1.Bioinformatics-based analysis of autophagy-related genes and prediction of potential Chinese medicines in diabetic kidney disease
Yufeng XING ; Zining PENG ; Chaoyang YE
Digital Chinese Medicine 2025;8(1):90-99
[Objective] :
To predict the autophagy-related pathogenesis and key diagnostic genes of diabetic kidney disease (DKD) through bioinformatics analysis, and to identify related Chinese medicines.
[Methods] :
Data from sequencing microarrays GSE30528, GSE30529, and GSE1009 in the Gene Expression Omnibus (GEO) were employed. Differentially expressed genes (DEGs) with adjusted P < 0.05 from GSE30528 and GSE30529 were identified. Combining these DEGs with the human autophagy gene database, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and protein-protein interaction (PPI) network analysis were conducted on the obtained DKD autophagy-related genes. Subsequently, the least absolute shrinkage and selection operator (LASSO) regression and support vector machine-recursive feature elimination (SVM-RFE) algorithms were adopted to select autophagy-related genes. The diagnostic capability of these genes was assessed through analysis with the external validation set from microarray GSE1009, and relevant Chinese medicines were inversely predicted using the SymMap database.
[Results] :
A total of 2 014 DEGs were selected from GSE30528 and GSE30529, leading to the
identification of 37 DKD autophagy-related genes. GO analysis indicated 681 biological
mechanisms, including autophagy regulation and plasma membrane microdomain activity.
KEGG enrichment analysis identified 112 related signaling pathways. PPI network analysis
showed a marked enrichment of autophagy-related genes in DKD. Through LASSO regression and SVM-RFE, four core diagnostic genes for autophagy in DKD were identified: protein
phosphatase 1 regulatory subunit 15A (PPP1R15A), hypoxia inducible factor 1 alpha subunit
(HIF1α), deleted in liver cancer 1 (DLC1), and ceroid lipofuscinosis neuronal 3 (CLN3). The
external validation set demonstrated high diagnostic efficiency for these genes. Finally, 146
kinds of potential Chinese medicines were predicted using the SymMap database, with heatclearing and detoxifying medicine and blood-activating and stasis-eliminating medicine accounting for the largest proportion (25/146 and 13/146, respectively).
[Conclusion]
This study analyzed and validated bioinformatics sequencing databases to elucidate the potential molecular mechanisms of DKD autophagy and predicted key diagnostic genes, potential therapeutic targets, and related Chinese medicines, laying a solid foundation for clinical research and application.
2.Research progress on macrophage metabolism and immune function in coronary heart disease with phlegm and blood stasis syndrome
Panxia CAO ; Zining PENG ; Jian LI ; Hong WU
Chinese Journal of Comparative Medicine 2024;34(9):157-164
In traditional Chinese medicine,coronary heart disease falls under the categories of"chest impediment and heart pain"and"true heart pain",with lipid metabolism disorder and the inflammatory response acting as biochemical manifestations of"phlegm and stasis"throughout the disease.The energy metabolism of macrophages is closely related to their immune function and is an important factor in regulating the metabolic disorder and inflammatory responses in coronary heart disease.This article reviews the role of macrophages in the pathophysiology of coronary heart disease.We discuss how these metabolic pathways affect the immune responses of macrophages and influence the disease.We delve into the different modes of macrophage energy metabolism in coronary heart disease,especially the metabolic characteristics and immune regulatory functions of pro-inflammatory M1 and anti-inflammatory M2 macrophages in the syndrome of phlegm and blood stasis.This provides a theoretical guidance for understanding the pathogenic mechanism of the syndrome of phlegm and blood stasis in coronary heart disease and developing new treatment strategies.
3.Exploring the Mechanism of Jianpi Shenshi Formula for the Treatment of Hyperuricemia Based on Network Pharmacology and Molecular Docking
Qian DENG ; Xingqiang WANG ; Weitian YAN ; Zining PENG ; Nian LIU ; Chunping WAN ; Jiangyun PENG
Traditional Chinese Drug Research & Clinical Pharmacology 2024;35(6):850-861
Objective To investigate the potential mechanism of Jianpi Shenshi Formula for the treatment of hyperuricemia(HUA)by using network pharmacology and molecular docking techniques.Methods The active ingredients of Jianpi Shenshi Formula were searched and screened by combining TCMSP,BATMAN,and TCM-ID database with literature,and then SwissTargetPrediction was used to obtain the corresponding targets of the ingredients.Cytoscape 3.8.0 was used to construct a"drug-ingredients"network to analyze and obtain the main active ingredients of Jianpi Shenshi Formula.The GeneCards,OMIM,and disgenet databases were used to obtain the relevant targets of hyperuricemia.The intersection targets of Jianpi Shenshi Formula and hyperuricemia were imported into the STRING database for protein-protein interaction(PPI)network analysis,and hub targets for network were screened by CytoHubba plug-in.Meanwhile,the GO function and KEGG pathway enrichment analysis of the intersection targets were carried out using R4.2.2 software.Molecular docking of hub targets and key ingredients was performed using CB-DOCK 2.Results A total of 90 active ingredients of Jianpi Shenshi Formula were screened,among which quercetin,kaempferol,luteolin,stigmasterol,and ethyl linoleate were the main active ingredients,and 837 targets corresponding to the ingredients were obtained,with a total of 64 intersecting targets.CASP3,IL1B,IL6,PPARG,SIRT1,MAPK3,TNF,STAT3,TGFβ1,PTGS2,and XDH were the hub targets.The potential targets of action are mainly enriched in signaling pathways such as inflammation,metabolism,environment,cellular processes,biological systems,and hyperuricemia-related pathways.Conclusion Jianpi Shenshi Formula may exert effects on inhibition of uric acid production,and/or enhancement of uric acid excretion,anti-inflammation,and amelioration of related complications through the modulation of hyperuricemia-related signaling pathways(including neoplastic,infectious,metabolic,and cardiovascular diseases),as well as metabolic,immune,inflammatory,and other biological pathways by a variety of active ingredients such as quercetin,kaempferol,luteolin,stigmasterol,and ethyl linoleate.
4.Study on fimbrial part′s morphology and function of fallopian tubes by using two-dimensional fundamental sonosalpingography combined with saline infusion pelvic sonosalpingography
Zining XU ; Chengzhong PENG ; Ya′er LYU ; Juan SUN ; Yan ZOU ; Bihui JIN
Chinese Journal of Ultrasonography 2020;29(10):881-886
Objective:To evaluate the performance of two-dimensional fundamental sonosalpingography combined with saline infusion pelvic sonosalpingography(abbreviated as "2DFS+ SIPS" in this article) for assessing fimbrial part′s morphology and function of fallopian tubes.Methods:A total of 246 infertile women were collected from Zhejiang Provincial People′s Hospital from May 2018 to December 2019. They underwent dynamic three-dimensional harmonic sonosalpingography(abbreviated as "4DHS" in this article) first. Cases which were diagnosed as bilaterally tubal obstruction would be excluded. 2DFS+ SIPS was performed in 230 patients. Among them, 21 underwent laparoscopy and dye test(LDT) within 6 months and the results were regarded as golden standard.Results:①Tubes which were diagnosed as complete obstruction would be excluded. The total display rate of remaining fimbrial parts by using 2DFS+ SIPS and 4DHS were 77.4% and 24.0% respectively, which had statistically difference( P<0.001). ②According to 2DFS+ SIPS, fimbrial parts were classified into 3 types: normal, suspected abnormal and abnormal.Normal fimbrial parts accounted for 86.4% while suspected abnormal ones accounted for 13.6% under the condition of patency; abnormal fimbrial parts accounted for 81.2% while suspected abnormal ones accounted for 18.8% under the condition of partial obstruction. The difference in the proportion of normal and abnormal fimbrial parts according to different tubal patency was statistically significant( P<0.001). ③Fimbrial parts were classified into normal (normal fimbrial parts) and abnormal (suspected abnormal and abnormal fimbrial parts) further according to 2DFS+ SIPS, the results were compared with LDT. Accuracy, sensitivity, specificity, positive predictive value, negative predictive value and Youden′s index were 92.0%, 100%, 88.2%, 80.0%, 100%, 0.88, respectively. The consistency analysis showed the results of 2DFS+ SIPS and LDT were highly consistent (Kappa=0.828). ④All the side effects occured during the procedure or within 30 minutes after the procedure were self-limited.No serious complications were observed. Conclusions:2DFS+ SIPS is a preferred method for assessment of fimbrial part′s morphology and function, with its advantages of non-invasiveness, intuition, and accuracy. This combination could provide objective imaging basis for choosing clinical treatment strategies and predicting prognosis.
5.Transcriptomic mechanisms and efficacy analysis of D-CAG regimen for treatment of acute myeloid leukemia after failure to initial induction of remission
Zhanqiang ZHANG ; Jundong ZHANG ; Peng ZHI ; Zining WANG ; Haoran CHEN ; Hongyi LI ; Xuechun LU
Journal of Leukemia & Lymphoma 2022;31(5):271-277
Objective:To investigate the transcriptomic mechanisms and clinical efficacy of D-CAG regimen for the treatment of acute myeloid leukemia (AML) after failure to initial induction of remission.Methods:The transcriptome data of AML cells before and after the use of dexitabine before August 28, 2021 was searched in Gene Expression Omnibus (GEO) database with "decitabine" as the search term. The R language package was used for differential expression analysis and Kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) enrichment analysis of the data. Protein-protein interaction network (PPI) analysis was conducted on the STRING online analysis website. The accurate treatment prediction platform designed based on logistic omics theory (EpiMed) was used to make drug-disease-target correlation analysis. The clinical data of 18 AML patients treated with D-CAG regimen after failure to induction of remission with standard anthracycline and cytarabine regimen ("3+7" regimen) in the 305th Hospital of Chinese PLA from October 8, 2015 to July 9, 2018 were searched and analyzed, and the curative effect was evaluated. The effects of the dose and duration of each drug on the efficacy were analyzed.Results:The transcriptome data of AML cells before and after the use of decitabine in GSE40442 dataset of the GPL5188 platform were finally selected, updated on July 10, 2014. A total of 366 differentially expressed genes were screened, including 201 up-regulated genes and 165 down-regulated genes. The differential genes were mainly related to cell cycle regulation, bone marrow leukocyte migration and differentiation, transcriptional regulation, bone marrow hematopoiesis and other signaling pathways. Ten core genes such as ANXA5, IL-10, THBS1, TLR4, JUN and CXCL12 were screened by PPI analysis. Drug-disease-target analysis showed that dexitabine had a potential therapeutic effect on various blood diseases such as diffuse large B-cell lymphoma, thrombocytopenia, T-cell acute lymphocytic leukemia, aplastic anemia, and AML. Of the 18 patients, after initial induction of remission, 7 (38.8%) patients achieved partial remission (PR), and 11 (61.2%) patients had no response (NR); after one cycle of re-induction remission therapy, 9 patients had complete remission (CR), 5 patients had PR, 4 patients had NR, and the overall response rate (ORR) was 77.8% (14/18). Compared with patients with NR, the CR rate was higher in patients with PR after initial induction therapy, which were 85.7% (6/7) and 27.3% (3/11), and the difference was statistically significant ( χ2=5.84, P = 0.025). The median duration of cytarabine in CR patients was longer than that in NR patients [10 d (7-14 d) vs. 5 d (2-8 d), Z = 3.89, P = 0.002] and the median ratio of the number of bone marrow blast cells to the duration cytarabine was lower in CR patients than that in NR patients [2.29 (0.89-9.10) vs. 8.10 (3.00-38.50), Z = -2.19, P = 0.006]; the median dose of cytarabine in CR patients was lower than NR patients, which were 50 mg·m -2·d -1 (30-150 mg·m -2·d -1) and 100 mg·m -2·d -1 (50-500 mg·m -2·d -1), and the difference was not statistically significant ( Z = -1.80, P = 0.074). Conclusions:AML patients with PR after initial induction and failure to initial induction of remission may be more likely to achieve CR after the treatment of D-CAG regimen, and this change may be related to the epigenetic regulation of decitabine.
6.Establishment of immune suppression-mediated infectious pneumonia model using resistant Acinetobacter baumannii strains
Zining TANG ; Xuewu LIU ; Qianqing LAN ; Hailiang TANG ; Sa XIAO ; Xiangzhong YUAN ; Dongdong PENG
Chinese Journal of Microbiology and Immunology 2023;43(12):908-917
Objective:To establish an animal model of pneumonia for research on clinical prevention and treatment of bacterial pneumonia by infecting immunocompromised rats with drug-resistant Acinetobacter baumannii ( Ab) strains. Methods:Drug-resistant Ab strains were selected. Forty-eight SD rats were randomly divided into four groups: normal group, cyclophosphamide control group (intraperitoneal injection of 45 mg/kg cyclophosphamide), bacterial infection group (intratracheal instillation of 1.5×10 8 CFU Ab suspension), and bacterial infection+ immunosuppression group (intraperitoneal injection of 45 mg/kg cyclophosphamide+ intratracheal instillation of 1.5×10 8 CFU Ab suspension). Flow cytometry analysis was used to detect the proportion of CD4 + , CD8 + and NK cells in rat peripheral blood before as well as 3 d and 7 d after infection. A lung function meter was used to detect peak inspiratory flow (PIF), peak expiratory flow (PEF), tidal volume (Vt ) and forced expiratory volume in the second second/forced vital capacity (FEV 200/FVC) at 3 d and 7 d after modeling. ELISA was used to detect the levels of IL-6, TNF-α and IL-10 in the alveolar lavage fluid. HE staining was used to observe the morphology of rat lung tissues in each group. Bacterial loads in rat lung tissues were counted by bacterial culturing. Results:A decrease in voluntary activity was observed in rats in the cyclophosphamide control group, bacterial infection group and bacterial infection+ immunosuppression group after modeling. Lung rales could be heard in the bacterial infection group and bacterial infection+ immunosuppression group. Compared with the normal group, the cyclophosphamide control group showed decreased proportion of CD4 + and CD11b + NK cells and increased CD8 + cells in peripheral blood; the bacterial infection group showed decreased PIF, PEF, Vt and FEV 200/FVC, increased IL-6 and TNF-α levels and decreased IL-10 level in the alveolar lavage fluid, and higher bacterial load in lung tissues with mild widening of alveolar walls and inflammatory cell infiltration ( P<0.05, P<0.01). Compared with the cyclophosphamide control group and the bacterial infection group, the bacterial infection+ immunosuppression group showed a lower proportion of CD4 + cells and a higher proportion of CD8 + cells in rat peripheral blood, decreased PIF, PEF, Vt and FEV 200/FVC, increased IL-6 and TNF-α levels and decreased IL-10 level in alveolar lavage fluid, higher bacterial load in lung tissues, and aggravated widening of alveolar walls and inflammatory cell infiltration ( P<0.05, P<0.01). The proportion of CD11b + NK cells in peripheral blood of rats in the bacterial infection+ immunosuppression group was significantly lower than that in the bacterial infection group ( P<0.05, P<0.01). Conclusions:A bacterial pneumonia model was successfully constructed by infecting rats with Ab alone or in combination with cyclophosphamide immunosuppression. In the model constructed with Ab and cyclophosphamide immunosuppression, the rats had more severe pneumonia, which might be related to the reduced cellular immune function and the aggravated bacterial infection in rat lung tissues by cyclophosphamide.
7.Involvement of oral flora in the role of betel nut-extract-induced ulcers in rats
Dongdong PENG ; Xiangchi CHEN ; Zining TANG ; Xuewu LIU ; Xiangzhong YUAN ; Meng LI ; Qiao LI ; Zeheng ZHANG
Chinese Journal of Comparative Medicine 2024;34(1):52-59
Objective A model for studying oral ulcers induced by betel nut-extract was constructed in rats.Changes in the structure and diversity of oral flora were observed to explore the involvement of oral flora and local inflammatory factors in the pathogenesis of oral ulcers induced by betel nut-extract and to provide theoretical support for the prevention and treatment of oral ulcers in the clinic.Methods Thirty SD rats were randomly divided into normal,model and intervention groups(Guilin watermelon cream,8 mg/d for 7 days),with 10 rats/group.The oral mucosa of rats was subcutaneously injected with 10 g/mL of betel nut-extract to generate an oral ulcer model.The histomorphological changes were observed,and ulcer area and ulcer scores were assessed.Local oral tissue tumor necrosis factor-α(TNF-α),interleukin(IL)-2 and IL-8 levels were determined.Oral mucosal tissues were sampled for HE staining and analyzed for the structural distribution of oral flora and the diversity of microbial communities using high-throughput sequencing method.Results Compared with rats in the normal group,those in the model group had an increased ulcer area,significantly increased ulcer scores(P<0.01),and significantly increased levels of TNF-α,IL-2 and IL-8 in the oral mucosal tissues(P<0.01).The amount Streptococcus(P<0.05)and Veillonella(P<0.001)in the oral saliva of the model group rats was significantly reduced.The model group rats showed oral mucosal epithelial cell hyperplasia or focal necrosis,mucosal lamina propria edema,and hemorrhage accompanied by mass neutrophil and monocyte infiltration.Compared with the model group rats,the intervention group rats had significantly reduced ulcerated area(P<0.05,P<0.01)and ulcer scores(P<0.05).And oral mucosal tissue levels of TNF-α(P<0.01),IL-2(P<0.05)and IL-8(P<0.05),as well as significantly increased Streptococcus(P<0.001)and Veillonella(P<0.01)and significantly reduced Staphylococcus(P<0.01)in the oral saliva.The degree of lesions in the oral mucosal tissues was significantly improved in the intervention group.Conclusions Betel nut-extract can be used to successfully reproduce a rat model of oral ulcer,and it is speculated that the development of oral ulcers after exposure to betel nut-extract may be related to an imbalance in the oral flora and local tissue inflammatory mediators.
8.Use of ferrets in nonclinical studies of anti-infective drugs
Xuewu LIU ; Zining TANG ; Dongdong PENG ; Yanhua DU ; Dejian JIANG
Acta Laboratorium Animalis Scientia Sinica 2024;32(6):799-818
Ferrets offer an advantage in nonclinical studies of anti-infective drugs because of their ability to be infected with and spread pathogenic microorganisms,especially viral strains,without the need for host adaptation.Additionally,the clinical symptoms exhibited by infected ferrets are very similar to those of humans.Although ferrets play a very important role in the research and development of antiviral drugs,the scope of their application remains limited.This may be related to the lack of corresponding national standards for laboratory animal feeding and application of ferrets as well as the lack of specific diagnostic and detection reagents.This paper summarizes the characteristics of ferrets as infectious disease models with a summary and analysis of the application direction of ferrets in anti-infective drug research.Our aim is to promote further standardization of the use of ferrets.
9.Construction and evaluation of an immunosuppression-mediated model of invasive Aspergillus niger lung disease in rats
Zining TANG ; Xiangchi CHEN ; Xuewu LIU ; Zhimin ZHOU ; Qiao LI ; Sa XIAO ; Dejian JIANG ; Dongdong PENG
Chinese Journal of Comparative Medicine 2024;34(6):63-72
Objective This study established a model of invasive Aspergillus niger lung disease in immunosuppressed rats to provide theoretical support for the pharmacodynamic evaluation of anti-invasive pulmonary aspergillosis drugs and mechanism studies.Methods Sixty SD rats were randomly divided into a normal control group;cyclophosphamide control group,and cyclophosphamide+fungal infection low,medium,and high dose groups,with 12 animals in each group.General clinical observations were performed daily,and the serum levels of immunoglobulin(Ig)G and IgM and galactomannan(GM)were detected by ELISA on the 3rd and 7th days of modeling.Simultaneously,the ratio of CD4+and CD8+cells,content of white blood cells(WBCs)and neutrophils(Neu)in peripheral blood,the Aspergillus niger load in alveolar lavage,and morphological changes to rat lung tissue were observed.Results Rats in the cyclophosphamide control and cyclophosphamide+fungal infection groups showed reduced voluntary activity and erect hair after modeling,and rats in the cyclophosphamide+fungal infection group also had shortness of breath and audible wet rhonchi in the lungs.Compared with the normal control group,rats in the cyclophosphamide control group showed significant reductions in the levels of CD4+,WBC,Neu,IgG,and IgM in the blood,and their proportion of CD8+cells was significantly higher(P<0.05,P<0.01).Compared with the cyclophosphamide control group,rats in the cyclophosphamide+fungal infection medium-and high-dose groups had significantly reduced blood levels of IgG,IgM,and CD4+cells(P<0.05,P<0.01);while the cyclophosphamide+fungal infection low-,medium-,and high-dose groups had significantly reduced blood levels of WBC and Neu(P<0.05,P<0.01).Additionally,rats in the cyclophosphamide+fungal infection medium-and high-dose groups had significantly increased blood CD8+cells(P<0.05,P<0.01),Blood GM levels and the alveolar lavage Aspergillus niger load were significantly increased in rats in the cyclophosphamide+fungal infection low-,medium-,and high-dose groups compared with the cyclophosphamide control group(P<0.05,P<0.01).The lung tissues of the cyclophosphamide+fungal infection low-,medium-,and high-dose groups showed mycelial distribution and destruction of alveolar epithelium,increase of bronchial epithelial cup cells in the alveoli,and infiltration of inflammatory cells,and the degree of lesions was positively correlated with the modeling dose.Conclusions In this study,we used Aspergillus niger combined with cyclophosphamide immunosuppressant to construct a model of invasive Aspergillus niger lung disease.The duration of the disease was positively correlated with the concentration of bacterial fluid and modeling time,confirming that cellular immunity plays an important role in the pathogenesis of the disease.At the same time,Ig can also affect the development of invasive pulmonary aspergillosis,and it is speculated that the pathogenesis may be related to the level of Ig produced by humoral immunity.