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. Benzyl isothiocyanate induces cell cycle arrest and apoptosis in cervical cancer through activation of p53 and AMPK-FOXO1a signaling pathways
Tamasha KURMANJIANG ; Xiao-Jing WANG ; Xin-Yi LI ; Hao WANG ; Guo-Xuan XIE ; Yun-Jie CHEN ; Ting WEN ; Xi-Lu CHENG ; Nuraminai MAIMAITI ; Jin-Yu LI
Chinese Pharmacological Bulletin 2024;40(1):114-158
Aim To investigate the effect of benzyl iso-thiocyanate (BITC) on the proliferation of mouse U14 cervical cancer cells and to explore the mechanism of cytotoxicity based on transcriptomic data analysis. Methods The effect of BITC on U14 cell activity was detected by MTT, nuclear morphological changes were observed by Hochest 33258 and fluorescent inverted microscope, cell cycle and apoptosis were determined by flow cytometry, and the transcriptome database of U14 cells before and after BITC (20 μmol · L
3.Rapid Screening of 34 Emerging Contaminants in Surface Water by UHPLC-Q-TOF-MS
Chen-Shan LÜ ; Yi-Xuan CAO ; Xiao-Xi MU ; Hai-Yan CUI ; Tao WANG ; Zhi-Wen WEI ; Ke-Ming YUN ; Meng HU
Journal of Forensic Medicine 2024;40(1):30-36
Objective To establish a rapid screening method for 34 emerging contaminants in surface water by ultra-high performance liquid chromatography-quadrupole-time of flight mass spectrometry(UHPLC-Q-TOF-MS).Methods The pretreatment conditions of solid phase extraction(SPE)were op-timized by orthogonal experimental design and the surface water samples were concentrated and ex-tracted by Oasis? HLB and Oasis? MCX SPE columns in series.The extracts were separated by Kine-tex? EVO C18 column,with gradient elution of 0.1%formic acid aqueous solution and 0.1%formic acid methanol solution.Q-TOF-MS'fullscan'and'targeted MS/MS'modes were used to detect 34 emerging contaminants and to establish a database with 34 emerging contaminants precursor ion,prod-uct ion and retention times.Results The 34 emerging contaminants exhibited good linearity in the con-centration range respectively and the correlation coefficients(r)were higher than 0.97.The limit of de-tection was 0.2-10 ng/L and the recoveries were 81.2%-119.2%.The intra-day precision was 0.78%-18.70%.The method was applied to analyze multiple surface water samples and 6 emerging contaminants were detected,with a concentration range of 1.93-157.71 ng/L.Conclusion The method is simple and rapid for screening various emerging contaminants at the trace level in surface water.
4.Effect of Bushen Quhan Huashi Prescription Combined with Methotrexate on Disease Activity and Serum Core-Binding Factor a1 Level in Patients with Ankylosing Spondylitis
Xuan LI ; Jun-Jie WANG ; Jing MAO ; Yun-Nan LI
Journal of Guangzhou University of Traditional Chinese Medicine 2024;41(4):862-867
Objective To investigate the effects of the Bushen Quhan Huashi Prescription(mainly composed of Drynariae Rhizoma,Eucommiae Cortex,Dipsaci Radix,Notopterygii Rhizoma et Radix,Zingiberis Rhizoma Recens,Coicis Semen,and Achyranthis Bidentatae Radix)in combination with Methotrexate on the disease activity and serum core-binding factor a1(Cbfa1)level of patients with ankylosing spondylitis(AS)of kidney deficiency and governor-vessel cold type.Methods Ninety AS patients with kidney deficiency and governor-vessel cold type were randomly divided into a trial group and a control group,with 45 patients in each group.The control group was given Methotrexate treatment,and the trial group was treated with Bushen Quhan Huashi Prescription on the basis of treatment for the control group.The course of treatment in the two groups lasted for 3 months.The changes of Bath ankylosing spondylitis disease activity index(BASDAI)scores,Bath