1.Construction of a Prognostic Model for Lysosome-dependent Cell Death in Gastric Cancer Based on Single-cell RNA-seq and Bulk RNA-seq Data.
Peng NI ; Kai Xin GUO ; Tian Yi LIANG ; Xin Shuang FAN ; Yan Qiao HUA ; Yang Ye GAO ; Shuai Yin CHEN ; Guang Cai DUAN ; Rong Guang ZHANG
Biomedical and Environmental Sciences 2025;38(4):416-432
OBJECTIVE:
To identify prognostic genes associated with lysosome-dependent cell death (LDCD) in patients with gastric cancer (GC).
METHODS:
Differentially expressed genes (DEGs) were identified using The Cancer Genome Atlas - Stomach Adenocarcinoma. Weighted gene co-expression network analysis was performed to identify the key module genes associated with LDCD score. Candidate genes were identified by DEGs and key module genes. Univariate Cox regression analysis, and least absolute shrinkage and selection operator regression and multivariate Cox regression analyses were performed for the selection of prognostic genes, and risk module was established. Subsequently, key cells were identified in the single-cell dataset (GSE183904), and prognostic gene expression was analyzed. Cell proliferation and migration were assessed using the Cell Counting Kit-8 assay and the wound healing assay.
RESULTS:
A total of 4,465 DEGs, 95 candidate genes, and 4 prognostic genes, including C19orf59, BATF2, TNFAIP2, and TNFSF18, were identified in the analysis. Receiver operating characteristic curves indicated the excellent predictive power of the risk model. Three key cell types (B cells, chief cells, and endothelial/pericyte cells) were identified in the GSE183904 dataset. C19orf59 and TNFAIP2 exhibited predominant expression in macrophage species, whereas TNFAIP2 evolved over time in endothelial/pericyte cells and chief cells. Functional experiments confirmed that interfering with C19orf59 inhibited proliferation and migration in GC cells.
CONCLUSION
C19orf59, BATF2, TNFAIP2, and TNFSF18 are prognostic genes associated with LDCD in GC. Furthermore, the risk model established in this study showed robust predictive power.
Stomach Neoplasms/pathology*
;
Humans
;
Prognosis
;
Lysosomes/physiology*
;
RNA-Seq
;
Cell Death
;
Single-Cell Analysis
;
Gene Expression Regulation, Neoplastic
;
Cell Proliferation
;
Single-Cell Gene Expression Analysis
2.Discussion on the mechanism of Danxing Zhichan Prescription in the treatment of Parkinson's disease based on network pharmacology and experimental verification
Zhouyuan HU ; Yifan YANG ; Tao PENG ; Nan HU ; Yedong YUN ; Jun YIN ; Yongmei YAN ; Tao LI ; Ni JIA
International Journal of Traditional Chinese Medicine 2025;47(2):205-212
Objective:To explore the mechanism of Danxing Zhishuang Prescription in the treatment of Parkinson's disease (PD) by combining network pharmacology with animal models.Methods:TCMSP, BATMAN database, Genecards, and OMIM databases were retrieved to obtain the active components and action targets of Danxing Zhishuang Prescription. Venny 2.1.0 was used to intersect drug targets and PD related genes, and a protein interaction network of the intersection targets was constructed using the STRING 12.0 platform. Topology analysis was performed using Cytoscape 3.10.0 software to identify the key targets of Danxing Zhishuang Prescription on PD; GO functional and KEGG pathway enrichment analysis was performed on key targets using the WeChat platform, and molecular docking was validated through AutoDockTools 1.5.7. Using a random number table method, mice were divided into a blank control group, a model group, and a Danxing Zhishuang Prescription group, with 20 mice in each group; except for the blank group, all other groups of mice were orally administered fisetin to prepare PD models; Danxing Zhishuang Prescription group was orally administered with concentrated Danxing Zhishuang Prescription at a dosage of 10.5 g/kg, while the blank group and model group were orally administered with 0.2 ml of physiological saline for 21 days; Western blot was used to detect the expressions of Akt1, Bcl-2, Bax, and α-Syn proteins.Results:359 intersection targets, 69 core targets, and 185 active components were obtained the treatment of PD with Danxing Zhishuang Prescription. The main active components included quercetin, kaempferol, phenylalanine, etc., and the key targets were AKT1, TP53, TNF, ESR1, etc. KEGG analysis revealed several key signaling pathways, such as AGE-RAGE, PI3K-Akt, fluid shear stress and atherosclerosis signaling pathways. The validation experiment results showed that compared with the model group, the expression of Bcl-2 protein was up-regulated ( P<0.01), and the expressions of Bax, Akt1, and α-Syn proteins were down-regulated in the Danxing Zhishuang Prescription group ( P<0.01). Conclusions:Danxing Zhishuang Prescription has the advantages of multi target and multi pathway treatment for PD. Its mechanism may be related to down-regulating the expressions of Bax, Akt1, and α-Syn proteins, improving brain blood supply, regulating neurotransmitter balance, inhibiting oxidative stress response, and promoting nerve regeneration.
