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.AMP-activated protein kinase mediates macrophage fatty acid oxidation:an approach to prevent and treat atherosclerosis with traditional Chinese medicine
Panxia CAO ; Zining PENG ; Shanshan LIU ; Tiantian FEI ; Tengyun LIANG ; Mengwen ZHANG ; Hong WU
Chinese Journal of Tissue Engineering Research 2025;29(18):3906-3914
BACKGROUND:The energy metabolism and polarization state of macrophages play a crucial role in the progression of atherosclerosis.Traditional Chinese Medicine(TCM)has shown significant therapeutic potential for prevention and treatment of atherosclerosis by regulating macrophage metabolic pathways.OBJECTIVE:To review the research progress in AMP-activated protein kinase regulation of macrophage energy metabolism and polarization and explore the mechanism of TCM in the prevention and treatment of atherosclerosis.METHODS:A computerized search was conducted on the databases including Web of Science,PubMed,and CNKI,covering relevant literature up to June 2024.The search terms were"AMPK,fatty acid oxidation,macrophage polarization,Traditional Chinese Medicine,atherosclerosis,coronary heart disease"in Chinese and English.A total of 62 articles were finally included for review.RESULTS AND CONCLUSION:The shiftin macrophage energy metabolism from oxidative phosphorylation to glycolysis plays a key role in the progression of atherosclerosis.The activation of AMP-activated protein kinase in macrophages promotes fatty acid oxidation and M2 polarization,exerting anti-inflammatory effects and stabilizing arterial plaques.TCM monomers(such as ginseng,astragalus,and polygonatum)and compounds(such as Huanglian Jiedu Decoction,Yangxin Shumai Granules,and Tiaogan Daozhuo Formula)influence macrophage metabolism and cellular function by regulating the AMP-activated protein kinase pathway and intervening in multiple signaling pathways,such as nuclear factor-κB,peroxisome proliferator-activated receptor γ,and mammalian target of rapamycin,thereby achieving therapeutic effects.Future research should focus on the interactions between AMP-activated protein kinase,metabolism,and polarization pathways,as well as how TCM exerts its therapeutic effects through these pathways,providing new strategies for the treatment of atherosclerosis.
3.Construction and comparative study of animal models of influenza A virus transmission and infection
Xiangzhong YUAN ; Dongdong PENG ; Zhuole WANG ; Ke LIU ; Meng LI ; Yuhan LI ; Xuewu LIU ; Zining TANG
Chinese Journal of Comparative Medicine 2025;35(9):82-90
Objective To establish a model of indirectly induced respiratory tract infection with influenza A subtypes H1N1 and H3N2 in animals,to screen influenza virus hosts,and to provide theoretical support for the clinical control of influenza viruses.Methods Fifty BALB/c mice and 50 Hartley guinea pigs were randomly divided into five groups(10 animals/group for each species):normal control group,virus infects 1 group,virus infects 2 group,close transmission 1 group,and close transmission 2 group.Mice and guinea pigs in virus infects 1 and 2 groups were administered influenza A(H1N1)and influenza A(H3N2)viruses via nasal drip.For both virus infects 1 and 2 groups,animals were housed together with those in the close transmission group at a 1∶1 ratio on the following day.On day 7,the lung function,viral titer and viral load of the nasal tissue,trachea,and lung tissue of each group were measured,and pathological changes of the trachea and lung tissue of animals in the close transmission group were evaluated.Results In mice,the viral titers and viral loads of nasal,tracheal,and lung tissues of virus infects 1 and 2 and the closely transmitted groups 1 and 2 were significantly higher(P<0.01),pathological scores of the trachea and lung tissues were significantly higher(P<0.01),and the FVC and FEV20 of virus infects l and 2 groups were significantly lower(P<0.01)than those in the normal control group.The nasal tissue,trachea and lung tissues of guinea pigs in virus infects 1 and 2 groups and close transmission groups 1 and 2 showed significantly higher viral titers and viral loads(P<0.01),significantly higher trachea and lung histopathological scores(P<0.01),and significantly lower FVC and FEV200(P<0.01)than those of the normal control group.Conclusions In this study,influenza A subtypes H1N1 and H3N2 were used to indirectly induce respiratory tract infections in mice and guinea pigs for analyses of animal lung function,respiratory viral titers,viral load,and pathology.The animal models of the indirect transmission of influenza viruses in the respiratory tract had certain limitations;for example,influenza viruses were transmitted less efficiently among mice than among guinea pigs.The guinea pig model was stable.These findings confirm that guinea pigs are suitable hosts for efficient virus replication and transmission.
4.Construction and comparative study of animal models of influenza A virus transmission and infection
Xiangzhong YUAN ; Dongdong PENG ; Zhuole WANG ; Ke LIU ; Meng LI ; Yuhan LI ; Xuewu LIU ; Zining TANG
Chinese Journal of Comparative Medicine 2025;35(9):82-90
Objective To establish a model of indirectly induced respiratory tract infection with influenza A subtypes H1N1 and H3N2 in animals,to screen influenza virus hosts,and to provide theoretical support for the clinical control of influenza viruses.Methods Fifty BALB/c mice and 50 Hartley guinea pigs were randomly divided into five groups(10 animals/group for each species):normal control group,virus infects 1 group,virus infects 2 group,close transmission 1 group,and close transmission 2 group.Mice and guinea pigs in virus infects 1 and 2 groups were administered influenza A(H1N1)and influenza A(H3N2)viruses via nasal drip.For both virus infects 1 and 2 groups,animals were housed together with those in the close transmission group at a 1∶1 ratio on the following day.On day 7,the lung function,viral titer and viral load of the nasal tissue,trachea,and lung tissue of each group were measured,and pathological changes of the trachea and lung tissue of animals in the close transmission group were evaluated.Results In mice,the viral titers and viral loads of nasal,tracheal,and lung tissues of virus infects 1 and 2 and the closely transmitted groups 1 and 2 were significantly higher(P<0.01),pathological scores of the trachea and lung tissues were significantly higher(P<0.01),and the FVC and FEV20 of virus infects l and 2 groups were significantly lower(P<0.01)than those in the normal control group.The nasal tissue,trachea and lung tissues of guinea pigs in virus infects 1 and 2 groups and close transmission groups 1 and 2 showed significantly higher viral titers and viral loads(P<0.01),significantly higher trachea and lung histopathological scores(P<0.01),and significantly lower FVC and FEV200(P<0.01)than those of the normal control group.Conclusions In this study,influenza A subtypes H1N1 and H3N2 were used to indirectly induce respiratory tract infections in mice and guinea pigs for analyses of animal lung function,respiratory viral titers,viral load,and pathology.The animal models of the indirect transmission of influenza viruses in the respiratory tract had certain limitations;for example,influenza viruses were transmitted less efficiently among mice than among guinea pigs.The guinea pig model was stable.These findings confirm that guinea pigs are suitable hosts for efficient virus replication and transmission.
5.AMP-activated protein kinase mediates macrophage fatty acid oxidation:an approach to prevent and treat atherosclerosis with traditional Chinese medicine
Panxia CAO ; Zining PENG ; Shanshan LIU ; Tiantian FEI ; Tengyun LIANG ; Mengwen ZHANG ; Hong WU
Chinese Journal of Tissue Engineering Research 2025;29(18):3906-3914
BACKGROUND:The energy metabolism and polarization state of macrophages play a crucial role in the progression of atherosclerosis.Traditional Chinese Medicine(TCM)has shown significant therapeutic potential for prevention and treatment of atherosclerosis by regulating macrophage metabolic pathways.OBJECTIVE:To review the research progress in AMP-activated protein kinase regulation of macrophage energy metabolism and polarization and explore the mechanism of TCM in the prevention and treatment of atherosclerosis.METHODS:A computerized search was conducted on the databases including Web of Science,PubMed,and CNKI,covering relevant literature up to June 2024.The search terms were"AMPK,fatty acid oxidation,macrophage polarization,Traditional Chinese Medicine,atherosclerosis,coronary heart disease"in Chinese and English.A total of 62 articles were finally included for review.RESULTS AND CONCLUSION:The shiftin macrophage energy metabolism from oxidative phosphorylation to glycolysis plays a key role in the progression of atherosclerosis.The activation of AMP-activated protein kinase in macrophages promotes fatty acid oxidation and M2 polarization,exerting anti-inflammatory effects and stabilizing arterial plaques.TCM monomers(such as ginseng,astragalus,and polygonatum)and compounds(such as Huanglian Jiedu Decoction,Yangxin Shumai Granules,and Tiaogan Daozhuo Formula)influence macrophage metabolism and cellular function by regulating the AMP-activated protein kinase pathway and intervening in multiple signaling pathways,such as nuclear factor-κB,peroxisome proliferator-activated receptor γ,and mammalian target of rapamycin,thereby achieving therapeutic effects.Future research should focus on the interactions between AMP-activated protein kinase,metabolism,and polarization pathways,as well as how TCM exerts its therapeutic effects through these pathways,providing new strategies for the treatment of atherosclerosis.
6.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.
7.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.
8.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.
9.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.
10.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.

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