Dataset Information

Impact of Qi-Invigorating Traditional Chinese Medicines on Diffuse Large B Cell Lymphoma Based on Network Pharmacology and Experimental Validation.

ABSTRACT: Background: It has been verified that deficiency of Qi, a fundamental substance supporting daily activities according to the Traditional Chinese Medicine theory, is an important symptom of cancer. Qi-invigorating herbs can inhibit cancer development through promoting apoptosis and improving cancer microenvironment. In this study, we explored the potential mechanisms of Qi-invigorating herbs in diffuse large B cell lymphoma (DLBCL) through network pharmacology and in vitro experiment. Methods: Active ingredients of Qi-invigorating herbs were predicted from the Traditional Chinese Medicine Systems Pharmacology Database. Potential targets were obtained via the SwissTargetPrediction and STITCH databases. Target genes of DLBCL were obtained through the PubMed, the gene-disease associations and the Malacards databases. Overlapping genes between DLBCL and each Qi-invigorating herb were collected. Hub genes were subsequently screened via Cytoscape. The Gene Ontology and pathway enrichment analyses were performed using the DAVID database. Molecular docking was performed among active ingredients and hub genes. Hub genes linked with survival and tumor microenvironment were analyzed through the GEPIA 2.0 and TIMER 2.0 databases, respectively. Additionally, in vitro experiment was performed to verify the roles of common hub genes. Results: Through data mining, 14, 4, 22, 22, 35, 2, 36 genes were filtered as targets of Ginseng Radix et Rhizoma, Panacis Quinquefolii Radix, Codonopsis Radix, Pseudostellariae Radix, Astragali Radix, Dioscoreae Rhizoma, Glycyrrhizae Radix et Rhizoma for DLBCL treatment, respectively. Then besides Panacis Quinquefolii Radix and Dioscoreae Rhizoma, 1,14, 10, 14,13 hub genes were selected, respectively. Molecular docking studies indicated that active ingredients could stably bind to the pockets of hub proteins. CASP3, CDK1, AKT1 and MAPK3 were predicted as common hub genes. However, through experimental verification, only CASP3 was considered as the common target of Qi-invigorating herbs on DLBCL apoptosis. Furthermore, the TIMER2.0 database showed that Qi-invigorating herbs might act on DLBCL microenvironment through their target genes. Tumor-associated neutrophils may be main target cells of DLBCL treated by Qi-invigorating herbs. Conclusion: Our results support the effects of Qi-invigorating herbs on DLBCL. Hub genes and immune infiltrating cells provided the molecular basis for each Qi-invigorating herb acting on DLBCL.

SUBMITTER: Huang Q

PROVIDER: S-EPMC8699731 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Although traditional Chinese medicine is effective and safe for the treatment of angiogenesis, the in vivo intervention mechanism is diverse, complex, and largely unknown. Therefore, we aimed to explore the active ingredients of traditional Chinese medicine and their mechanisms of action against angiogenesis. Data on angiogenesis-related targets were collected from GeneCards, Therapeutic Target Database, Online Mendelian Inheritance in Man, DrugBank, and DisGeNET. These were matched to related molecular compounds and ingredients in the traditional Chinese medicine system pharmacology platform. The data were integrated and based on the condition of degree > 1, and relevant literature, target-compound, compound-medicine, and target-compound-medicine networks were constructed using Cytoscape. Molecular docking was used to predict the predominant binding combination of core targets and components. We obtained 79 targets for angiogenesis; 41 targets were matched to 3839 compounds, of which 110 compounds were selected owing to their high correlation with angiogenesis. Fifty-five combinations in the network were obtained by molecular docking, among which PTGS2-astragalin (-9.18 kcal/mol), KDR-astragalin (-7.94 kcal/mol), PTGS2-quercetin (-7.41 kcal/mol), and PTGS2-myricetin (-7.21 kcal/mol) were top. These results indicated that the selected potential core compounds have good binding activity with the core targets. Eighty new combinations were obtained from the network, and the top combinations based on affinity were KDR-beta-carotene (-10.13 kcal/mol), MMP9-beta-sitosterol (-8.04 kcal/mol), MMP9-astragalin (-7.82 kcal/mol), and MMP9-diosgenin (-7.51 kcal/mol). The core targets included PTGS2, KDR, VEGFA, and MMP9. The essential components identified were astragalin, kaempferol, myricetin, quercetin, and β-sitosterol. The crucial Chinese medicines identified included Polygoni Cuspidati Rhizoma et Radix, Morus alba Root Bark, and Forsythiae Fructus. By systematically analysing the ingredients of traditional Chinese medicine and their targets, it is possible to determine their potential mechanisms of action against pathological angiogenesis. Our study provides a basis for further research and the development of new therapeutics for angiogenesis.

Project description:BackgroundThis study used a combination of network pharmacology and experimental confirmation to clarify the mechanism of the compound kidney-invigorating granule (CKG) in treating osteoporosis (OP).MethodsThe main bioactive compounds and corresponding targets of CKG were collected and screened via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Yet another Traditional Chinese Medicine (YaTCM), and UniProt databases. Disease targets of OP were summarized in GeneCards and the Comparative Toxicogenomics Database (CTD). Targets of CKG for OP were obtained by Venn diagram. The protein-protein interaction (PPI) network was constructed by the STRING database and then screened for hub genes through Cytoscape 3.7.2 software. The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were analyzed and visualized by R software. Then, CB-Dock was used for molecular docking verification. Finally, we confirmed the antiosteoporosis effect of CKG through animal and cell experiments.ResultsA total of 250 putative targets were obtained from 65 bioactive compounds in CKG. Among them, 140 targets were related to OP. Topological analysis of the PPI network yielded 23 hub genes. Enrichment analysis showed the targets of CKG in treating OP might concentrate on the MAPK signaling pathway, the TNF signaling pathway, the PI3K-Akt signaling pathway, etc. The results of molecular docking showed the bioactive components in CKG had good binding ability with the key targets. The experimental results showed that CKG-medicated serum had a promoting effect on proliferating hBMSCs, increasing the expression of AKT, PI3K, ERK1, and IkB in cells and decreasing the expression of IKK in cells.ConclusionCKG has a complex of multicomponent, multitarget, and multipathway. This study lays the theoretical foundation for further in vitro and in vivo experimental studies and further expands the clinical applications of CKG.

Dataset Information

Impact of Qi-Invigorating Traditional Chinese Medicines on Diffuse Large B Cell Lymphoma Based on Network Pharmacology and Experimental Validation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets