Untargeted Metabolomics and Targeted Quantitative Analysis of Temporal and Spatial Variations in Specialized Metabolites Accumulation in Poria cocos (Schw.) Wolf (Fushen)

Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams

Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.

Ling-Gui-Qi-Hua formula alleviates left ventricular myocardial fibrosis in rats with heart failure with preserved ejection fraction by blocking the transforming growth factor-β1 /Smads signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Ling-Qui-Qi-Hua (LGQH) decoction, composed of Poria cocos (Schw.) Wolf, Cinnamomum cassia (L.) J. Presl, Paeonia veitchii Lynch, and Atractylodes macrocephala Koidz., is a compound formula derived from Ling-Gui-Zhu-Gan decoction recorded in the Treatise on Febrile and Miscellaneous. It has shown cardioprotective effects on patients or rats with heart failure with preserved ejection fraction (HFpEF). Nevertheless, the active ingredients of LGQH and its anti-fibrotic mechanism remain unknown.

AIM OF THE STUDY

To determine the active ingredients in LGQH decoction and verify that LGQH decoction may inhibit left ventricular (LV) myocardial fibrosis in HFpEF rats by blocking the transforming growth factor-β1 (TGF-β1)/Smads signaling pathway from the perspective of animal experiments.

MATERIALS AND METHODS

First, liquid chromatography-mass spectrometry (LC-MS) technology was used to identify active components in the LGQH decoction. Secondly, a rat model of the metabolic syndrome-associated HFpEF phenotype was established and subsequently received LGQH intervention. The mRNA and protein expression of targets in the TGF-β1/Smads pathway were detected by quantitative real-time polymerase chain reaction and western blot analysis. Finally, molecular docking was conducted to examine the interactions between the active ingredients in the LGQH decoction and key proteins of the TGF-β1/Smads pathways.

RESULTS

According to LC-MS analysis, the LGQH decoction contained 13 active ingredients. In animal experiments, LGQH attenuated LV hypertrophy, enlargement, and diastolic function in HEpEF rats. Mechanically, LGQH not only down-regulated TGF-β1, Smad2, Smad3, Smad4, α-SMA, Coll I, and Coll III mRNA expressions and TGF-β1, Smad2, Smad3, P-Smad2/Smad3, Smad4, α-SMA, and Coll I protein expressions, but also up-regulated Smad7 mRNA and protein expressions, which ultimately led to myocardial fibrosis. Furthermore, molecular docking confirmed that 13 active ingredients in the LGQH decoction have excellent binding activities to the critical targets of the TGF-β1/Smads pathway.

CONCLUSION

LGQH is a modified herbal formulation with multiple active ingredients. It might alleviate LV remodeling and diastolic dysfunction and inhibit LV myocardial fibrosis by blocking TGF-β1/Smads pathways in HFpEF rats.

Integrated omic profiling of the medicinal mushroom Inonotus obliquus under submerged conditions

BACKGROUND

The Inonotus obliquus mushroom, a wondrous fungus boasting edible and medicinal qualities, has been widely used as a folk medicine and shown to have many potential pharmacological secondary metabolites. The purpose of this study was to supply a global landscape of genome-based integrated omic analysis of the fungus under lab-growth conditions.

RESULTS

This study presented a genome with high accuracy and completeness using the Pacbio Sequel II third-generation sequencing method. The de novo assembled fungal genome was 36.13 Mb, and contained 8352 predicted protein-coding genes, of which 365 carbohydrate-active enzyme (CAZyme)-coding genes and 19 biosynthetic gene clusters (BCGs) for secondary metabolites were identified. Comparative transcriptomic and proteomic analysis revealed a global view of differential metabolic change between seed and fermentation culture, and demonstrated positive correlations between transcription and expression levels of 157 differentially expressed genes involved in the metabolism of amino acids, fatty acids, secondary metabolites, antioxidant and immune responses. Facilitated by the widely targeted metabolomic approach, a total of 307 secondary substances were identified and quantified, with a significant increase in the production of antioxidant polyphenols.

CONCLUSION

This study provided the comprehensive analysis of the fungus Inonotus obliquus, and supplied fundamental information for further screening of promising target metabolites and exploring the link between the genome and metabolites.

Untargeted metabolomics reveals sour jujube kernel benefiting the nutritional value and flavor of Morchella esculenta

Nucleosides, organic acids, and amino acids separated from Morchella esculenta are well known for their nutritional value and flavor. However, how to increase their content in a better way has been a challenge. In this study, the effect of adding jujube kernel on the active components of M. esculenta was investigated by untargeted metabolomics using UPLC-MS/MS. A total of 1,243 metabolites were identified, of which 262 metabolites (21.078%) were organic acids and derivatives, 245 metabolites (19.71%) were lipids and lipid-like molecules, and 26 metabolites (2.092%) were nucleosides, nucleotides, and analogues. Subsequently, differential metabolites between groups were screened by the orthogonal partial least squares-discriminant analysis model, which showed that 256 metabolites were identified as significantly different for the positive ion model and 149 for the negative ion model. Moreover, significant differential metabolites (VIP > 1, P < 0.05) in annotation of kyoto encyclopedia of genes and genomes pathway were investigated, which showed that ABC transporters were the most commonly observed transporters, followed by pyrimidine metabolism and purine metabolism. The results indicated that the main components of jujube kernel might be conducive to the accumulation of nucleoside organic acids and amino acid metabolites in M. esculenta. These results provide important information for the understanding of more suitable way for cultivation of M. esculenta.

Pharmacokinetics-derived absorbed components responsible for Guizhi-Fuling capsule target PI3K/Akt-Erk to exert an anti-dysmenorrhea effect

ETHNOPHARMACOLOGICAL RELEVANCE

Guizhi-Fuling capsule (GZFL), a well-known herbal remedy, has been widely used to treat primary dysmenorrhea (PD). Hence, systematic identifying multiple active ingredients and the involved mechanism is essential and urgently needed for GZFL.

AIM OF THE STUDY

This study was planned to assess the pharmacokinetics of GZFL in rats, and identify whether these GZFL-derived absorbed components (ACs) contribute to the efficacy of source herbs and relevant mechanism.

MATERIALS AND METHODS

The in vivo pharmacokinetic profile of 11 phytochemicals and 13 metabolites in healthy and PD rats were evaluated using liquid chromatography with mass spectrometry (LC-MS/MS). Whereafter, the introduced contribution strategy assessed ACs' effect (doses = their contents in GZFL) in PD rats with the mechanism.

RESULT

The pharmacokinetic profiles of prototypes and metabolites differed in healthy and PD rats. As a main proxy of GZFL, 11ACs exerted an anti-PD effect (improvement of indexes for writhing latency, writhing time, PGF_2α/PGE₂, TXB₂/6-keto-PGF_1α and β-EP) by regulating PI3K-Akt/ERK pathway.

CONCLUSION

As a paradigmatic example, 11ACs contributed an average of 113.55% to GZFL in terms of anti-PD efficacy, providing an approach to rapidly, accurately and consistently identify the bioactive components and their pathway from herbs.

Effects of Poria cocos extract on metabolic dysfunction-associated fatty liver disease via the FXR/PPARα-SREBPs pathway

Despite the increase in the global prevalence of metabolic dysfunction-associated fatty liver disease (MAFLD), no approved drug currently exists for the disease. Poria cocos (Schw.) Wolf (P. cocos) is a medicinal mushroom belonging to a family of polyporaceae widely used in TCM clinics to protect the liver and treat obesity. However, its efficacy, practical components, and underlying mechanism against MAFLD are yet to be determined. In this study, we evaluated the effects of Poria cocos (P. cocos) ethanol extract (EPC) on hepatic dyslipidemia, steatosis, and inflammation by both bioinformatics analysis and MAFLD rats induced by HFD feeding. We found EPC treatment dramatically reduced lipid accumulation, inflammatory cell infiltration, and liver injury. EPC reduced serum TC, TG levels, and hepatic TG, TBA, and NEFA contents. UHPLC Q-Trap/MS examination of BA profiles in serum and feces showed that EPC increased fecal conjugated BAs, decreased free BAs, and improved BA metabolism in HFD-fed rats. Western blot and RT-qPCR analysis showed that EPC could activate hepatic FXR and PPARα expression and reduce CYP7A1 and SREBP-1c expression. Systemic pharmacology combined with molecular docking suggested that poricoic acid B and polyporenic acid C, the major active compounds in EPC, could ameliorate lipid homeostasis by activating the nuclear receptor PPARα. We further confirmed their inhibition effects of lipid droplet deposition in steatized L-02 hepatocytes. In summary, EPC alleviated HFD-induced MAFLD by regulating lipid homeostasis and BA metabolism via the FXR/PPARα-SREBPs signaling pathway. P. cocos triterpenes, such as poricoic acid B and polyporenic acid C, were the characteristic substances of P. cocos for the treatment of MAFLD.

Gender Discrimination of Flower Buds of Mature Populus tomentosa by HPLC Fingerprint Combined with Chemometrics

A high performance liquid chromatography-diode array detector (HPLC-DAD) was used to establish the HPLC fingerprint. Chemometrics methods were used to discriminate against the gender of flower buds of Populus tomentosa based on areas of common peaks calibrated with the HPLC fingerprint. The score plot of principal component analysis (PCA) showed a clear grouping trend (R²X, 0.753; Q², 0.564) between female and male samples. Two groups were also well discriminated with orthogonal partial least squares-discriminant analysis (OPLS-DA) (R²X, 0.741; R²Y, 0.980; Q², 0.970). As the hierarchical clustering analysis (HCA) heatmap showed, all samples were separated into two groups. Four compounds were screened out by S-plot and variable importance in projection (VIP > 1.0). Two of them were identified as siebolside B and tremulacin. This study demonstrated that HPLC fingerprints combined with chemometrics can be applied to discriminate against dioecious plants and screen differences, providing a reference for identifying the gender of dioecious plants.

An integrated approach for investigating pharmacodynamic material basis of Lingguizhugan Decoction in the treatment of heart failure

ETHNOPHARMACOLOGICAL RELEVANCE

As a classical formula of traditional Chinese medicine (TCM), Lingguizhugan Decoction (LGZGD) has been used for treating heart failure (HF) because it has an efficiency of yang-warming and fluid-dispersing. However, the pharmacodynamic material basis of LGZGD responsible for the therapeutic benefits is not well understood.

AIM OF THE STUDY

The aim of this study was to elucidate the pharmacodynamic material basis of LGZGD by an integrated approach.

MATERIALS AND METHODS

Following oral administration of LGZGD in mice, ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS) was used to identify prototype substances. A heart failure (HF) model was established, followed by an untargeted metabolomics study to determine potential targets of LGZGD. The network pharmacology method was performed to screen substances that interacted with potential targets of LGZGD treating HF. Molecular docking technology was applied to further screen substances based on binding energy. Cell viability assays were conducted to verify pharmacodynamic effects of selected substances.

RESULTS

In all, forty-two prototype substances were identified in the blood, urine, and fecal samples of mice. A total of fifty-five differential metabolites were identified using heart tissue untargeted metabolomics. Twenty-five substances of LGZGD were screened relating to thirty-three targets treating HF. Twenty-two substances were filtered according to their binding energy using molecular docking technology. Cell experiments revealed cinnamaldehyde, glycyrrhetinic acid, kaempferol, daidzein, caffeic acid, and catechin could significantly improve the survival rate of H9c2 cells, which might be the pharmacodynamic material basis of LGZGD.

CONCLUSIONS

A scientific approach that integrated in vivo substances identification, metabolomics, network pharmacology, molecular docking, and cell pharmacodynamic assay has been developed to study the pharmacodynamic material basis of LGZGD in the treatment of HF.

