1.Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer
Chuang-Ming ZHENG ; Ho Won KANG ; Seongmin MOON ; Young Joon BYUN ; Won Tae KIM ; Yung Hyun CHOI ; Sung-Kwon MOON ; Xuan-Mei PIAO ; Seok Joong YUN
Investigative and Clinical Urology 2025;66(3):272-280
Purpose:
This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.
Materials and Methods:
A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry.Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.
Results:
WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.
Conclusions
WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.
2.Therapeutic Effect of Wenweishu Granules on Functional Dyspepsia Rats with Spleen-stomach Deficiency Cold Syndrome Based on Bioinformatics Analysis and Experimental Validation
Xinyu YANG ; Xiaoyi JIA ; Zihua XUAN ; Shuangying GUI ; Yanfang WU ; Yuhan MA ; Qin RUAN ; Jia ZHENG ; Zhiyong JIAO
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(18):30-40
ObjectiveThis study aims to investigate the therapeutic effects of Wenweishu granule (WWSG) on functional dyspepsia (FD) with spleen-stomach deficiency cold syndrome in rats by integrating network pharmacology, molecular docking, and animal experiments. MethodsActive components and corresponding targets of WWSG were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and the Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine (BATMAN-TCM). Disease-related targets for FD with spleen-stomach deficiency cold syndrome were screened using GeneCards and the Integrative Pharmacology-based Research Platform of Traditional Chinese Medicine (TCMIP). Core therapeutic targets were identified via Cytoscape and validated by molecular docking. A rat model of FD with spleen-stomach deficiency cold syndrome was established using vinegar gavage combined with tail-clamping. The rats were randomly divided into a model group, low-, medium-, and high-dose WWSG groups (2.0, 4.0, 8.0 g·kg-1), a domperidone group (3.0 mg·kg-1), a Fuzi Lizhong pillwan (0.8 g·kg-1), and a normal control group (n=10 per group). Drugs were administered once daily by gavage for 14 consecutive days. After treatment, body weight, symptom scores, and gastrointestinal motility indices were recorded. Gastric and duodenal pathologies changes were observed via hematoxylin-eosin (HE) staining. Brain-gut peptides were measured in serum and tissue using enzyme-linked immunosorbent assay (ELISA). Immunohistochemistry and Western blot were performed to assess stem cell factor (SCF) and receptor tyrosine kinase (c-Kit) protein expression in gastric tissues. ResultsA total of 305 drug targets, 1 140 disease targets, and 116 overlapping targets were identified. Cytoscape analysis revealed 104 core targets. Enrichment analysis indicated that the SCF/c-Kit signaling pathway was the key mechanism. Molecular docking confirmed a strong binding affinity between active components of WWSG and SCF/c-Kit proteins (binding energy<-5.1 kcal·mol-1). Compared with the normal group, model rats exhibited slower weight gain (P<0.05), reduced gastric emptying and intestinal propulsion (P<0.01), mild gastric mucosal shedding, duodenal inflammatory cell infiltration, decreased levels of gastrin (GAS), 5-hydroxytryptamine (5-HT), and vasoactive intestinal peptide (VIP) (P<0.05, P<0.01), and elevated somatostatin (SS) expression (P<0.05, P<0.01). WWSG treatment ameliorated weight gain, symptom scores, and low-grade inflammation in gastric/duodenal tissues. High-dose WWSG significantly improved gastric emptying and intestinal propulsion, upregulated GAS, 5-HT, and VIP, and downregulated SS expression in serum and tissues (P<0.05, P<0.01). Immunohistochemistry and Western blot demonstrated that SCF and c-Kit protein expression was decreased in the model group (P<0.05, P<0.01), which was reversed by WWSG intervention (P<0.05). ConclusionWWSG exerts therapeutic effects on FD with spleen-stomach deficiency cold syndrome in rats, potentially by regulating the SCF/c-Kit signaling pathway to enhance gastrointestinal motility.
3.Application of artificial intelligence in medical education for pediatric surgery
Chinese Journal of Medical Education Research 2024;23(5):589-593
This article focuses on the application of artificial intelligence in pediatric surgery education. In view of the current situation of medical education in pediatric surgery, combining the advantages of artificial intelligence technology, we present the prospects of artificial intelligence in pediatric surgery education from the perspectives of clinical decision-making, teaching assistance, virtual simulation training, and question library construction, and also discuss associated possible problems in teaching practice.