ankylosing spondylitis function index(BASFI)scores and serum levels of Cbfa1,type I collagen carboxy-terminal peptide(CTX-Ⅰ)and Dickkopf1 protein(DKK1)of the two groups were observed before and after treatment.After treatment,the clinical efficacy and the incidence of adverse effects were compared between the two groups.Results(1)After 3 months of treatment,the total effective rate of the trial group was 97.78%(44/45)and that of the control group was 82.22%(37/45).The intergroup comparison by chi-square test)showed that the therapeutic efficacy of the trial group was significantly superior to that of the control group,and the difference was statistically significant(P<0.05).(2)After treatment,the disease activity scores of BASDAI and BASFI in the two groups of patients were significantly decreased compared with those before treatment(P<0.05),and the trial group's reduction of BASDAI scores and BASFI scores were significantly superior to those of the control group,and the differences were statistically significant(P<0.01).(3)After treatment,the serum levels of serological indicators of Cbfa1,CTX-Ⅰ,and DKK1 in the two groups were decreased compared with those before treatment(P<0.05),and the decrease of Cbfa1,CTX-Ⅰ and DKK1 levels in the trial group was significantly superior to that in the control group,the differences being all statistically significant(P<0.01).(4)During the treatment,the incidence of adverse reactions in the trial group was 6.66%(3/45)and that in the control group was 11.11%(5/45),and the difference of the incidence of adverse reactions between the two groups was not statistically significant(P>0.05).Conclusion Bushen Quhan Huashi Prescription combined with Methotrexate exerts certain effect in treating AS patients with kidney deficiency and governor-vessel cold type,and the therapy can effectively control the disease activity and reduce the level of serum Cbfa1 expression in the patients.
5.Median effective dose of remimazolam combined with sufentanil for inhibition of nasopharyngeal airway insertion reaction in elderly patients
Shuwen QIAN ; Xuan GUO ; Yun SHEN ; Mazhong ZHANG
The Journal of Clinical Anesthesiology 2024;40(1):61-64
Objective To calculate median effective dose(ED50)of remimazolam combined with sufentanil for inhibition of nasopharyngeal airway insertion reaction in elderly patients.Methods Thirty-eight patients,aged≥65 years,BMI 18-25 kg/m2,ASA physical statusⅠ-Ⅲ,undergoing elective cata-ract surgery under nasopharyngeal airway were selected.Patients received intravenous sufentanil injections of 0.1 μg/kg,followed by intravenous remimazolam injection 3 minutes later,then nasopharyngeal airway in-sertion after 2 minutes.The initial dose of remimazolam was 0.2 mg/kg and adjusted by 0.01 mg/kg,based on the modified Dixon sequential method.A positive reaction was defined as head shaking,choking,body movement,an increase in HR>20%of the basal value,or an increase in SBP or DBP>20%of the basal value at the time of nasopharyngeal airway placement.The procedure was stopped after seven crossovers.The ED50,95%effective dose(ED95)of remimazolam,and 95%confidence intervals(CI)were calculated by probabilistic unit(Probit)regression analysis.Results When combined with sufentanil,the ED50 and ED95 of remimazolam for inhibition of nasopharyngeal airway insertion in elderly patients was 0.193 mg/kg(95%CI 0.191-0.195 mg/kg)and 0.209 mg/kg(95%CI 0.205-0.213 mg/kg),respectively.Conclusion The ED50 of remimazolam combined with sufentanil for inhibition of nasopharyngeal airway in-sertion reaction in elderly patients were 0.193 mg/kg(95%CI 0.191-0.195 mg/kg).
6.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.
7.Application of Functionalized Liposomes in The Delivery of Natural Products
Cheng-Yun WANG ; Xin-Yue LAN ; Jia-Xuan GU ; Xin-Ru GAO ; Long-Jiao ZHU ; Jun LI ; Bing FANG ; Wen-Tao XU ; Hong-Tao TIAN
Progress in Biochemistry and Biophysics 2024;51(11):2947-2959
Plant natural products have a wide range of pharmacological properties, not only can they be used as plant dietary supplements to meet the nutritional needs of the human body in the accelerated pace of life, but also occupy an important position in the research and development of therapeutic drugs for the treatment of tumors, inflammation and other diseases, and have been widely accepted by the public due to their good safety. However, despite the above advantages of plant natural products, limiting factors such as low solubility, poor stability, lack of targeting, high toxicity and side effects, and unacceptable odor have greatly impeded their conversion to clinical applications. Therefore, the development of new avenues for the application of new natural products has become an urgent problem to be solved at present. In recent years, with the continuous development of research, various strategies have been developed to improve the bioavailability of natural products. Among them, nanocarrier delivery system is one of the most attractive strategies at present. In past studies, a large number of nanomaterials (organic, inorganic, etc.) have been developed to encapsulate plant-derived natural products for their efficient delivery to specific organs and cells. Up to now, nanotechnology has not only been limited to pharmaceutical applications, but is also competing in the fields of nanofood processing technology and nanoemulsions. Among the various nanocarriers, liposomes are the largest nanocarriers with the largest market share at present. Liposomes are bilayer nanovesicles synthesized from amphiphilic substances, which have advantages such as high drug loading capacity and stability. Attractively, the flexible surface of liposomes can be modified with various functional elements. Functionalized modification of liposomes with different functional elements such as antibodies, nucleic acids, peptides, and stimuli-responsive moieties can bring out the excellent drug delivery function of liposomes to a greater extent. For example, the modification of functional elements with targeting function such as nucleic acids and antibodies on the surface of liposomes can deliver natural products to the target location and improve the bioavailability of drugs; the modification of stimulus-responsive groups such as photosensitizers, magnetic nanoparticles, pH-responsive groups, and temperature sensitizers on the surface of liposomes can achieve controlled release of drugs, localized targeting, and synergistic thermotherapy. In addition to the above properties, by using functionalized liposomes to encapsulate natural products with irritating properties can also effectively mask the irritating properties of natural products, improve public acceptance, and increase the possibility of application of irritating natural products. There are various strategies for modifying liposomes with functional elements, and the properties of functionalized liposomes constructed by different construction strategies differ. The commonly used construction strategies for functionalized liposomes include covalent modification and non-covalent modification. These two types of construction strategies have their own advantages and disadvantages. Covalent modification has better stability than non-covalent modification, but its operation is cumbersome. With the above background, this review focuses on the three typical problems faced by plant natural products at present, and summarizes the specific applications of functionalized liposomes in them. In addition, this paper summarizes the construction strategies for building different types of functionalized liposomes. Finally, this paper will also review the opportunities and challenges faced by functionalized liposomes to enter clinical therapy, and explore the opportunities to overcome these problems, with a view to better realizing the precise control of plant nanomedicines, and providing ideas and inspirations for researchers in related fields as well as relevant industrial staff.
8.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.
9.The taste correction process of ibuprofen oral solution based on the combination of electronic tongue technology and artificial taste comprehensive evaluation
Rui YUAN ; Yun-ping QU ; Yan WANG ; Ya-xuan ZHANG ; Wan-ling ZHONG ; Xiao-yu FAN ; Hui-juan SHEN ; Yun-nan MA ; Jin-hong YE ; Jie BAI ; Shou-ying DU
Acta Pharmaceutica Sinica 2024;59(8):2404-2411
This experiment aims to study the taste-masking effects of different kinds of corrigent used individually and in combination on ibuprofen oral solution, in order to optimize the taste-masking formulation. Firstly, a wide range of corrigent and the mass fractions were extensively screened using electronic tongue technology. Subsequently, a combination of sensory evaluation, analytic hierarchy process (AHP)-fuzzy mathematics evaluation, and Box-Behnken experimental design were employed to comprehensively assess the taste-masking effects of different combinations of corrigent on ibuprofen oral solution, optimize the taste-masking formulation, and validate the results. The study received ethical approval from the Review Committee of the Beijing University of Chinese Medicine (ethical code: 2024BZYLL0102). The results showed that corrigent fractions and types were screened separately through single-factor experiments. Subsequently, a Box-Behnken response surface design combined with AHP and fuzzy mathematics evaluation was used to fit a functional model:
10.Tetrandrine ameliorates pulmonary fibrosis by inhibiting ROS-mediated fibroblast activation
Ye-chao YAN ; Chun-yi GUO ; Jia-ming ZHANG ; Yun-xuan LI ; Ke LI
Acta Pharmaceutica Sinica 2024;59(8):2216-2226
Pulmonary fibrosis is a chronic and progressive lung disease that poses a threat to human health. Current treatment options are limited, highlighting the urgent need for more effective therapeutic strategies. Tetrandrine (TET), a bis-benzylisoquinoline alkaloid extracted from

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