Exploiting omic-based approaches to decipher Traditional Chinese Medicine

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Chinese Medicine (TCM), an ancient health system, faces significant research challenges due to the complexity of its active components and targets, as well as a historical lack of detailed annotation. However, recent advances in omics technologies have begun to unravel these complexities, providing a more informed and nuanced understanding of TCM's therapeutic potential in contemporary healthcare.

AIM OF THE REVIEW

This review summarizes the application of omics technologies in TCM modernization, emphasizing components analysis, quality control, biomarker discovery, target identification, and treatment optimization. In addition, future perspectives on using omics for precision TCM treatment are also discussed.

MATERIALS AND METHODS

We have explored several databases (including PubMed, ClinicalTrials, Google Scholar, and Web of Science) to review related articles, focusing on Traditional Chinese Medicine, Omics Strategy, Precision Medicine, Biomarkers, Quality Control, and Molecular Mechanisms. Paper selection criteria involved English grammar, publication date, high citations, and broad applicability, exclusion criteria included low credibility, non-English publications, and those full-text inaccessible ones.

RESULTS

TCM and the popularity of Chinese herbal medicines (CHMs) are gaining increasing attention worldwide. This is driven, in part, by a large number of technologies, especially omics strategy, which are aiding the modernization of TCM. They contribute to the quality control of CHMs, the identification of cellular targets, discovery of new drugs and, most importantly, the understanding of their mechanisms of action.

CONCLUSION

To fully integrate TCM into modern medicine, further development of robust omics strategies is essential. This vision includes personalized medicine, backed by advanced computational power and secure data infrastructure, to facilitate global acceptance and seamless integration of TCM practices.

Paeoniflorin improves ulcerative colitis via regulation of PI3K‑AKT based on network pharmacology analysis

Paeoniflorin (PF) is the primary component derived from Paeonia lactiflora and white peony root and has been used widely for the treatment of ulcerative colitis (UC) in China. UC primarily manifests as a chronic inflammatory response in the intestine. In the present study, a network pharmacology approach was used to explore the specific effects and underlying mechanisms of action of PF in the treatment of UC. A research strategy based on network pharmacology, combining target prediction, network construction, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and molecular docking simulation was used to predict the targets of PF. A total of 288 potential targets of PF and 599 UC-related targets were identified. A total of 60 therapeutic targets of PF against UC were identified. Of these, 20 core targets were obtained by protein-protein interaction network construction. GO and KEGG pathway analyses showed that PF alleviated UC through EGFR tyrosine kinase inhibitor resistance, the IL-17 signaling pathway, and the PI3K/AKT signaling pathway. Molecular docking simulation showed that AKT1 and EGFR had good binding energy with PF. Animal-based experiments revealed that the administration of PF ameliorated the colonic pathological damage in a dextran sulfate sodium-induced mouse model, resulting in lower levels of proinflammatory cytokines including IL-1β, IL-6, and TNF-α, and higher levels of IL-10 and TGF-β. PF decreased the mRNA and protein expression levels of AKT1, EGFR, mTOR, and PI3K. These findings suggested that PF plays a therapeutic protective role in the treatment of UC by regulating the PI3K/AKT signaling pathway.

Protective effect of vitamin B6 against doxorubicin-induced cardiotoxicity by modulating NHE1 expression

Doxorubicin (DOX) has been used to treat various types of cancer, but its application is limited due to its heart toxicity as well as other drawbacks. Chronic inhibition of Na+ /H+ exchanger (NHE1) reduces heart failure and reduces the production of reactive oxygen species (ROS); vitamin B6 (VitB6 ) has been demonstrated to have a crucial role in antioxidant mechanism. So, this study was designed to explore the effect of VitB6 supplement on the DOX-induced cardiotoxicity and to imply whether NHE1 is involved. Ultrasonic cardiogram analysis revealed that VitB6 supplement could alleviate DOX-induced cardiotoxicity; hematoxylin and eosin (HE) and Masson's staining further confirmed this effect. Furthermore, VitB6 supplement exhibited significant antioxidative stress and antiapoptosis effect, which was evidenced by decreased serum malondialdehyde (MDA) content and increased serum superoxide dismutase (SOD) content, and decreased Bcl-2-associated X protein/B-cell lymphoma-2 ratio, respectively. Collectively, VitB6 supplement may exert antioxidative and antiapoptosis effects to improve cardiac function by decreasing NHE1 expression and improve DOX-induced cardiotoxicity.