4.Predictive value of serum Actinin-4 and NDRG4 for postoperative recurrence and metastasis in early stage lung cancer patients undergoing radical surgery
Xiaoqiang WANG ; Yuman SUN ; Xuan ZHENG ; Xinxin ZHAO ; Jingjing ZHENG
International Journal of Laboratory Medicine 2024;45(22):2743-2746
Objective To investigate the predictive value of serum Actinin-4 and N-myc downscream regu-lated gene 4(NDRG4)for recurrence and metastasis in early stage lung cancer patients.Methods A total of 110 patients who underwent early lung cancer radical surgery in the hospital from January 2020 to January 2022 were collected as the study subjects.They were separated into a recurrence group of 62 patients and a non recurrence group of 48 patients based on whether they experienced recurrence or metastasis during a one-year follow-up.Enzyme-linked immunosorbnent assay(ELISA)method was applied to detect serum Actinin-4 and NDRG4 levels.Pearson and Spearman methods were used for correlation analysis.Logistic regression was applied to analyze the influencing factors of recurrence and metastasis in early stage lung cancer patients after radical surgery.Receiver operating characteristic(ROC)curve was applied to analyze the predictive value of serum Actinin-4 and NDRG4 levels for recurrence and metastasis in early stage lung cancer patients after radi-cal surgery.Results Compared with the non recurrence group,the serum Actinin-4 level in the recurrence group was obviously increased,while the NDRG4 level was obviously reduced,and there was a obvious differ-ence in TNM staging and lymph node metastasis between the two groups(P<0.05).Pearson analysis showed that there was a negative correlation between serum Actinin-4 and NDRG4 levels in the recurrence group(r=-0.566,P<0.05).Spearman analysis showed that Actinin-4 was positively correlated with lymph node me-tastasis and clinical staging(r=0.429,0.396,P<0.05),while NDRG4 was negatively correlated with lymph node metastasis and clinical staging(r=-0.411,-0.431,P<0.05).Logistic regression analysis showed that lymph node metastasis,clinical staging,Actinin-4,and NDRG4 levels could all be used as influencing fac-tors for postoperative recurrence and metastasis in early stage lung cancer patients after radical surgery(P<0.05).ROC curve analysis showed that the area under the curve(AUC)of serum Actinin-4 and NDRG4 in predicting postoperative recurrence and metastasis in early stage lung cancer patients after radical surgery was 0.857 and 0.848,respectively,and the AUC of combined prediction was 0.950,which was better than those of the two single predictions(P<0.05).Conclusion Serum Actinin-4 level increases and NDRG4 level decrea-ses in early stage lung cancer patients with postoperative recurrence and metastasis after radical surgery.The combined detection of the two could serve as an auxiliary indicator for predicting postoperative recurrence and metastasis in early stage lung cancer patients after radical surgery.
5.The RNA binding protein QKI can promote gastric cancer by regulating cleavage of EMT-related gene transcripts to form circRNAs
Yi-Shuang CUI ; Xuan ZHENG ; Ya-Nan WU ; Yi-Han YAO ; Jun WANG ; Zi-Qing LIU ; Guo-Gui SUN
Chinese Pharmacological Bulletin 2024;40(8):1462-1473
Aim To study the proliferation,invasion and migration ability of Quaking(QKI)in gastric cancer(GC)via elucidating the molecular mechanisms associated with QKI in the occurrence and development of GC through bioinformatics.Methods Differential expression analysis of QKI was performed across vari-ous human cancer samples by merging data from the TCGA and GTEx databases.The correlation was ana-lyzed between QKI protein expression and tumor muta-tion burden(TMB)score,microsatellite instability(MSI)score,and ESTIMATE score,and the correla-tion was also explored between QKI protein expression and overall survival(OS),disease free survival(DFS),and progression free survival(PFS).EMT related genes that could encode DECircRNAs were ob-tained through bioinformatics analysis to construct a QKI-EMT-circRNAs regulatory network.The differenti-ally expressed circRNAs and EMT related genes in TMK1 cells were verified.The proliferation,invasion and migration ability of the QKI was studied by using the knockdown system.Results QKI was differential-ly expressed in the vast majority of tumors and was closely related to TMB,MSI,and tumor microenviron-ment(TME);QKI emerged as a high-risk factor for predicting OS,DFS,and PFS in individuals with com-mon human cancers.QKI regulated the splicing of 6 EMT related gene transcripts to form eight circRNAs,all of which were significantly associated with the prog-nosis of gastric cancer patients.Cell experiments showed that compared to normal gastric epithelial cells,only hsa_ccirc_0004015,CALD1,and CDK14 were down-regulated in TMK1 cells.Knocking down QKI inhibited the proliferation,invasion and migration ability of TMK1 cells.Conclusion QKI exerts regu-latory control over the transcription of six EMT-related genes,resulting in the formation of circRNAs,thereby promoting the pathogenesis and progression of GC.QKI is highly expressed in TMK1 cells,and knock-down of QKI can inhibit the proliferation,invasion and migration ability of TMK1 cells.
