The mechanism of the Wenshenyang recipe in the treatment of infertility by transcriptome analysis and network pharmacology
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ABSTRACT:
PROVIDER: PRJNA836852 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19154600.fastq.gz | Fastqsanger.gz | |||
| SRR19154544.fastq.gz | Fastqsanger.gz | |||
| SRR19154545.fastq.gz | Fastqsanger.gz | |||
| SRR19154546.fastq.gz | Fastqsanger.gz | |||
| SRR19154547.fastq.gz | Fastqsanger.gz |
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Project description:The Wenshenyang recipe (WSYR) has the effect of treating infertility, but the mechanisms underlying this activity have not been fully elucidated. In this study, network pharmacology and RNA sequencing were combined, with database-based “dry” experiments and transcriptome analysis-based “wet” experiments used conjointly to analyse the mechanism of WSYR in the treatment of infertility. In the dry analysis, 43 active compounds in WSYR and 44 therapeutic targets were obtained through a database search, 15 infertility pathways were significantly enriched, and key targets, such as ESR1, TP53, AKT1, IL-6, and IL-10 were identified. In the wet experimental analysis, HK-2 cells were treated with the three herbs of WSYR. Using the transcriptome sequencing platform, the expression level changes in 412 genes from 15 infertility pathways were observed, and 92 DEGs were finally obtained. Additionally, key targets, such as ESR2, STAT1, STAT3, and IL6, were identified. RT-qPCR experiments further verified that WSYR played an anti-inflammatory role by upregulating IL-4 and IL-10. By building the molecular docking model of ESR1, ESR2 and screening compounds, it was further found that xanthogalenol in Drynaria fortunei (Kunze) J.Sm. (Gusuibu), arachidonate in Cistanche deserticola Y.C.Ma (Roucongrong), and anhydroicaritin in Epimedium brevicornu Maxim. (Yinyanghuo) have good affinity for estrogen receptors. These findings provide evidence that WSYR exerts an estrogen-regulating role. By integrating the results of dry and wet experiments, it was found that the WSYR treats infertility by regulating hormone levels and inflammatory responses.
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Project description:This study explores how quercetin may treat endometriosis (EMs) by combining network pharmacology and transcriptome sequencing approaches. Through network pharmacology, 132 shared targets between quercetin and EMs were identified, with KEGG pathway analysis suggesting that the MAPK signaling pathway could be a significant therapeutic target. Transcriptome sequencing revealed that PDGFRB was highly expressed in ectopic endometrial tissue, a finding confirmed by immunohistochemistry (IHC) showing elevated levels of PDGFRB, RAS, RAF1, and ERK1/2 in ectopic lesions. In an EMs mouse model, quercetin treatment led to a marked reduction in ectopic lesion volume, lowered adhesion scores, and decreased expression of PDGFRB, RAS, RAF1, and ERK1/2 in endometrial tissues. Additionally, the knockdown of PDGFRB in endometriosis cells inhibited their proliferation, invasion, and migration, processes critical to EMs pathology. Quercetin treatment further suppressed cell viability and downregulated the protein expression of RAS, phosphorylated RAF1, RAF1, phosphorylated ERK, and ERK1/2. These findings collectively suggest that quercetin exerts its therapeutic effect in endometriosis by regulating the MAPK signaling pathway via PDGFRB, thereby reducing EMs cell proliferation, invasion, and migration. This study provides insights into quercetin’s multi-targeted mechanism of action in endometriosis treatment.
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Project description:MicroRNAs (miRNAs) have emerged as potential therapeutic targets for non-alcoholic fatty liver disease/non-alcoholic steatohepatitis (NAFLD/NASH). Traditional Chineses Medicine (TCM) plays an important role in the prevention or treatment of NAFLD/NASH. However, miRNA targets of TCM against NASH still remain largely unknown. Here, we showed that Yiqi-Bushen-Tiaozhi (YBT) recipe effectively attenuated diet-induced NASH in C57BL/6 mice. To identify the miRNA targets of YBT and understand the potential underlying mechanisms, we performed network pharmacology using miRNA and mRNA deep sequencing data combined with Ingenuity Pathway Analysis (IPA). Mmu-let-7a-5p, mmu-let-7b-5p, mmu-let-7g-3p and mmu-miR-106b-3p were screened as the main targets of YBT. Our results suggested that YBT might alleviate NASH by regulating the expression of these miRNAs that potentially modulate inflammation/immunity and oxidative stress. This study provides useful information for guiding future studies on the mechanism of YBT against NASH by regulating miRNAs.
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Project description:Mechanism of quercetin in the treatment of endometriosis based on network pharmacology and transcriptome sequencing
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Project description:Wang Bi Tablet (WBT) exhibits effective power in clinic during the treatment of rheumatoid arthritis (RA) in China. We aimed to employ the “integrative pharmacology strategy”, including rapid analysis of chemical composition, pharmacological experiment, and network pharmacology analysis, to delineate the main active components and reveal the underlying mechanism of WBT acting on RA. UPLC-QTOF-MS/MS provided the chemical fingerprint of WBT and UNIFI 1.8 software assisted in chemical composition identification by matching the MSE raw data to the in-house library. The anti-inflammatory effect of WBT was evaluated in TNF-α- stimulated RAW264.7 cells by ELISA and transcriptome sequencing. Network pharmacology analysis was carried out based on Integrative Pharmacology-based Network Computational Research Platform of Traditional Chinese Medicine (TCMIP V2.0, http://www.tcmip.cn/). Functional enrichment and network visualization was performed by DAVID v6.8 and NaviGator v3.0 respectively. Altogether, 293 chemical constituents were preliminarily identified or tentatively characterized in the extract of WBT, and it could effectively against inflammatory response in TNF-α-stimulated RAW264.7 cells. One hundred and thirty-five hub genes were delineated based on the network construction of “Anti-inflammatory Core Genes-Putative Targets-RA genes”, which were mainly involved in inflammation-immune regulation, closely relating to the occurrence and development of RA, such as Cytokine-cytokine receptor interaction, Chemokine signaling pathway, etc., Forty-eight key active constituents were selected according to the frequency binding to hub targets and contents in WBT, corresponding to 13 herbal medicines. In summary, it is the first time to explore the active constituents and underlying mechanism of WBT acting on RA using integrative pharmacology strategy, which may provide an efficient way for the analysis of chemical constituents and exploration of pharmacological mechanism of TCM.
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