Integrated metabolomics and network pharmacology to reveal the therapeutic mechanism of Dingkun Pill on polycystic ovary syndrome

Integration of metabolomics and transcriptomics to reveal the mechanism of Gerberae piloselloidis herba in alleviating bronchial asthma

ETHNOPHARMACOLOGICAL RELEVANCE

Gerberae Piloselloides Herba (GPH) is derived from Gerbera piloselloides (Linn.) Cass. It is a commonly used traditional medicine in China, featured by its special bioactivities as antitussive, expectorant, anti-asthma, anti-bacterial and anti-tumor. It is often used as an effective treatment for cough and sore throat as well as bronchial asthma (BA) in China. It was demonstrated in our previous studies that GPH exerted significant effects on the treatment of BA, but its underlying mechanism remains unclear.

AIM OF THE STUDY

This study was aimed at revealing the mechanism through which GPH protects against BA.

MATERIALS AND METHODS

The protective effect of GPH against BA was evaluated in a mouse model of BA induced by ovalbumin. Through integrated metabolomics and transcriptomics analysis, the most critical pathways were discovered. The effects of GPH in regulating these pathways was verified through molecular biology experiments and molecular docking.

RESULTS

GPH have anti-BA effects. In plasma and lung tissue, 5 and 17 differentially expressed metabolites (DEMs), respectively, showed a reversed tendency in the GPH group compared with the model group; apart from gamma-aminobutyric acid and butyrylcarnitine, these DEMs might aid in BA diagnosis. The DEMs were involved primarily in the regulation of lipid metabolism, followed by glucose metabolism and amino acid metabolism. Transcriptomic analysis indicated that GPH modulated 268 differentially expressed genes (DEGs). Integration analysis of metabolomics and transcriptomics revealed that GPH might regulate the PPAR signaling pathway, thus affecting the expression of key gene targets such as Cyp4a12a, Cyp4a12b, Adh7, Acaa1b and Gpat2; controlling fatty acid degradation, unsaturated fatty acid biosynthesis, glycerophospholipid metabolism and other lipid metabolic pathways; and ameliorating BA. This possibility was confirmed through reverse-transcription quantitative polymerase chain reaction, western blotting, immunofluorescence and molecular docking.

CONCLUSION

GPH was found to activate the PPAR signaling pathway, decrease the levels of Cyp4a12a and Cyp4a12b, and increase the levels of Adh7, Acaa1b and Gpat2, thereby regulating lipid metabolism disorder, decreasing the generation of inflammatory mediators and limiting lung injury.

Prediction of shared gene signatures and biological mechanisms between polycystic ovary syndrome and asthma: Based on weighted gene coexpression network analysis

OBJECTIVE

Several clinical studies have shown an association between polycystic ovary syndrome (PCOS) and asthma; however, the molecular link between these conditions remains unclear. In this study, we conducted a reanalysis and repurposing of existing databases in order to depict the common key genes, related signaling pathways, and similarity of the immune microenvironment between PCOS and asthma.

METHODS

PCOS and asthma data sets were downloaded, and common signal pathways were identified by using gene set enrichment analysis. Identified common susceptibility genes were explored by intersecting the weighted gene coexpression network analysis module genes for both diseases. Then, we performed protein-protein interaction, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses of the common susceptibility genes. Finally, we analyzed the immune environment of PCOS and asthma.

RESULTS

We identified five hub genes, namely, MMP9, CDC42, CD44, CD19, and BCL2L1, and uncovered that these five hub genes showed a tendency to be upregulated in both PCOS and asthma and possessed good diagnostic ability. In addition, we revealed that both PCOS and asthma were significantly enriched in the FcεRI-mediated signaling pathway. Moreover, we found that both PCOS and asthma exhibited infiltration of similar types of immune cells, such as monocytes, suggesting that the two diseases have similar pathological features.

CONCLUSION

PCOS and asthma share common causative genes with a similar immune environment. Taken together, we uncovered previously unsuspected traits for comprehensive diagnosis and treatment of PCOS and asthma in the future.

