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.Kinase modulators approved by FDA in 2022
Acta Pharmaceutica Sinica 2024;59(1):61-75
The FDA approved a total of 37 new drugs in 2022, including 22 new molecular entities and 15 new biological products. This is the year with the lowest number of new drugs approved by the FDA since 2017. Among these approved drugs, 21 new drugs belong to the "first-in-class" category, accounting for 56% of the total approved drugs, which is the highest ratio in the past 10 years. Among the drugs approved in 2022, there are 5 small molecule kinase modulators, including the tyrosine kinase 2 (TYK2) allosteric inhibitor deucravacitinib, the first oral pyruvate kinase (PK) activator mitapivat, the Janus kinase 1 (JAK1) selective inhibitor abcrocitinib, the JAK2 selective inhibitor pacritinib and the broad-spectrum fibroblast growth factor receptor (FGFR) inhibitor futibatinib. This review briefly describes the discovery background, research and development process, synthesis routes and clinical efficacy and safety of small molecule kinase modulators approved by the FDA in 2022, hoping to provide ideas and methods for further research on kinase modulators.
4.Gadopiclenol,a new radiological diagnostic drug used in magnetic resonance imaging
Lu ZHENG ; Ting YANG ; Chao-Yang CHEN ; Ran WEI ; Xuan-Ling ZHANG ; Jing-Zhong DENG ; Ying ZHOU
The Chinese Journal of Clinical Pharmacology 2024;40(11):1661-1664
Gadopiclenol was used in adults and pediatric patients 2 years of age and older during magnetic resonance imaging(MRI)to detect and view lesions of the central nervous system(brain,spine,and associated tissues)and body(head and neck,chest,abdomen,pelvis,and musculoskeletal system)with abnormal vascular properties.Gadopiclenol is a new type of macrocyclic gadolinium-based contrast agent(GBCA).In this article,the molecular structure,principle of action,pharmacodynamics,pharmacokinetics,clinical studies,safety and other aspects of Gadopiclenol were reviewed,in order to introduce the current research status and existing achievements of Gadopiclenol.
5.Effects of enamel adhesives with different components on Porphyromonas gingivalis and Streptococcus mutans
Zhiyao LI ; Zheng HU ; Xuan LI ; Peijun LU
Chinese Journal of Tissue Engineering Research 2024;28(3):329-335
BACKGROUND:The light curing and fluoride light curing enamel adhesives have a certain sealing effect on the etched enamel surface.The fluoride light curing enamel adhesives can also achieve the anti-caries function by releasing fluoride ions.However,the existing researches lack the long-term tracing of fluoride release effect,especially the amount of local pathogenic bacteria after 1-3 months of local fluoride application. OBJECTIVE:To analyze the changes in the expression of Porphyromonas gingivalis and Streptococcus mutans in subgingival plaque of the upper anterior teeth adhered by different components of enamel adhesives in adolescent patients with fixed appliance. METHODS:Ninety adolescent patients who received orthodontic treatment in Shanghai Stomatological Hospital from January to December 2016 were enrolled,including 43 males and 47 females,with a mean age of(13.27±1.12)years.These patients were randomly divided into three groups(n=30 per group).In the chemical curing group,Unite? bonding resin was used to bond fixed appliances.In the light curing group,Transbond XT light curing resin was used to bond the fixed appliance.In the fluoride light curing group,GC light curing orthodontic adhesive was used to bond the fixed appliance with cement.The subgingival plaque was collected on the day of bonding,1st,2nd,and 3rd month follow-up reviews.The expressions of Porphyromonas gingivalis and Streptococcus mutans in subgingival plaque were detected by PCR. RESULTS AND CONCLUSION:(1)Intragroup comparison:With the increase of bonding time,Porphyromonas gingivalis expression increased significantly in the 3rd month in the chemical curing group(P<0.05).In the light curing group,Porphyromonas gingivalis showed a significant decrease in the 1st month(P<0.05).Porphyromonas gingivalis expression decreased significantly in the 1st and 2nd months compared with initial data in the fluoride light curing group(P<0.05).The expression of Streptococcus mutans was higher in the chemical curing group in the 1st,2nd,and 3rd months compared with the initial data(P<0.05).In the fluoride light curing group,the expression of Streptococcus mutans was lower in the 1st,2nd,and 3rd months compared with the initial data(P<0.05).There was no significant difference in the proliferation and expression of Streptococcus mutans during follow-up in the light curing group compared to the initial adhesion(P>0.05).(2)Intergroup comparison:In the 1st month,the expression of Porphyromonas gingivalis was lower in the light curing group and fluoride light curing group than that in the chemical curing group(P<0.05).In the 2nd and 3rd months,the expression of Porphyromonas gingivalis was lower in the fluoride light curing group than that in the light curing group and chemical curing group(P<0.05).In the 1st,2nd,and 3rd months,the expression of Streptococcus mutans was lower in the light curing group and fluoride light curing group than that in the chemical curing group(P<0.05).The expression of Streptococcus mutans was lower in the fluoride light curing group than that in the light curing group(P<0.05).(3)The results show that in the fixed orthodontic process,the use of different components of enamel adhesives has different effects on the proliferation and expression of oral Porphyromonas gingivalis and Streptococcus mutans in the short term.Fluoride light curing enamel adhesives at the initial stage can reduce the occurrence of enamel demineralization,caries,and periodontal inflammation.