Anshen Dingzhi prescription in the treatment of PTSD in mice: Investigation of the underlying mechanism from the perspective of hippocampal synaptic function

BACKGROUND

Anshen Dingzhi prescription (ADP) is an important prescription for the treatment of mental diseases in traditional Chinese medicine and is widely used to treat neuropsychiatric disorders.

PURPOSE

To explore the ameliorative effect of ADP on post-traumatic stress disorder (PTSD)-like behaviors in mice and determine the underlying mechanism.

METHODS

The constituents of ADP were analyzed by UPLC-Q-TOF/MS. The PTSD-like behaviors of mice subjected to single prolonged stress (SPS) were evaluated using behavioral tests. Potential pathological changes in the hippocampus were assessed by hematoxylin and eosin (H&E) staining. Western blotting and immunohistochemistry (IHC) were employed to detect the expression of proteins involved in relevant signaling pathways.

RESULTS

Five quality control markers (ginsenoside Rg1, ginsenoside Rb1, tenuifolin, poricoic acid B, and α-asarone) were detected in the ADP solution. The ginsenoside Rg1 content in ADP was found to be 0.114 mg/g. Mice subjected to SPS showed obvious fear generalization and anxiety-like behaviors. ADP treatment prevented the behavioral changes caused by exposure to SPS. Compared with control animals, the number of normal pyramidal cells in the hippocampal CA1 region of mice exposed to SPS was decreased and the number of degenerating pyramidal cells was increased; however, ADP administration could counteract these effects. Furthermore, the protein expression of BDNF, p-TrkB, μ-calpain, PSD95, GluN2A, GluA1, p-AKT, p-mTOR, and ARC was decreased, while that of PTEN and GluN2B was increased in the hippocampus of mice subjected to SPS compared with that in control animals; however, these changes in protein expression were reversed following ADP treatment. Importantly, the ameliorative effect of ADP on PTSD-like behaviors and synaptic protein expression were inhibited by rapamycin administration.

CONCLUSIONS

ADP administration improves PTSD-like behaviors in mice and this effect may be mediated through an mTOR-dependent improvement in synaptic function in the hippocampus.

The Application of UHPLC-HRMS for Quality Control of Traditional Chinese Medicine

UHPLC-HRMS (ultra-high-performance liquid chromatography-high resolution mass spectrometry) is a new technique that unifies the application of UHPLC with HRMS. Because of the high sensitivity and good separation ability of UHPLC and the sensitivity of HRMS, this technique has been widely used for structure identification, quantitative determination, fingerprint analysis, and elucidation of the mechanisms of action of traditional Chinese medicines (TCMs) in recent years. This review mainly outlines the advantages of using UHPLC-HRMS and provides a survey of the research advances on UHPLC-HRMS for the quality control of TCMs.

An Evaluation of Traits, Nutritional, and Medicinal Component Quality of Polygonatum cyrtonema Hua and P. sibiricum Red

Polygonati rhizoma (Huangjing in Chinese) is a traditional and classic dual-purpose material used in food and medicine. Herbalists in China and Japan have noticed several different rhizome types in Huangjing with different qualities. Rhizome of Polygonatum cyrtonema Hua and P. sibiricum Red. is divided into five types: "Jitou-type" Polygonati rhizoma (JTPR), atypical "Jitou-type" Polygonati rhizoma (AJTPR), "Jiang-type" Polygonati rhizoma (JPR), "Cylinder-type" Polygonati rhizoma (CPR), and "Baiji-type" Polygonati rhizoma (BJPR). This study observed the microstructure and histochemical localization of polysaccharides, saponins, and proteins in Huangjing. Nutritional and medicinal component data and antioxidant capacity (DPPH and ABTS) were analyzed to evaluate the quality of different types of Huangjing. The results showed that the comprehensive quality of the rhizomes, BJPR and JTPR, was better, regardless of their nutritional or medicinal values. Altogether, these results could recommend future breeding efforts to produce Huangjing with improved nutritional and medicinal qualities.