject, multivariate functional magnetic resonance imaging (fMRI) time series data with subject-level covariates. In Stage 1, we analyze the fMRI multivariate time series for each subject individually via a unified SEM model by combining longitudinal pathways represented by a multivariate autoregressive (MAR) model, and contemporaneous pathways represented by a conventional SEM. In Stage 2, the resulting subject-level path coefficients are merged with subject-level covariates such as gender, age, IQ, etc., to examine the impact of these covariates on effective connectivity via a GLM. Our approach is exemplified via the analysis of an fMRI visual attention experiment. Furthermore, the significant path network from the unified SEM analysis is compared to that from a conventional SEM analysis without incorporating the longitudinal information as well as that from a Dynamic Causal Modeling (DCM) approach.

Attention↗

PubMed2006

B cells play a cooperative role via CD40L-CD40 interaction in T cell-mediated experimental autoimmune neuritis in Lewis rats.

The expression of co-stimulatory molecules CD40 and CD40L was examined over the course of experimental autoimmune neuritis (EAN) induced in Lewis rats by immunization with bovine peripheral nerve myelin. In draining lymph nodes, highest level of CD40L expression was seen on day 7 post immunization (p.i.), i.e. before onset of clinical signs of EAN, while CD40 expression was increased on day 14 p.i., i.e. at peak of clinical disease. In contrast, both CD40 and CD40L expressing cells in sciatic nerves, a target organ of EAN, peaked on day 14 p.i., large numbers of both expressing cells were mainly detected on day 14-21 p.i. After co-culture with EAN rat B cells bearing CD40, P0 peptide 180-199-specific T cell line cells exhibited a rapid down-regulation of CD40L expression. Furthermore, EAN rats had enhanced P0 peptide 180-199-specific antibody responses on day 14 p.i., which might have contributed to their aggravated EAN and further demonstrated the role of antibodies in EAN. The results indicate that CD40L-CD40 interactions are involved in the initiation of the antigen-specific T cell responses associated with the generation and development of EAN, and may mediate autoantibody production in EAN. Evidently, B cells play a cooperative role via CD40L-CD40 interaction in T cell-mediated EAN of Lewis rats.

Acute Disease↗

PubMed2006

Evidence that brain MAO A activity does not correspond to MAO A genotype in healthy male subjects.

BACKGROUND: A functional polymorphism in the promoter region of the monoamine oxidase A (MAO A) gene has two common alleles that are referred to as the high and low MAO A genotypes. We report the first in vivo human study to determine whether there is an association between MAO A genotype and brain MAO A activity in healthy male subjects. METHODS: Brain MAO A activity was measured with positron emission tomography and [(11)C]clorgyline in 38 healthy adult male nonsmokers genotyped for MAO A polymorphism. RESULTS: There was no significant difference in brain MAO A activity between the high (n = 26) and low (n = 12) MAO A genotypes. CONCLUSIONS: The lack of an association between the high and low MAO A genotype and brain MAO A activity suggests that this polymorphism by itself does not contribute to differences in brain MAO A activity in healthy adult male subjects.

Adult↗

PubMed2006

The TIGR Rice Genome Annotation Resource: improvements and new features.

In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42,653 non-transposable element-related genes encoding 49,472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13,237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31,739 gene models), representing approximately 50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

DNA Transposable Elements↗

PubMed2006

IKr and IKs remodeling differentially affects QT interval prolongation and dynamic adaptation to heart rate acceleration in bradycardic rabbits.

Bradycardic ventricular electrical remodeling predisposes to lethal tachyarrhythmias. We investigated the early temporal sequence and reversibility of electrical remodeling in a rabbit complete heart block model subjected to bradycardic ventricular pacing for either 2 or 8 days, with a third group of animals undergoing 8 days of bradycardic pacing followed by 8 days of physiological-rate pacing. At specified time points after complete heart block induction and pacing initiation, steady-state QT interval measurements and variability as well as dynamic QT interval adaptation to abrupt heart rate acceleration were assessed in the absence and presence of isoproterenol. Rapidly (I(Kr)) and slowly (I(Ks)) activating delayed rectifier repolarizing K(+) tail current densities were evaluated using whole cell patch clamp in isolated right ventricular myocytes. Steady-state QT interval prolongation at both 2 and 8 days was associated with moderate I(Kr) reduction. I(Ks) downregulation was apparent by day 2 but more profound at day 8. Dynamic QT interval adaptation was impaired under baseline conditions at day 8 but only during isoproterenol administration at day 2. Both in vivo and cellular manifestations of remodeling reverted toward control values after 8 days of physiological-rate pacing. In conclusion, in this bradycardic model, I(Ks) downregulation 1) proceeds more gradually but more extensively than that of I(Kr) and 2) is most prominently associated with impaired dynamic QT interval adaptation to heart rate acceleration. Isoproterenol blunts the dynamic QT interval response in animals with partially downregulated I(Ks), consistent with stress-related phenomena in known I(Ks)-impaired states. Relative early sparing of I(Ks) could explain the delay in the onset of lethal tachyarrhythmia predisposition in bradycardic electrical remodeling. Reversibility of remodeling supports the potential utility of preventive pacing intervention soon after bradycardia onset.

