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Wei Zhu

Publications and source records attributed to Wei Zhu.

7 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↗