Yi-Xin-Shu capsule ameliorates cardiac hypertrophy by regulating RB/HDAC1/GATA4 signaling pathway based on proteomic and mass spectrometry image analysis

BACKGROUND

Cardiac hypertrophy (CH) forms the main pathological basis of chronic heart failure (CHF). Mitigating and preventing CH is the key strategy for the treatment of ventricular remodeling in CHF. Yi-Xin-Shu capsule (YXS) has been commonly applied in the clinical treatment of CHF in Asian countries for several decades. However, the underlying mechanism of YXS has not been revealed yet.

PURPOSE

To assess the efficiency of YXS in CH and identify its potential therapeutic targets for the managing of CH.

METHOD

Ultrasonic cardiogram was used to evaluate the cardiac function of CH rats. Hematein Eosin (HE)-staining, Masson-staining and transmission electron microscope were used to measure the morphological changes, cardiac fibrosis degree and ultrastructure characteristics of cardiomyocytes, respectively. ELISA was used to detect the myocardial injury biomarkers. Then, the potential targets regulated by YXS were screened out via proteomic analysis and mass spectrometry image analysis. Finally, the targets were validated by real-time quantitative (RT-q) PCR, immunofluorescence, immunohistochemistry, and western-blotting methods.

RESULTS

YXS improved the cardiac function of CH rats and attenuated the injuries in morphology and subcellular structure of cardiomyocytes. A core protein-protein interaction network was established on differentially expressed proteins (DEP) using proteomics analysis. GATA binding protein 4 (GATA4) was identified as the key target regulated by YXS. The results of mass spectrometry image analysis indicated that the expressions of histone deacetylase 1 (HDAC1) and retinoblastoma (RB) could also be regulated by YXS. Further valuative experiments showed that YXS may attenuate CH by regulating the RB/HDAC1/GATA4 signaling pathway.

CONCLUSIONS

For the first time, this study discloses the precise mechanism investigation of the efficacy of YXS against CH. These data demonstrate that YXS may protect against CH by regulating the RB/HDAC1/GATA4 signaling pathway.

Efficacy and Mechanism of Buyang Huanwu Decoction in Patients With Ischemic Heart Failure: A Randomized, Double-Blind, Placebo-Controlled Trial Combined With Proteomic Analysis

Objective: Buyang Huanwu Decoction (BYHW), a famous herbal prescription in traditional Chinese medicine (TCM), has been used for 200 years for treating ischemic heart failure (IHF). This study aims to assess the efficacy and safety of BYHW combined with guideline-guided pharmacotherapy in patients with IHF and explore the biological mechanism by which BYHW exerts its efficacy. Methods: In the multicenter, double-blind, randomized controlled trial, a total of 80 patients with IHF were randomized to receive BYHW or placebo for 3 months. The primary efficacy endpoints were New York Heart Association (NYHA) classification, TCM syndrome scores, N-terminal pro-B-type natriuretic peptide (NT-ProBNP), whereas the mechanism exploration endpoints included energy metabolism parameters and coagulation function parameters. In addition, we performed the proteomic study of the serum of patients after treatment by label-free quantification technology to verify the candidate target proteins and pathways. Results: After 3 months of treatment, the NYHA classification, TCM syndrome scores, and the percentage of subjects with at least 30% reduction in NT-ProBNP were significantly improved in the BYHW group, compared with the control group (p < 0.05); BYHW treatment also significantly regulated blood glucose, blood lipid levels, ameliorated energy metabolism and improved coagulation function parameters. There were no significant differences in safety endpoints between the two groups. In addition, we obtained 56 differentially expressed proteins by proteomics, including 20 upregulated proteins and 36 downregulated proteins. Bioinformatic analysis revealed the mechanism of BYHW treatment was significantly related to complement and coagulation cascades, cholesterol metabolism, NF-kappa B signaling pathway, PI3K-Akt signaling pathway, and metabolic pathways. Among these differentially regulated proteins, fibrinogen gamma (FGG), fibrinogen beta (FGB), Carboxypeptidase B2 (CPB2), Coagulation factor XIII A (F13A1), Intercellular adhesion molecule1 (ICAM1), Apolipoprotein C-II(APOC2), Apolipoprotein C-I(APOC1), and CD44 were found to be signature proteins associated with the efficacy of BYHW against IHF. Conclusion: BYHW treatment can further improve cardiac dysfunction and clinical symptoms in IHF based on standard therapy without apparent adverse effects. Additionally, BYHW may play a therapeutic role in IHF by improving energy metabolism and regulating coagulation function through multiple targets and pathways.

Precise Investigation of the Efficacy of Multicomponent Drugs Against Pneumonia Infected With Influenza Virus

Background: Viral pneumonia is one of the most serious respiratory diseases, and multicomponent traditional Chinese medicines have been applied in the management of infected patients. As a representative TCM, HouYanQing (HYQ) oral liquid shows antiviral activity. However, the unclear mechanisms, as well as the ambiguous clinical effects, limit widespread application of this treatment. Therefore, in this study, a proteomics-based approach was utilized to precisely investigate its efficacy.