3.Analysis of a case with oocyte maturation disorder caused by a heterozygous c.728C>T (p.P243L) missense variant of TUBB8 gene and literature review.
Wei JIANG ; Yali NI ; Jinwei YANG ; Bo YAN ; Chuan ZHANG ; Zhiqiang WANG
Chinese Journal of Medical Genetics 2025;42(8):924-930
OBJECTIVE:
To explore the genetic basis for a woman with oocyte maturation disorder during assisted reproductive treatment (ART), and to verify the source of the variant and its impact on oocyte maturation through family verification.
METHODS:
A 35-year-old infertile woman presented at the Reproductive Medicine Center of Gansu Provincial Maternal and Child Health Care Hospital on 20 October 2023 for a 10-year history of infertility despite unprotected intercourse was selected as study subject. Peripheral venous blood sample was collected from the proband. Next-generation sequencing (NGS) was used to detect the potential variant. Candidate variants were validated within her family by Sanger sequencing, and their deleteriousness was assessed with comprehensive bioinformatic analyses to elucidate their origin and impact on oocyte maturation. According to the Standards and Guidelines for the Interpretation of Sequence Variants (hereinafter referred to as ACMG Guidelines) formulated by the American College of Medical Genetics and Genomics (ACMG), the pathogenicity of the candidate variant was rated. This study was approved by the Medical Ethics Committee of Gansu Provincial Maternal and Child Health Care Hospital (Ethics No.: 2023GSFYLS78).
RESULTS:
The proband underwent three controlled ovarian-stimulation cycles as part of assisted reproductive technology, yielding a total of 29 oocytes, among which only three were mature, whilst the remainders exhibited maturation arrest. Targeted sequencing of peripheral-blood DNA revealed a heterozygous c.728C>T (p.P243L) missense variant of the TUBB8 gene. While the same variant was detected in the proband's father. Based on the ACMG guidelines, the variant was classified to be likely pathogenic (PS4_Supporting+PM2_Supporting+PP2+PP3+PP4).
CONCLUSION
The heterozygous c.728C>T (p.P243L) missense variant of the TUBB8 gene probably underlay the oocyte maturation disorder in the proband, which may be either autosomal dominant or autosomal recessive. For probands with oocyte maturation disorders caused by the heterozygous c.728C>T variant of the TUBB8 gene, oocyte donation may be considered.
Humans
;
Female
;
Adult
;
Mutation, Missense
;
Oocytes/metabolism*
;
Heterozygote
;
Tubulin/genetics*
;
Infertility, Female/genetics*
;
High-Throughput Nucleotide Sequencing
;
Pedigree
4.Clinical phenotype and genetic analysis of a patient with Oocyte maturation defect due to a novel variant of PATL2 gene.
Fangzhu WANG ; Yali NI ; Lin ZHANG ; Bo YAN ; Jinwei YANG ; Chuan ZHANG ; Zhiqiang WANG
Chinese Journal of Medical Genetics 2025;42(10):1244-1251
OBJECTIVE:
To investigate the clinical phenotype and genetic etiology of a patient with primary infertility accompanied by Oocyte maturation defect (OOMD).