6.SWOT analysis of construction of intelligent vaccination clinics in Zhejiang Province
ZHENG Shuhan ; SHEN Lingzhi ; DENG Xuan ; SU Ying ; LUO Feng ; ZHOU Yang ; TANG Xuewen ; YAN Rui ; ZHU Yao ; HE Hanqing
Journal of Preventive Medicine 2024;36(8):669-673
Objective:
To analyze the strengths, weaknesses, opportunities and threats of the construction on intelligent vaccination clinics in Zhejiang Province, so as to provide countermeasures for promoting the construction of intelligent vaccination clinics in Zhejiang Province.
Methods:
By reviewing the annual reports of Zhejiang immunization planning, survey data from Zhejiang Centers for Disease Control and Prevention and Immunization Intelligent Service System, data of human resources of immunization planning, vaccine procurement, construction progress of intelligent vaccination clinics and vaccination were collected. The relevant literature was searched to gather information on the construction standards and norms of intelligent vaccination clinics. The analysis of the strengths, weaknesses, opportunities and threats (SWOT) of the construction of intelligent vaccination clinics was conducted, and corresponding countermeasures and suggestions were proposed.
Results:
The National Immunization Program reported vaccine rate in Zhejiang Province is more than 99%, and standardized vaccination clinics have been popularized throughout the province. The vaccination staff are professional, and a province-wide intelligent immunization service information system has been established, providing the resources and conditions for the construction of intelligent vaccination clinics. However, there are problems such as low data quality and matching efficiency in vaccination, insufficient data interoperability and sharing, unbalanced regional capabilities in intelligent transformation, and uneven distribution of talent and resources. It is crucial to seize the opportunities presented by the development of big data and artificial intelligence, rely on the regional development of the Internet and health industry, seize the opportunity of rapid growth in demand for intelligent vaccination services and high public acceptance, accelerate the construction of intelligent vaccination clinics, and establish intelligent vaccination service standards as soon as possible.
Conclusion
We should seize the opportunities presented by the digital reform and development, fully utilize the existing vaccination resources and strengths, address the shortcomings, and accelerate the construction of intelligent vaccination clinics in Zhejiang Province.
7.A Prognostic Model Based on Colony Stimulating Factors-related Genes in Triple-negative Breast Cancer
Yu-Xuan GUO ; Zhi-Yu WANG ; Pei-Yao XIAO ; Chan-Juan ZHENG ; Shu-Jun FU ; Guang-Chun HE ; Jun LONG ; Jie WANG ; Xi-Yun DENG ; Yi-An WANG
Progress in Biochemistry and Biophysics 2024;51(10):2741-2756
ObjectiveTriple-negative breast cancer (TNBC) is the breast cancer subtype with the worst prognosis, and lacks effective therapeutic targets. Colony stimulating factors (CSFs) are cytokines that can regulate the production of blood cells and stimulate the growth and development of immune cells, playing an important role in the malignant progression of TNBC. This article aims to construct a novel prognostic model based on the expression of colony stimulating factors-related genes (CRGs), and analyze the sensitivity of TNBC patients to immunotherapy and drug therapy. MethodsWe downloaded CRGs from public databases and screened for differentially expressed CRGs between normal and TNBC tissues in the TCGA-BRCA database. Through LASSO Cox regression analysis, we constructed a prognostic model and stratified TNBC patients into high-risk and low-risk groups based on the colony stimulating factors-related genes risk score (CRRS). We further analyzed the correlation between CRRS and patient prognosis, clinical features, tumor microenvironment (TME) in both high-risk and low-risk groups, and evaluated the relationship between CRRS and sensitivity to immunotherapy and drug therapy. ResultsWe identified 842 differentially expressed CRGs in breast cancer tissues of TNBC patients and selected 13 CRGs for constructing the prognostic model. Kaplan-Meier survival curves, time-dependent receiver operating characteristic curves, and other analyses confirmed that TNBC patients with high CRRS had shorter overall survival, and the predictive ability of CRRS prognostic model was further validated using the GEO dataset. Nomogram combining clinical features confirmed that CRRS was an independent factor for the prognosis of TNBC patients. Moreover, patients in the high-risk group had lower levels of immune infiltration in the TME and were sensitive to chemotherapeutic drugs such as 5-fluorouracil, ipatasertib, and paclitaxel. ConclusionWe have developed a CRRS-based prognostic model composed of 13 differentially expressed CRGs, which may serve as a useful tool for predicting the prognosis of TNBC patients and guiding clinical treatment. Moreover, the key genes within this model may represent potential molecular targets for future therapies of TNBC.