6.Research progress of cement-augmented pedicle screw instrumentation technique
Yong-Cun WEI ; Yan-Chun XIE ; An-Wu XUAN ; Hong-Wen GU ; Bin ZHENG ; Yi LIAN ; Ze-Ning WANG ; Hai-Long YU
Journal of Regional Anatomy and Operative Surgery 2024;33(5):455-459
Osteoporosis is an important cause of internal fixation loosening after spinal surgery.Cement-augmented pedicle screw instru-mentation(CAPSI)technique is the most widely used technique in clinical practice to improve the stability of pedicle screw,mainly applied in osteoporosis and revision surgery,which included conventional solid pedicles crews and fenestrated/cannulated pedicle screws technique.CAPSI technique may cause cement leakage and pulmonary embolism,and there is no consensus on its indications or technical points.Therefore,this article reviews the research progress of CAPSI,in order to provide relevant reference for clinical practice.
7.Roles of Pyroptosis in Oral Diseases
Zheng-Sen WANG ; Yu XUE ; Yi-Xuan CHEN
Chinese Journal of Biochemistry and Molecular Biology 2024;40(9):1230-1239
Oral diseases are usually caused by external physical and chemical factors,the invasion of pathogens,dento-maxillofacial deformities and systemic diseases.Oral infections and orofacial pain triggered by oral diseases seriously reduce the quality of life.Pyroptosis is a kind of programmed cell death,which is characterized by swelling of the cell until the cell membrane ruptures,releasing the cell contents and activating a strong inflammatory response.Previous studies have shown that pyroptosis is widely involved in the occurrence and development of oral diseases.In this review,four types of cellular pyroptosis pathways are described in detail,including the canonical pathway,non-canonical pathway,caspase-3/8 mediated pathway and caspase independent pathway.Different pyroptosis pathways form complex signal networks,which regulate the functions of periodontal membrane cells,gingival fibroblasts,macrophages and other cells in the oral cavity,thus affecting the occurrence and development of oral diseases.This review summarizes the latest research about the pathways of pyroptosis and its roles in oral diseases,aiming to provide a theoretical basis and direction for searching effective methods to treat and prevent oral diseases.
8.A QCM Biosensor for Screening Arsenic(Ⅲ)Aptamers and Detecting Arsenic(Ⅲ)
Chu-Jun ZHENG ; Shi-Quan QIAN ; Xin-Pei LI ; Xu YAN ; Hai-Xuan HUANG ; Yu-Xuan WANG ; Yu-Wei YE ; Min YUAN
Chinese Journal of Biochemistry and Molecular Biology 2024;40(9):1282-1288
A quartz crystal microbalance(QCM)-systematic evolution of ligands by the exponential en-richment(SELEX)technique was developed to screen out aptamers with high affinity for arsenic(Ⅲ).A random single strand DNA library was designed and fixed on the mercaptoethylamine-modified crystal plate with arsenic(Ⅲ)as the target,and the free aptamer was captured in the solution,and the QCM-SELEX screening method was constructed.After 6 rounds of screening,the secondary library was se-quenced with high throughput method,and the 6S1 dissociation coefficient Kd value was 0.36 μmol/L based on QCM resonance frequency.Using 6S1 as a probe,the QCM biosensor was constructed for the detection of arsenic(Ⅲ).The sensor has a good linear relationship in the range of 0.01 μmol/L~0.2μmol/L,and the detection limit of arsenic(Ⅲ)is 5.2 nmol/L(3σ),indicatinggood selectivity.
9.Clinical Characteristics and Prognosis of Children with Hypodip-loid B-cell Precursor Acute Lymphoblastic Leukemia
Cheng-Xuan CHEN ; Kai-Zhi WENG ; Hong WEN ; Shu-Quan ZHUANG ; Xing-Guo WU ; Yong-Zhi ZHENG
Journal of Experimental Hematology 2024;32(5):1356-1364
Objective:To analyze the clinical characteristics and prognosis of children with hypodiploid B-cell precursor acute lymphoblastic leukemia(BCP-ALL).Methods:The clinical data of 1 287 children with BCP-ALL admitted to five hospital in Fujian province from April 2011 to December 2020 were retrospectively analyzed.According to the results of chromosome karyotype,all the patients were grouped into hypodiploid subgroup and non-hypodiploid subgroup.The clinical characteristics,early treatment response[minimal residual disease(MRD)on middle stage of induction chemotherapy and end of induction chemotherapy]and long-term efficacy[overall survival(OS)and event-free survival(EFS)]were compared.The prognostic factors of hypodiploid BCP-ALL were further explored.Results:Among 1 287 BCP-ALL patients,28 patients(2.2%)were hypodiploid BCP-ALL.The proportion of patients with white blood cell count(WBC)≥50 x 109/L in the hypodiploid subgroup was significantly higher than that in the non-hypodiploid subgroup(P=0.004),while there was no statistically significant difference in gender ratio,age group at initial diagnosis,and early treatment response between the two groups(all P>0.05).The 5-year EFS and OS rate of the hypodiploid subgroup were 75.0%(95%CI:66.8%-83.2%)and 77.8%(95%CI:69.8%-85.8%),respectively,which were lower than those of non-hypodiploid subgroup[EFS:79.6%(95%CI:78.4%-80.8%);OS:86.4%(95%CI:85.4%-87.5%)],but the difference was not statistically significant(all P>0.05).Further subgroup analysis by risk stratification showed that the 5-year EFS and OS rates of the hypodiploid subgroup were significantly lower than those in the low-risk(LR)group[LR group EFS:91.4%(95%CI:88.4%-93.6%),P<0.001;OS:94.7%(95%CI:92.1%-96.4%),P<0.001];it was similar to that of BCP-ALL children stratified into intermediate-risk(IR)excluding hypodiploid[IR group EFS:79.4%(95%CI:74.9%-83.2%),P=0.343;OS:87.3%(95%CI:83.6%-90.2%),P=0.111];while was higher than that of EFS in HR group,but the difference was not statistically significant[HR group EFS:58.7%(95%CI:52.6%-64.8%),P=0.178.OS:69.9%(95%CI:63.5%-75.4%),P=0.417].Univariate analysis showed that gender,age,white blood cell count,and MRD on middle stage of induction chemotherapy had no significant impact on OS and EFS;chromosome count<40 was a risk factor for lower OS(P=0.026),but has no significant effect on EFS;MRD≥0.01%after induction therapy was a risk factor for lower OS and EFS(P=0.002,and 0.001,respectively).Conclusion:Children with hypodiploid BCP-ALL have an intermediate prognosis,and MRD ≥0.01%after induction chemotherapy may be a risk factors for poor prognosis.
10.Application value of RMNES combined with comprehensive rehabilitation for consciousness disorders caused by senile brain injury
Qian ZHANG ; Xuan LI ; Xinrui ZHENG ; Yu WANG
Chinese Journal of Geriatric Heart Brain and Vessel Diseases 2024;26(7):784-788
Objective To explore the application value of RMNES combined with comprehensive rehabilitation for consciousness impairment caused by senile brain injury.Methods A retrospec-tive analysis was conducted on 160 elderly patients with consciousness disorders caused by brain injury admitted in our hospital between January 2020 and November 2023.According to treatment regiments,they were divided into comprehensive rehabilitation group(Group Ⅰ,53 cases),com-prehensive rehabilitation followed by RMNES group(Group Ⅱ,54 patients),and simultaneous indoor comprehensive rehabilitation and RMNES(Group Ⅲ,53 patients).At 1 week after treat-ment,electroencephalogram(EEG)grade,brainstem auditory induction(BAEP)grade,cerebral hemodynamic parameters[including relative cerebral blood flow(rCBF),relative cerebral blood volume(rCBV),and mean blood flow velocity(Vm)],Disability Rating Scale(DRS)score,and Glasgow Coma Scale(GCS)score were compared among the three groups.Results After 1 week of treatment,the ratios of EEG grade Ⅰ,EEG grade Ⅱ and BAEP grade Ⅰ,rCBV,rCBF and Vm values and GCS score were increased,while the ratios of EEG grade V and BAEP grade Ⅲ,and DRS score were decreased when compared with the levels before treatment(P<0.05).Significant differences were observed in EEG grade and BAEP grade among the 3 groups after 1 week of treatment(P<0.01);Group Ⅲ had obviously higher rCBV,rCBF,Vm and GCS score and lower DRS score than Groups Ⅰ and Ⅱ(P<0.05).There was no statistical difference in the incidence of adverse reactions in Groups Ⅰ,Ⅱ and Ⅲ(3.77%vs 7.41%vs 7.55%,x2=0.830,P=0.660).Conclusion Simultaneous indoor comprehensive rehabilitation and RMNES treatment achieves more significant efficacy for elderly patients with brain injury-caused consciousness disorders,and it can improve electrophysiological activities of brain nerves,enhance cerebral hemodynamics,and promote the recovery of consciousness.

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