Shizao decoction for cirrhotic ascites: assessing potential targets based on network analysis combined with pharmacokinetics and metabolomics

Introduction: Shizao decoction (SZD) is a traditional Chinese medicine decoction that has therapeutic effects on cirrhotic ascites (CAS). Because of the unclear treatment mechanism, in the current study, the anti-CAS activity of SZD and molecular mechanisms were analyzed by network analysis combined with pharmacokinetics and metabolomics. Methods: Firstly, we assessed the anti-CAS efficacy of SZD by hematoxylin-eosin (H&E), liver function tests, NO and ET-1 levels, and portal venous pressure. Secondly, network analysis was applied to dig out the metabolites, targets, and pathways related to SZD and CAS. Then, the pharmacokinetics of the pharmacokinetically relevant metabolites (PRM) were analyzed. Thirdly, the serum and urine metabolic biomarkers of rats with CAS were identified using metabolomics by comparing them with the SZD treatment group. In addition, MetaboAnalyst was utilized to conduct metabolic pathway analysis. Finally, the correlation analysis established a dynamic connection between absorbed PRM from SZD and CAS-associated endogenous metabolites. Results: Pharmacodynamic analysis indicated that SZD effectively mitigated liver injury symptoms by ameliorating inflammatory cell infiltration in CAS rats. The network analysis results indicated that twelve RPM contribute to the therapeutic efficacy of SZD against CAS; the key signaling pathways involved might be hepatitis B and PI3K-Akt. Pharmacokinetics results showed that the 12 RPM were efficiently absorbed into rat plasma, ensuring desirable bioavailability. The metabolomic analysis yielded 21 and 23 significantly distinct metabolites from the serum and urine, respectively. The 12 bioavailable SZD-PRM, such as luteolin, apigenin, and rutin, may be associated with various CAS-altered metabolites related to tryptophan metabolism, alpha-linolenic acid metabolism, glycine metabolism, etc. Discussion: A novel paradigm was provided in this study to identify the potential mechanisms of pharmacological effects derived from a traditional Chinese medicine decoction.

Biomarkers based on multiplatform comprehensive analysis: A systematic analysis of Geng-Nian-Shu in perimenopausal syndrome

Although Geng-Nian-Shu has been shown to be clinically effective in perimenopausal syndrome, its active components and mechanism have not yet been elucidated. To demonstrate the mechanism-based biomarkers of Geng-Nian-Shu in treating perimenopausal syndrome, a total of 135 chemical constituents including 52 prototype blood constituents were identified via high-performance liquid chromatography-quadrupole-time of flight/mass spectrometry. Then, network pharmacology showed significant enrichment for the PhosphoInositide-3 Kinase/Akt pathway, suggesting that it may be the main regulatory pathway for the Geng-Nian-Shu treatment of the perimenopausal syndrome. Subsequently, multivariate analysis was performed between the Geng-Nian-Shu sham-treated and Geng-Nian-Shu ovariectomy-treated groups and further screened out 18 prototype blood constituents by correlation analysis with plasma estrogen levels to identify potential biomarkers associated with Geng-Nian-Shu treat the ovariectomy-induced perimenopausal syndrome. Finally, the results of pharmacological experimental verification and Pearson correlation analysis indicated that catalpol, ligustilide, paeoniflorin, and gallic acid were selected as biomarkers of Geng-Nian-Shu which were strongly and positively correlated with PhosphoInositide-3 Kinase/Akt signaling pathway. In this study, based on high-performance liquid chromatography-quadrupole-time of flight/mass spectrometry combined with pharmacodynamics, network pharmacology, pharmacology, and other disciplines, we explored the effects and mechanisms of Geng-Nian-Shu in the treatment of perimenopausal syndrome at multiple levels. Using multiplatform technology to investigate the role of Geng-Nian-Shu represents a new strategy for the selection and verification of biomarkers of Geng-Nian-Shu and provides a basis for further development and utilization of Geng-Nian-Shu.

A screening strategy for bioactive components of Bu-Zhong-Yi-Qi-Tang regulating spleen-qi deficiency based on "endobiotics-targets-xenobiotics" association network

ETHNOPHARMACOLOGICAL RELEVANCE

Bu-Zhong-Yi-Qi-Tang is a famous traditional Chinese medicine formula that has been prevalent in China for over 700 years to treat spleen-qi deficiency related diseases, such as gastrointestinal and respiratory disorders. However, the bioactive components responsible for regulating spleen-qi deficiency remain unclear and have puzzled many researchers.