METHODS:
A 24-year-old female patient who visited the Reproductive Medicine Center of Gansu Provincial Maternity and Child Care Hospital in April 2024 was selected as the study subject. Whole-exome sequencing (WES) was performed on the proband and her husband. Candidate gene variants were validated in the family using Sanger sequencing, and compound heterozygous variants were confirmed through vector construction. Candidate variants were classified for pathogenicity according to the "Standards and Guidelines for the Interpretation of Sequence Variants" established by the American College of Medical Genetics and Genomics (ACMG). This study was approved by the Medical Ethics Committee of the Hospital [Ethics No.: (2023) GSFYLS(78)].
RESULTS:
The proband, a 24-year-old female, had been unable to conceive for four years without contraception after marriage. She had undergone two ovarian stimulation cycles using the antagonist protocol and the PPOS protocol, respectively. A total of 74 oocytes were retrieved, with all showing OOMD and some oocytes exhibiting abnormal morphology and poor quality. WES results revealed two heterozygous missense variants in exons 14 and 16 of the PATL2 gene: c.1127G>A (p.R376Q) and c.1388C>G (p.A463G). Family validation results indicated that the missense variant in exon 14 was inherited from the proband's father, while the variant in exon 16 was de novo.
CONCLUSION
The compound heterozygous variants of the PATL2 gene probably underlay the OOMD and infertility in this proband. Further analysis based on the variant sites and protein structures is needed to determine whether PATL2 gene variants can fully affect oocyte development, thereby providing a personalized treatment plan for the proband.
Female
;
Humans
;
Young Adult
;
Exome Sequencing
;
Infertility, Female/genetics*
;
Oocytes/metabolism*
;
Pedigree
;
Phenotype
5.Clinical trial of halperidol combined with ondansetron in postoperative controlled intravenous analgesia
Zhen-Yong CHENG ; Er-Wei GU ; Hong XIE ; Xiao-Yan WANG ; Bo HU ; Long-Ni CHENG ; Fei YANG
The Chinese Journal of Clinical Pharmacology 2024;40(5):649-653
Objective To investigate the efficacy of flupentixol combined with ondansetron in preventing postoperative nausea and vomiting(PONV)in patients receiving sufentanil and dezocine patient-controlled intravenous analgesia(PCIA).Methods Surgical patients receiving sufentanil and dezocine PCIA were randomly divided into treatment and control groups using a random number table.The control group received sufentanil 150 μg,dezocine 20 mg,and ondansetron 8 mg for PCIA,while the treatment group received sufentanil 150 μg,dezocine 20 mg,flupentixol 5 mg,and ondansetron 8 mg for PCIA.The incidence of PONV,severity of PONV,heart rate(HR),mean arterial pressure(MAP),blood oxygen saturation(SPO2)levels at different time points after surgery,surgery-related indicators,visual analogue scale(VAS)scores,Ramsay scores,PCIA pressing times,and incidence of adverse drug reactions were compared between the two groups.Results The incidence of PONV in the treatment group and the control group at 2,12,24,36 and 48 hours after surgery were 1.64%,4.84%,6.56%,3.28%,0 and 14.75%,18.03%,19.67%,16.39%,9.84%,respectively.The HR at 24 hours after surgery in the treatment group and the control group were(91.42±8.75)and(98.13±9.62)beat·min-1,respectively;the MAP were(91.98±4.56)and(99.05±4.17)mmHg;SPO2 were(98.13±1.65)%and(98.95±1.82)%;VAS scores were 2.68±0.49 and 2.97±0.63;Ramsay scores were 2.27±0.65 and 2.05±0.32;PCIA pressing times were(2.14±0.37)and(4.36±0.78)times,respectively.The differences in the above indicators between the treatment group and the control group were statistically significant(all P<0.05).The incidence of total adverse drug reactions after surgery in the treatment group and the control group were 13.12%and 8.20%,respectively,with no statistically significant difference(P>0.05).Conclusion Flupentixol combined with ondansetron can reduce the risk of PONV caused by sufentanil combined with dezocine PCIA after surgery,ensuring good analgesic effects and safety.
6.The role of macrophage polarization in the pathogenesis and treatment of periodontitis
Ruiyang GE ; Can NI ; Kun YANG ; Fuhua YAN
Chinese Journal of Tissue Engineering Research 2024;28(20):3246-3251
BACKGROUND:Host immune response triggered by plaque biofilm is an initiator of periodontitis progression and destruction.Macrophages are an important component of the innate immune response,which play an important role in inflammation occurrence and development. OBJECTIVE:To review the relationship between macrophage polarization and periodontitis and the related progress in the treatment of periodontitis by regulating macrophage polarization. METHODS:PubMed and CNKI databases were searched for relevant literature published from 1990 to 2023,with"macrophage polarization,M1/M2 macrophage,periodontitis,periodontitis treatment,macrophage polarization and periodontitis,osteoimmunology,ferroptosis,macrophage polarization and ferroptosis,periodontitis and ferroptosis"as the English and Chinese search terms.After the initial screening,96 articles were selected for review. RESULTS AND CONCLUSION:The switch between different phenotypes of macrophages is closely related to the tissue destruction caused by periodontitis,and various cytokines and inflammatory mediators secreted from macrophages are involved in the destruction and repair of periodontal tissue.Therefore,regulation of macrophage polarization and cytokine secretion in inflammatory state helps to alleviate periodontitis inflammation and improve the periodontal microenvironment,thereby reducing tissue destruction or promoting periodontal tissue regeneration.Many studies have been conducted to develop drugs or biomaterials to modulate macrophage function for the purpose of immunomodulatory treatment of periodontitis.However,macrophages act throughout the development of periodontitis and play an important role in the process of anti-infection,bone destruction and bone repair,and polarization is a complex and dynamic process influenced by many factors.Therefore,further exploration on possible mechanisms is still needed to clarify the interaction between materials or drugs and macrophages.
7.Application of Allograft Endometriosis Rat Model in Pharmaco-dynamic Evaluation of GnRH Agonists
Ruihua ZHONG ; Guoting LI ; Wenjie YANG ; Xiangjie GUO ; Jieyun ZHOU ; Yingyi HU ; Qicheng NI ; Ye YANG ; Min ZHANG ; Yan ZHU
Laboratory Animal and Comparative Medicine 2024;44(2):127-138
Objective To establish an allogeneic rat model of endometriosis and to evaluate the effects of gonadotropin-releasing hormone (GnRH) agonist GenSci006 on experimental rat endometriosis. Methods Endometrium from SPF grade donor female SD rats were transplanted onto the abdominal wall of recipient female rats to construct an allogeneic endometriosis model. The rats undergoing sham surgery were divided into the sham group. Three weeks later, the length, width and height of the ectopic endometrium were measured, and the volume of the endometrium (V1) was calculated before drug administration. The modeling rats were randomly divided into four groups: model group, triptorelin group (0.25 mg/kg), GenSci006-1 group (0.125 mg/kg) and GenSci006-2 group (0.25 mg/kg). Each group had 16 rats and received a single dose of the corresponding drug. The sham group and model group were administered an equal volume of solvent. Three weeks after administration, ectopic endometrium was measured to calculate the volume V2 and inhibition rate. The effect of GenSci006 on rat uterus and ovarian tissues was assessed by comparing organ coefficients and changes in pathological sections. Enzyme-linked immunosorbent assay (ELISA) was used to measure the levels of serum estradiol (E2), progesterone (P4), follicle stimulating hormone (FSH), and luteinizing hormone (LH). Real-time fluorescent quantitative PCR was used to detect the expression of GnRH receptor (GnRHR) mRNA in the hypothalamus and pituitary. Western blot was used to detect the expression of estradiol receptor alpha (ERα), beta (ERβ) and progesterone receptor (PR) in ectopic endometrium. Results Three weeks after administration, compared with the model group, the body weight of rats in the triptorelin and GenSci006-2 groups significantly increased (P < 0.05), while the volume of ectopic endometrium significantly decreased (P < 0.05). Compared with the sham group, the model group showed no significant changes in uterine and ovarian organ coefficients or endometrial thickness (P > 0.05). Compared with the model group, the uterine organ coefficients and endometrial thickness were significantly reduced in the triptorelin and GenSci006-2 groups (P < 0.05). Compared with the sham group, the serum levels of E2, P4, FSH and LH in the model group showed no significant changes (P > 0.05). Compared with the model group, the ovarian organ coefficient and serum P4 levels of rats in the Triptorelin, GenSci006-1, and GenSci006-2 groups were significantly reduced (P < 0.05), while the serum LH levels of rats in the GenSci006-1 group were significantly increased (P < 0.05). However, there were no significant changes in serum E2 and FSH levels in each group (P > 0.05). Compared with the model group, the expression levels of GnRHR mRNA in the pituitary tissue of rats in the triptorelin and GenSci006-2 groups were significantly downregulated (P < 0.05), with no significantly changes in the hypothalamus (P > 0.05). There were no significant changes in the expression level of GnRHR mRNA in the hypothalamus or the protein levels of ERα, ERβ and PR in the ectopic endometrial tissue in any group (P > 0.05). Conclusion The allogeneic endometriosis rat model is a suitable animal model for screening and evaluating drugs for treating endometriosis. The volume of ectopic endometrium, inhibition rate, uterine and ovarian organ coefficients, and serum E2 levels may serve as indicators for detecting drug efficacy.
8.Prognostic factors of patients with muscle invasive bladder cancer with intermediate-to-high risk prostate cancer
Junyong OU ; Kunming NI ; Lulin MA ; Guoliang WANG ; Ye YAN ; Bin YANG ; Gengwu LI ; Haodong SONG ; Min LU ; Jianfei YE ; Shudong ZHANG
Journal of Peking University(Health Sciences) 2024;56(4):582-588
Objective:To investigate the prognostic factors for all-cause mortality in patients with muscle-invasive bladder cancer(MIBC)with intermediate-to-high-risk primary prostate cancer.Methods:From January 2012 to October 2023,the clinical data of the patients with MIBC with intermediate-to-high-risk primary prostate cancer in Peking University Third Hospital were retrospectively analyzed.All the patients were monitored and the occurrence of all-cause death was documented as the outcome event in the prognostic study.Univariate and multivariate Cox proportional risk regression analysis models were implemented to search for independent influences on the prognosis of patients.For significant influencing factors(pathological T stage,M stage and perineural invasion of bladder cancer),survival curves were plotted before and after multifactorial Cox regression adjusting for confounding factors.Results:A total of 32 patients were included in this study.The mean age was(72.5±6.6)years;the median preoperative total prostate specific antigen(tPSA)was 6.68(2.47,6.84)μg/L;the mean preoperative creatinine was(95±36)μmol/L,and the median survival time was 65 months.The majority of the patients(87.5%)had high-grade bladder cancer,53.1%had lymphatic invasion,and 31.3%had perineural invasion.Prostate involvement was observed in 25.0%of the cases,and the positive rate of soft-tissue surgical margin was 37.5%.Multivariate Cox analysis revealed that preoperative creatinine level(HR=1.02,95%CI:1.01-1.04),pathological stage of bladder cancer T3(HR=11.58,95%CI:1.38-97.36)and T4(HR=19.53,95%CI:4.26-89.52)metastasis of bladder cancer(HR=9.44,95%CI:1.26-70.49)and perineural invasion of bladder cancer(HR=6.26,95%CI:1.39-28.27)were independent prognostic factors(P<0.05).Survival curves with Log-rank test after adjusting for confounding factors demonstrated that bladder cancer pathology T3,T4,M1,and perineural invasion were unfavorable factors affecting the patients'survival prognosis(P<0.05).Conclusion:Patients with MIBC with intermediate-to-high risk primary prostate cancer generally portends a poor prognosis.High preoperative serum creatinine,T3 or T4 pathological stage of bladder cancer,metastasis of bladder cancer and bladder cancer perineural invasion are poor prognostic factors for patients with MIBC with intermediate-to-high risk primary prostate cancer.
