New omic and network paradigms for deep understanding of therapeutic mechanisms for Fangji of traditional Chinese medicine

Integrating transcriptomics and metabolomics to reveal the protective effect and mechanism of Bushen Kangshuai Granules on the elderly people

Background: Aging is characterized by a decline in the adaptability and resistance of the body. In this study, Bushen Kangshuai Granules (BKG), as a kind of Chinese herbal formula, was developed and shown to alleviate aging-related symptoms. Methods: Self-controlled study combined with RNA-seq and metabonomics were used to expound the efficacy and safety of BKG and revealed the regulation mechanism of BKG treating aging. In vitro experiments were used to confirm the analytical results. The aging cell model of AC16 cells were treated with D-galactose. The RT-qPCR was used to detect the impact of BKG on telomere length. The DCFH-DA staining was used for detecting intracellular ROS. The targeted signaling pathway was selected and verified using Western blot. Results: After 8 weeks of treatment, BKG significantly reduced SOD level (p = 0.046), TCM aging symptoms (p < 0.001) and TNF-α level (p = 0.044) in the elderly participants. High-throughput sequencing showed that BKG reversed the expression of 70 and 79 age-related genes and metabolites, respectively. Further enrichment analysis indicated that BKG downregulated the PI3K-AKT signaling pathway, extracellular matrix (ECM)-receptor interaction, and Rap1 signaling pathway, while up-regulating sphingolipid metabolism. The results of in vitro experiments show that, after D-gal treatment, the viability and telomere length of AC16 cells significantly decreased (p < 0.05), while the expression of ROS increased (p < 0.05), BKG significantly increased the telomere length of AC16 cells and reduced the level of ROS expression (p < 0.05). In addition, BKG decreased the expression of THBS1, PDGFRA, and EPS8L1(p < 0.05), consistent with the RNA-seq results. Our results also showed that BKG affects PI3K-AKT signaling pathway. Conclusion: BKG can significantly improve aging-related symptoms and increase SOD levels, which may be associated with the reversal of the expression of various aging-related genes. The PI3K-AKT signaling pathway and sphingolipid metabolism may be potential mechanisms underlying BKG anti-aging effects.

Buyang Huanwu Decoction alleviates blood stasis, platelet activation, and inflammation and regulates the HMGB1/NF-κB pathway in rats with pulmonary fibrosis

ETHNOPHARMACOLOGICAL RELEVANCE

Qi deficiency and blood stasis are identified to be pathological factors of pulmonary fibrosis (PF) in traditional Chinese medicine (TCM) theory. Buyang Huanwu Decoction (BYHWD) is a traditional Chinese prescription ameliorating Qi deficiency and blood stasis.

AIM OF THE STUDY

The objective of this study was to investigate the anti-fibrosis effect of BYHWD and the potential molecular mechanism in rats.

MATERIALS AND METHODS

Bleomycin was used to construct PF rat models. 27 PF rats were randomly divided into three groups based on treatments: model group (saline solution, n = 9), low-dose BYHWD group (3.5 g/kg, n = 9), and high-dose BYHWD group (14.0 g/kg, n = 9). Moreover, 9 normal rats were used as the blank group. The blood viscosity, coagulation indexes (APTT, TT, PT, and FIB), platelet-related parameters (PLT, PDW, MPV, PCT, and PLCR), platelet microparticles (PMPs), and inflammatory factors (IL-2, IL-10, IL-1β, IL-6, IL-8, IL-17, IFN-γ, TNF-α, PAC-1, HMGB1, NF-κB, and TF) were determined. The lung tissue samples of rats were observed after hematoxylin-eosin (HE) staining. The full component analysis of the BYHWD extract was performed using the ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method. The signaling pathway included into the study was selected on the basis of bioinformatics analysis and the results of the phytochemical analysis. The expression levels of genes and proteins involved in the selected signaling pathway were detected.

RESULTS

Compared to the blank group, the whole blood viscosity, PLR, PDW, MPV, PCT, PLCR, PMPs, and the levels of IL-1β, IL-6, IL-8, IL-17, TNF-α, PAC-1, HMGB1, NF-κB, and TF were increased, while the levels of IL-2 and IL-10 were decreased in the model group. Both low-dose BYHWD and high-dose BYHWD reversed these PF-induced effects in spite of the fact that low-dose BYHWD had no significant effect on the level of NF-κB. In addition, BYHWD ameliorated PF-induced inflammation in the rat lung tissue. The phytochemical analysis of the BYHWD extract combined with the bioinformatics analysis suggested that the therapeutical effect of BYHWD on PF was related to the HMGB1/NF-κB pathway, which consisted of NF-κB, IKBKB, ICAM1, VCAM1, HMGB1, and TLR4. Both RT-qPCR and western blot analyses showed that PF induced increases in the expression levels of NF-κB, ICAM1, VCAM1, HMGB1, and TLR4, but a decrease in the expression level of IKBKB. Moreover, both low-dose BYHWD and high-dose BYHWD exerted the opposite effects, and recovered the expression levels of NF-κB, ICAM1, VCAM1, HMGB1, TLR4, and IKBKB, despite the fact that low-dose BYHWD had no effects on the mRNA expression levels of NF-κB or TLR4.