8.Efficacy evaluation of comprehensive treatment for chronic dacryocystitis with meibomian gland dysfunction
Yi ZHANG ; Xiaozhao YANG ; Hua YANG ; Xuan ZHENG ; Haiqing LU ; Chao LIU
International Eye Science 2024;24(11):1836-1841
AIM: To investigate the efficacy of lacrimal duct laser dacryoplasty combined with intubation and postoperative meibomian gland treatment in patients with chronic dacryocystitis complicated by meibomian gland dysfunction.METHODS: Data were collected from 128 patients with chronic dacryocystitis complicated by meibomian gland dysfunction treated at Xi'an No.1 Hospital from March 2021 to December 2022. All patients underwent lacrimal duct laser dacryoplasty combined with intubation. Postoperatively, those patients were randomly divided into two groups: group A(64 cases, without meibomian gland treatment)and group B(64 cases, with meibomian gland treatment). The lacrimal intubation was removed at 3 mo after surgery to evaluate the patency rate of lacrimal irrigation. Additionally, changes in the ocular surface disease index(OSDI)score, non-invasive tear film break-up time, tear meniscus height, conjunctival hyperemia analysis, meibomian gland analysis, tear lipid layer thickness, tear ferning test, and conjunctival impression cytology were compared between the two groups.RESULTS: The lacrimal irrigation patency rates in the group A and group B were 78.1% and 81.2% respectively, with no statistically significant difference between the two groups(P>0.05); compared with the group A, group B showed a significant extension in non-invasive tear breakup time at 3 mo after surgery, and the OSDI score, conjunctival hyperemia analysis, tear ferning test and conjunctival impression cytology grading were all significantly decreased(all P<0.05), while there was no significant difference in tear meniscus height, tear lipid layer thickness and meibomian gland loss score between the two groups(all P>0.05).CONCLUSION: Comprehensive treatment for patients with chronic dacryocystitis combined with meibomian gland dysfunction have improved patients' comfort, tear film stability, and reduces local inflammatory response. It is important to simultaneously address ocular surface microenvironment abnormalities during surgical treatment to achieve satisfactory efficacy.
9.Full-length transcriptome sequencing and bioinformatics analysis of Polygonatum kingianum
Qi MI ; Yan-li ZHAO ; Ping XU ; Meng-wen YU ; Xuan ZHANG ; Zhen-hua TU ; Chun-hua LI ; Guo-wei ZHENG ; Jia CHEN
Acta Pharmaceutica Sinica 2024;59(6):1864-1872
The purpose of this study was to enrich the genomic information and provide a basis for further development and utilization of
10.Schisandrin A ameliorates DSS-induced acute ulcerative colitis in mice via regulating the FXR signaling pathway
Jia-rui JIANG ; Kua DONG ; Yu-chun JIN ; Xin-ru YANG ; Yi-xuan LUO ; Shu-yang XU ; Xun-jiang WANG ; Li-hua GU ; Yan-hong SHI ; Li YANG ; Zheng-tao WANG ; Xu WANG ; Li-li DING
Acta Pharmaceutica Sinica 2024;59(5):1261-1270
Inflammatory bowel disease (IBD) is characterized by chronic relapsing intestinal inflammation and encompasses ulcerative colitis (UC) and Crohn's disease (CD). IBD has emerged as a global healthcare problem. Clinically efficacious therapeutic agents are deficient. This study concentrates on models of ulcerative colitis with the objective of discovering novel therapeutic strategies. Previous investigations have established that schisandrin A demonstrates anti-inflammatory effects


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