Methods: Based on the efficacy evaluation of HYQ in a mouse model of pneumonia caused by influenza A virus (H1N1) and the subsequent proteomics analysis, specific signatures regulated by HYQ treatment of viral pneumonia were identified.

Results: Experimental verifications indicate that HYQ may show distinctive effects in viral pneumonia patients, such as elevated galectin-3-binding protein and glutathione peroxidase 3 levels.

Conclusion: This study provides a precise investigation of the efficacy of a multicomponent drug against viral pneumonia and offers a promising alternative for personalized management of viral pneumonia.

Proteomic Analysis Reveals the Protective Effects of Yiqi Fumai Lyophilized Injection on Chronic Heart Failure by Improving Myocardial Energy Metabolism

Yiqi Fumai lyophilized injection (YQFM) is the recombination of Sheng mai san (SMS).YQFM has been applied clinically to efficaciously and safely treat chronic heart failure (CHF). However, the mechanism of YQFM is still not fully elucidated. The purpose of our study was to investigate the protective mechanism of YQFM against abdominal aortic coarctation (AAC) in rats by proteomic methods. After YQFM treatment, the cardiac function were obviously meliorated. One hundred and fifty-seven important differentially expressed proteins (DEPs) were identified, including 109 in model rat compared with that in control rat (M:C) and 48 in YQFM-treated rat compared with that in model rat (T:M) by iTRAQ technology to analyze the proteomic characteristics of heart tissue. Bioinformatics analysis showed that DEPs was mainly involved in the body’s energy metabolism and was closely related to oxidative phosphorylation. YQFM had also displayed efficient mitochondrial dysfunction alleviation properties in hydrogen peroxide (H₂O₂)-induced cardiomyocyte damage by Transmission Electron Microscope (TEM), Metabolic assay, and Mitotracker staining. What’s more, the levels of total cardiomyocyte apoptosis were markedly reduced following YQFM treatment. Furthermore, Western blot analysis showed that the expressions of peroxisome proliferator activated receptor co-activator-1α(PGC-1α) (p < 0.01 or p < 0.001), perixisome proliferation-activated receptor alpha (PPAR-α) (p < 0.001)and retinoid X receptor alpha (RXR-α) were upregulated (p < 0.001), PGC-1α as well as its downstream effectors were also found to be upregulated in cardiomyocytes after YQFM treatment(p < 0.001).These results provided evidence that YQFM could enhance mitochondrial function of cardiomyocytes to play a role in the treatment of CHF by regulating mitochondrial biogenesis-related proteins.

Traditional Chinese medicine for acute coronary syndrome: A meta-analysis of clinical manifestations and objective indicators

BACKGROUND

Modern clinical trials and experimental researches of traditional Chinese medicine (TCM) have been conducted for decades and provided support for the prevention and treatment of acute coronary syndrome (ACS). However the level of evidence and the proper application of TCM were still barely satisfactory.

METHODS

In this study, we divided ACS into 3 different stages, including unstable angina, acute myocardial infarction, and post myocardial infarction. Then we systematically reviewed and meta-analyzed the existing randomized controlled trials on both clinical manifestations and objective indicators, in these 3 aspects.

RESULTS

The results indicate that TCM can both improve the clinical manifestations and ameliorate the objective parameters in different courses of ACS, including C-reactive protein in unstable angina, left ventricular ejection fraction in acute myocardial infarction and post myocardial infarction. And the incidence of short-term cardiovascular events are lower in TCM intervention group. Some of the improvements lead to potential long-term benefits.

CONCLUSION

TCM treatment is beneficial to different courses of ACS. To acquire more solid and comprehensive evidence of TCM in treating ACS, more rigorously designed randomized controlled trials with longer follow-up duration are warranted.

Pharmacokinetics/pharmacometabolomics-pharmacodynamics reveals the synergistic mechanism of a multicomponent herbal formula, Baoyuan decoction against cardiac hypertrophy