CONCLUSIONS

In summary, BYHWD alleviated PF-induced blood stasis, platelet activation, and inflammation in the rats. Our study suggested BYHWD had a therapeutic effect on PF and was a good alternative for the complementary therapy of PF, and the potential molecular mechanism was modulation of HMGB1/NF-κB signaling pathway, and it needs further study.

Complementary authentication of Chinese herbal products to treat endometriosis using DNA metabarcoding and HPTLC shows a high level of variability

Traditional Chinese Medicine (TCM) is popular for the treatment of endometriosis, a complex gynecological disease that affects 10% of women globally. The growing market for TCMs has yielded a significant incentive for product adulteration, and although emerging technologies show promise to improve their quality control, many challenges remain. We tested the authenticity of two traditional Chinese herbal formulae used in women's healthcare for the treatment of endometriosis, known as Gui Zhi Fu Ling Wan (FL) and Ge Xia Zhu Yu Tang (GX). Dual-locus DNA metabarcoding analysis coupled with high-performance thin-layer chromatography (HPTLC) were used to authenticate 19 FL and six GX commercial herbal products, as well as three ad hoc prepared artificial mixtures. HPTLC was able to detect most of the expected ingredients via comparative component analysis. DNA metabarcoding was able to detect an unexpected species diversity in the products, including 38 unexpected taxa. Chromatography has a resolution for all species indirectly through the identification of marker compounds for the different species ingredients. Metabarcoding on the other hand yields an overview of species diversity in each sample, but interpretation of the results can be challenging. Detected species might not be present in quantities that matter, and without validated quantification, some detected species can be hard to interpret. Comparative analysis of the two analytical approaches also reveals that DNA for species might be absent or too fragmented to amplify as the relevant chemical marker compounds can be detected but no amplicons are assigned to the same species. Our study emphasizes that integrating DNA metabarcoding with phytochemical analysis brings valuable data for the comprehensive authentication of Traditional Chinese Medicines ensuring their quality and safe use.

Phenome-wide association study and precision medicine of cardiovascular diseases in the post-COVID-19 era

SARS-CoV-2 infection causes injuries of not only the lungs but also the heart and endothelial cells in vasculature of multiple organs, and induces systemic inflammation and immune over-reactions, which makes COVID-19 a disease phenome that simultaneously affects multiple systems. Cardiovascular diseases (CVD) are intrinsic risk and causative factors for severe COVID-19 comorbidities and death. The wide-spread infection and reinfection of SARS-CoV-2 variants and the long-COVID may become a new common threat to human health and propose unprecedented impact on the risk factors, pathophysiology, and pharmacology of many diseases including CVD for a long time. COVID-19 has highlighted the urgent demand for precision medicine which needs new knowledge network to innovate disease taxonomy for more precise diagnosis, therapy, and prevention of disease. A deeper understanding of CVD in the setting of COVID-19 phenome requires a paradigm shift from the current phenotypic study that focuses on the virus or individual symptoms to phenomics of COVID-19 that addresses the inter-connectedness of clinical phenotypes, i.e., clinical phenome. Here, we summarize the CVD manifestations in the full clinical spectrum of COVID-19, and the phenome-wide association study of CVD interrelated to COVID-19. We discuss the underlying biology for CVD in the COVID-19 phenome and the concept of precision medicine with new phenomic taxonomy that addresses the overall pathophysiological responses of the body to the SARS-CoV-2 infection. We also briefly discuss the unique taxonomy of disease as Zheng-hou patterns in traditional Chinese medicine, and their potential implications in precision medicine of CVD in the post-COVID-19 era.

Applying cooperative module pair analysis to uncover compatibility mechanism of Fangjis: An example of Wenxin Keli decoction

ETHNOPHARMACOLOGICAL RELEVANCE

Fangji is an ancient combinatorial formula. The compatibility mechanisms that how component herbs of Fangji work cooperatively to achieve the executive framework remain unexplored.

AIM OF THE STUDY

Toexplore compatibility mechanism and systematical effects of Fangjis by taking Wenxin Keli decoction (WXKL), a classical Fangji constituted by Codonopsis Radix, PolygonatiRhizoma, Notoginseng Radix Et Rhizoma, Ambrum, and Nardostachyos Radix Et Rhizoma., as example.

MAIN METHODS

Here, we employed bioinformatics approach, including cluster analysis, cooperative module pair analysis, primary module identification, and proximity examination among target profile of herbs, to investigate compatibility characterization and anti-arrhythmia mechanism of WXKL. Finally, core mechanisms of WXKL were validatedby in vivo experiments.