Adaptation, Physiological↗

PubMed2006

The TIGR Plant Transcript Assemblies database.

The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed sequence tags (ESTs) and full-length and partial cDNAs, but exclude computationally predicted gene sequences. The TA database includes all plant species for which more than 1000 EST or cDNA sequences are publicly available. The EST and cDNA sequences are first clustered based on an all-versus-all pairwise sequence comparison, followed by the generation of consensus sequences (TAs) from individual clusters. The clustering and assembly procedures use the TGICL tool, Megablast and the CAP3 assembler. The UniProt Reference Clusters (UniRef100) protein database is used as the reference database for the functional annotation of the assemblies. The transcription orientation of each TA is determined based on the orientation of the alignment with the best protein hit. The TA sequences and annotation are available via web interfaces and FTP downloads. Assemblies can be retrieved by a text-based keyword search or a sequence-based BLAST search. The current version of the TA database is Release 2 (July 17, 2006) and includes a total of 215 plant species.

DNA, Complementary↗

PubMed2006

Gastric stimulation in obese subjects activates the hippocampus and other regions involved in brain reward circuitry.

The neurobiological mechanisms underlying overeating in obesity are not understood. Here, we assessed the neurobiological responses to an Implantable Gastric Stimulator (IGS), which induces stomach expansion via electrical stimulation of the vagus nerve to identify the brain circuits responsible for its effects in decreasing food intake. Brain metabolism was measured with positron emission tomography and 2-deoxy-2[18F]fluoro-D-glucose in seven obese subjects who had the IGS implanted for 1-2 years. Brain metabolism was evaluated twice during activation (on) and during deactivation (off) of the IGS. The Three-Factor Eating Questionnaire was obtained to measure the behavioral components of eating (cognitive restraint, uncontrolled eating, and emotional eating). The largest difference was in the right hippocampus, where metabolism was 18% higher (P < 0.01) during the "on" than "off" condition, and these changes were associated with scores on "emotional eating," which was lower during the on than off condition and with "uncontrolled eating," which did not differ between conditions. Metabolism also was significantly higher in right anterior cerebellum, orbitofrontal cortex, and striatum during the on condition. These findings corroborate the role of the vagus nerve in regulating hippocampal activity and the importance of the hippocampus in modulating eating behaviors linked to emotional eating and lack of control. IGS-induced activation of regions previously shown to be involved in drug craving in addicted subjects (orbitofrontal cortex, hippocampus, cerebellum, and striatum) suggests that similar brain circuits underlie the enhanced motivational drive for food and drugs seen in obese and drug-addicted subjects, respectively.

Adult↗

PubMed2006

Simultaneous determination of 5-hydroxyindoleacetic acid and 5-hydroxytryptamine in urine samples from patients with acute appendicitis by liquid chromatography using poly(bromophenol blue) film modified electrode.

The fabrication and application of a novel electrochemical detection (ED) system with a poly(bromophenol blue) (PBPB) film chemically modified electrode (CME) for high performance liquid chromatography (HPLC) were described. The electrochemical behaviors of 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) at this CME were investigated by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). It was found that the PBPB CME efficiently exhibited electrocatalytic effect on the current responses of 5-HT and 5-HIAA with relatively high sensitivity, stability and long life of activity. In HPLC-ED, the two analytes had good and stable current responses at the CME and their linear ranges were over four orders of magnitude (R> or =0.9992) with the detection limits being 0.25 nmol L(-1) for 5-HT and 0.50 nmol L(-1) for 5-HIAA. The application of this method for the determination of 5-HT and 5-HIAA in urine samples from patients with acute appendicitis (AA) was satisfactory.

Acute Disease↗

PubMed2006

Evidence for stroke-induced neurogenesis in the human brain.

Experimental stroke in rodents stimulates neurogenesis and migration of newborn neurons from their sites of origin into ischemic brain regions. We report that in patients with stroke, cells that express markers associated with newborn neurons are present in the ischemic penumbra surrounding cerebral cortical infarcts, where these cells are preferentially localized in the vicinity of blood vessels. These findings suggest that stroke-induced compensatory neurogenesis may occur in the human brain, where it could contribute to postischemic recovery and represent a target for stroke therapy.

Adult↗