9.Establishment of UPLC-DAD fingerprint of raw and vinegar Bupleurum bupleurum and study on spectral effect relationship of anti-hepatic fibrosis
Ni-Ping CHEN ; Yan WANG ; Yan DONG ; Yang-Xin XIAO ; Ji-Yuan TU ; Yan-Ju LIU ; Zhong-Shi ZHOU
Chinese Pharmacological Bulletin 2024;40(6):1145-1152
Aim To establish the fingerprint of raw bupleurum and vinegar bupleurum,investigate the difference in their anti-liver fibrosis effects,and ex-plore the relationship between the chemical composition of raw bupleurum and vinegar bupleurum and their an-ti-liver fibrosis efficacy.Methods The fingerprints of 10 batches of raw bupleuri and 10 batches of bupleuri were established by UPLC method.The liver fibrosis cell model in vitro was established by TGF-β induced LX-2 hepatic stellate cells.The liver fibrosis cell mod-el was analyzed with collagen type Ⅰ(col1a1)and α-smoothmuscleactin.The expression of α-SMA protein was used as the pharmacodynamic index.MetaboAna-lyst5.0 was used to screen the difference markers af-fecting the quality of raw bupledges and vinegar bu-pledges with VIP value>1 as the criterion.Orthogo-nal partial least squares discriminant analysis(OPLS-DA)was used to screen the main components of raw bupleurum and vinegar bupleurum against liver fibro-sis.Results There were 18 peaks in the UPLC fin-gerprints of raw bupleurum and vinegar bupleurum,and the analysis results showed that there were nine main differences between raw bupleurum and vinegar bupleurum,among which peaks 9,7 and 6 could be considered as bupleurin d,bupleurin a and bupleurin f.The results of spectral effect relationship showed that the main components of bupleurum anti-liver fibrosis were peaks 11,12,14,15 and 18.Conclusions The established fingerprint method of raw bupleurum and vinegar bupleurum is simple and feasible,and the important components of anti-liver fibrosis activity are screened through the spectrum effect relationship,which provides a basis for clarifying the material basis of anti-liver fibrosis effect of raw bupleurum and vine-gar bupleurum.
10.Analysis of causes of bleeding after endoscopic duodenal papillary adenoma resection and establishment of prediction model
Chun-Yan JIN ; Hua YANG ; Lei WANG ; Qin YIN ; Meng-Yun HU ; Xu FANG ; Mu-Han NI
Modern Interventional Diagnosis and Treatment in Gastroenterology 2024;29(4):398-402,406
Objective The causes of bleeding after endoscopic duodenal papilloma resection were analyzed and discussed,and the prediction model of nomogram was established.Methods A total of 233 patients who underwent endoscopic duodenal papilloma resection in our hospital from January 2018 to December 2023 were retrospectively analyzed,and they were divided into bleeding group(n=31 cases)and non-bleeding group(n=202 cases)according to whether postoperative bleeding occurred.The clinical data of the two groups were compared,the independent risk factors for postoperative bleeding were analyzed by multi-factor logistic regression,the risk nomogram prediction model was constructed,and the Bootstrap method was used for 1000 repeated samples to carry out internal verification.Results Anticoagulant drugs(OR=9.063,95%CI:2.132-38.525),lesion diameter ≥2 cm(OR=2.802,95%CI:1.073-7.321),intraoperative fragment resection(OR=27.653,95%CI:3.055~619.174)and pancreatic complications(OR=6.859,95%CI:1.930~24.377)were independent risk factors for postoperative bleeding after endoscopic duodenal papilloma resection(P<0.05).A risk prediction nomogram model was constructed according to the Logistic regression analysis results.The samples were repeatedly sampled 1000 times through Bootstrap method for internal verification.The area under the ROC curve was 0.850,and the 95%CI was 0.780-0.913,indicating good differentiation ability of the model.Calibration curve analysis indicated that the prediction probability of postoperative bleeding predicted by the nomogram prediction model was in good agreement with the actual probability of postoperative bleeding,and Hosmer-Lemeshow showed good goodness of fit(x2=3.304 9,P=0.913 8).Conclusion Taking anticoagulant drugs,lesion diameter ≥2 cm,intraoperative segmentary resection,and postoperative combination of pancreas were independent risk factors for bleeding after endoscopic duodenal papilloma resection.A nomogram prediction model was established to help clinical assessment of postoperative bleeding risk in patients and improve decision-making basis for early prevention.

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