RESULTS

As a result, we identified 695 putative target proteins and 27 clusters (W-modules) inWXKL target network (W-network), in which W-module 1, 2, 4, 8, 10 were primary modules. The cooperative module pairs were W-module 2 and 4, W-module 2 and 8, and W-module 2 and 1, all of which existed in Codonopsis Radix- or Notoginseng Radix Et Rhizoma.-condition. And Nardostachyos Radix Et Rhizoma only yielded cooperation between W-module 1 and 2. The proximity of herbs' target profiles of Codonopsis Radix and Notoginseng Radix Et Rhizoma were similar, and Nardostachyos Radix Et Rhizoma and Ambrum were similar. For the compatibility framework, Codonopsis Radix general regulated 70.67% targets and majority W-modules (81.48%) as sovereign herb, contributing to primary therapeutic effect, mainly involving neurohormonal regulation, vasomotor, inflammation and oxidative stress. Other herbs assisted Codonopsis Radix to enhance major outcomes through common modules, and acted as complementary roles through unique process including mitotic cell cycle, biosynthetic and catabolic process, etc. Furthermore, WXKL regulated 66.67% hub proteins of arrhythmia-network, 68.18% and 47.37% proteins in primary arrhythmia-module 1 and 2, mainly involving ion channel activity, neurohormonal regulation, and stress response processes, to constitute regulatory network focusing on cardiovascular, renal, nervous system, to reverse the pathological process of arrhythmia. In vivo experiments demonstrated WXKL can attenuate adrenergic activation induced sympathetic atrial fibrillation by inhibiting calmodulin expression (CaM) and ryanodine receptor 2 (RYR2) phosphorylation to regulate neurohormonal action.

CONCLUSION

This strategy provided an overarching view of anti-arrhythmia mechanism of WXKL and its internal compatibility, and may facilitate the understanding of compatibility in Fangjis from the perspectives of modern biology.

Network-based modeling of herb combinations in traditional Chinese medicine

Traditional Chinese medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein–protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.

Traditional Chinese medicine for dementia

In Western medicine, dementia refers to a spectrum of diseases affecting cognition, mental health, and physical abilities. Ancient medical literatures of traditional Chinese medicine (TCM) also recorded dementia-like symptoms, but described the disease from a totally distinct theoretical point of view. The earliest records of memory loss in ancient China can be traced back 2000 years earlier. In TCM, dementia can be attributed mainly to the Brain dystrophy, Spleen-Kidney weakness, Blood stasis, and Phlegm stagnation. Of interest, ancient Chinese physicians have proposed that dementia manifests as not only cognitive but also noncognitive symptoms including psychiatric disorders and sleep disturbance, which have been investigated widely nowadays in Western medicine. Various TCM prescriptions, herbal medicines, and acupunctures have also been proposed for dementia prevention and therapy. Some of these strategies are still used in current clinical practice. Reviewing and highlighting the unique TCM recognition of treating dementia may shed light on future dementia research.

Network Patterns of Herbal Combinations in Traditional Chinese Clinical Prescriptions

As a well-established multidrug combinations schema, traditional Chinese medicine (herbal prescription) has been used for thousands of years in real-world clinical settings. This paper uses a complex network approach to investigate the regularities underlying multidrug combinations in herbal prescriptions. Using five collected large-scale real-world clinical herbal prescription datasets, we construct five weighted herbal combination networks with herb as nodes and herbal combinational use in herbal prescription as links. We found that the weight distribution of herbal combinations displays a clear power law, which means that most herb pairs were used in low frequency and some herb pairs were used in very high frequency. Furthermore, we found that it displays a clear linear negative correlation between the clustering coefficients and the degree of nodes in the herbal combination network (HCNet). This indicates that hierarchical properties exist in the HCNet. Finally, we investigate the molecular network interaction patterns between herb related target modules (i.e., subnetworks) in herbal prescriptions using a network-based approach and further explore the correlation between the distribution of herb combinations and prescriptions. We found that the more the hierarchical prescription, the better the corresponding effect. The results also reflected a well-recognized principle called “Jun-Chen-Zuo-Shi” in TCM formula theories. This also gives references for multidrug combination development in the field of network pharmacology and provides the guideline for the clinical use of combination therapy for chronic diseases.

Genomic data mining approaches for the discovery of anticancer peptides from Ganoderma sinense

Drug discovery from traditional Chinese medicine (TCM) typically involves the extraction of active ingredients from natural products with high biological activity and function from the vast repertoire of traditional Chinese medicine. This strategy cannot fully exploit the vast resources of TCM. Known as the longevity mushroom, Ganoderma spp. has been used as medicine for thousands of years. Recent studies have demonstrated its anticancer activity. While most research on Ganoderma spp. has focused on their polysaccharides or small molecules as potential anticancer components, possible anticancer peptides (ACPs) or proteins have been neglected. In this study, genomic data mining approaches were used to discover potential ACPs from Ganoderma sinense. A search against known ACPs identified 477 proteins in the G. sinense proteome that possess putative ACP sequences and that thus may serve as parent proteins. After in silico digestion by trypsin, 34 G. sinense proteins were predicted to release putative ACPs (by the mACPpred program). A subsequent sequence similarity comparison against known ACPs identified 15 trypsin-digested fragments as possible ACPs, of which 3 sequences were identical to known ACPs. The results indicated that ACPs may be involved in the anticancer activity of G. sinense and that genomic mining approaches can be effective strategies for discovering active components in TCM resources. The accumulation of genomic and proteomic data will undoubtedly accelerate drug discovery from TCM resources.