AIM OF THE STUDY

The current study focuses on efficacy evaluation of regulating spleen-qi deficiency and screening the bioactive components of Bu-Zhong-Yi-Qi-Tang.

MATERIALS AND METHODS

The effects of Bu-Zhong-Yi-Qi-Tang were evaluated through blood routine examination, immune organ index, and biochemical analysis. Metabolomics was utilized to analyze the potential endogenous biomarkers (endobiotics) in the plasma, and the prototypes (xenobiotics) of Bu-Zhong-Yi-Qi-Tang in the bio-samples were characterized using ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry. Then, these endobiotics were used as "bait" to predict targets based on network pharmacology and to screen potential bioactive components from the absorbed prototypes in the plasma by constructing an "endobiotics-targets-xenobiotics" association network. Further, the anti-inflammatory activities of representative compounds (calycosin and nobiletin) were validated through poly(I:C)-induced pulmonary inflammation mice model.

RESULTS

Bu-Zhong-Yi-Qi-Tang exhibited immunomodulatory and anti-inflammatory activities in spleen-qi deficiency rat, as supported by the observation of increased levels of D-xylose and gastrin in serum, an increase in the thymus index and number of lymphocytes in blood, as well as a reduction in the level of IL-6 in bronchoalveolar lavage fluid. Furthermore, plasma metabolomic analysis revealed a total of 36 Bu-Zhong-Yi-Qi-Tang related endobiotics, which were mainly enriched in primary bile acids biosynthesis, the metabolism of linoleic acid, and the metabolism of phenylalanine pathways. Meanwhile, 95 xenobiotics were characterized in plasma, urine, small intestinal contents, and tissues of spleen-qi deficiency rat after Bu-Zhong-Yi-Qi-Tang treatment. Using an integrated association network, six potential bioactive components of Bu-Zhong-Yi-Qi-Tang were screened. Among them, calycosin was found to significantly reduce the levels of IL-6 and TNF-α in the bronchoalveolar lavage fluid, increase the number of lymphocytes, while nobiletin dramatically decreased the levels of CXCL10, TNF-α, GM-CSF, and IL-6.

CONCLUSION

Our study proposed an available strategy for screening bioactive components of BYZQT regulating spleen-qi deficiency based on "endobiotics-targets-xenobiotics" association network.

Network pharmacology, molecular docking, and experimental pharmacology explored Ermiao wan protected against periodontitis via the PI3K/AKT and NF-κB/MAPK signal pathways

ETHNOPHARMACOLOGICAL RELEVANCE

Ermiao Wan (EMW), a classic and famous traditional Chinese medicine (TCM)-based herbal formula combined Phellodendron chinense C.K.Schneid. (Cortex Phellodendri Chinsis, CP) and Atractylodes lancea (Thunb.) DC. (Rhizoma Atractylodis, RA) with the weight composition of 1:1, has been used for the treatment of periodontitis in China for a long time. However, its efficacy and mechanism of action are still unclear now.

AIM OF THE STUDY

This study explored the efficacy and pharmaceutical mechanism of action of EMW against periodontitis.

MATERIALS AND METHODS

The efficacy of EMW against periodontitis was evaluated using the ligature-induced periodontitis (LIP) mice, and inflammatory-related factors in gingiva and alveolar bone loss were determined using the qRT-PCR and micro-CT assays. The potential pharmacological mechanisms were predicted by bioinformatics analysis and further confirmed by the qRT-PCR and western blotting assays.

RESULTS

EMW exhibited inhibitory effects on periodontitis in the LIP mice. Bio-informational analysis showed the core compounds (berberine and chlorogenic acid) targeted the key genes (AKT, MAPK1, MAPK14, NF-κB, TNF, IL-2, and IL1B) through regulating the PI3K/AKT and NF-κB/MAPK signal pathways, which were validated using the qRT-PCR and western blotting assays.

CONCLUSIONS

EMW could eliminate alveolar bone loss and inhibit inflammation, thereby preventing the development of periodontitis. The mechanism of action may be achieved by regulating the PI3K/AKT and NF-κB/MAPK signal pathways. Therefore, EMW was a potential therapy for the treatment of periodontitis.