Multicomponent herbal formulas (MCHFs) have earned a wide reputation for their definite efficacy in preventing or treating chronic complex diseases. However, holistic elucidation of the causal relationship between the bioavailable ingredients of MCHFs and their multitarget interactions is very challenging. To solve this problem, pharmacokinetics/pharmacometabolomics-pharmacodynamics (PK/PM-PD) combined with a multivariate biological correlation-network strategy was developed and applied to a classic MCHF, Baoyuan decoction (BYD), to clarify its active components and synergistic mechanism against cardiac hypertrophy (CH). First, multiple plasma metabolic biomarkers for β-adrenergic agonist-induced CH rats were identified by using untargeted metabolomic profiling, and then, these CH-associated endogenous metabolites and the absorbed BYD-compounds in plasma at different treatment stages after oral administration of BYD were analyzed by using targeted PK and PM. Second, the dynamic relationship of BYD-related compounds and CH-associated endogenous metabolites and signaling pathways was built by using multivariate and bioinformatic correlation analysis. Finally, metabolic-related PD indicators were predicted and further verified by biological tests. The results demonstrated that the bioavailable BYD-compounds, such as saponins and flavonoids, presented differentiated and distinctive metabolic features and showed positive or negative correlations with various CH-altered metabolites and PD-indicators related to gut microbiota metabolism, amino acid metabolism, lipid metabolism, energy homeostasis, and oxidative stress at different treatment stages. This study provides a novel strategy for investigating the dynamic interaction between BYD and the biosystem, providing unique insight for disclosing the active components and synergistic mechanisms of BYD against CH, which also supplies a reference for other MCHF related research.

Yixin-Shu Capsules Ameliorated Ischemia-Induced Heart Failure by Restoring Trx2 and Inhibiting JNK/p38 Activation

Traditional Chinese medicine has shown great safety and efficacy in the treatment of heart failure (HF), whereas the mechanism remains unclear. In this study, the protective effect of Yixin-shu (YXS) capsules, a conventional medicine for various cardiovascular diseases, against myocardial ischemia-induced HF in rats was systematically investigated by RNA-seq technology. HF rats treated with YXS (0.8 or 1.6 g/kg/d, ig) for 6 weeks had significantly decreased brain natriuretic peptide (BNP) and atrial natriuretic peptide (ANP) and collagen III and attenuated cardiac structure rupture and collagen deposition. Additionally, YXS treatment decreased the levels of interleukin-1β (IL-1β), interleukin 6 (IL-6), tumor necrosis factor-α (TNF-α), and lactate dehydrogenase (LDH) and TUNEL-positive rate and the nitrotyrosine staining, but increased levels of glutathione (GSH), total antioxidant capacity (T-AOC) activity, and mitochondrial membrane potential. Further experiments demonstrated that YXS restored Trx2 and inhibited the phosphorylation of JNK and p38, thereby improving cardiac function in the rats with HF. Silencing Trx2 decreased the protection of YXS in the response to H2O2 as evidenced by the increase of caspase-3 activity and decrease of GSH level. Thus, YXS enhanced heart function and decreased myocardial damage through restoring Trx2 and inhibiting JNK and p38 activation in ischemia-induced HF.

Network Pharmacology-Based Investigation into the Mechanisms of Quyushengxin Formula for the Treatment of Ulcerative Colitis

Objective

Ulcerative colitis (UC) is a chronic idiopathic inflammatory bowel disease whose treatment strategies remain unsatisfactory. This study aims to investigate the mechanisms of Quyushengxin formula acting on UC based on network pharmacology.

Methods

Ingredients of the main herbs in Quyushengxin formula were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Absorption, distribution, metabolism, and excretion properties of all ingredients were evaluated for screening out candidate bioactive compounds in Quyushengxin formula. Weighted ensemble similarity algorithm was applied for predicting direct targets of bioactive ingredients. Functional enrichment analyses were performed for the targets. In addition, compound-target network, target-disease network, and target-pathway network were established via Cytoscape 3.6.0 software.

Results

A total of 41 bioactive compounds in Quyushengxin formula were selected out from the TCMSP database. These bioactive compounds were predicted to target 94 potential proteins by weighted ensemble similarity algorithm. Functional analysis suggested these targets were closely related with inflammatory- and immune-related biological progresses. Furthermore, the results of compound-target network, target-disease network, and target-pathway network indicated that the therapeutic effects of Quyushengxin on UC may be achieved through the synergistic and additive effects.

Conclusion

Quyushengxin may act on immune and inflammation-related targets to suppress UC progression in a synergistic and additive manner.

Integrated UPLC-Q/TOF-MS Technique and MALDI-MS to Study of the Efficacy of YiXinshu Capsules Against Heart Failure in a Rat Model

Background: Yixinshu Capsules (YXSC) are widely used in Chinese medicine for the treatment of cardiovascular diseases. However, the therapeutic mechanisms of action are not well understood. Method: In this study, a metabonomic approach based on integrated UPLC-Q/TOF-MS technique and MALDI-MS was utilized to explore potential metabolic biomarkers that may help increase the understanding of heart failure (HF) and in order to assess the potential mechanisms of YXSC against HF. Plasma metabolic profiles were analyzed by UPLC-Q/TOF-MS with complementary hydrophilic interaction chromatography and reversed-phase liquid chromatography. Moreover, time-course analysis at the 2nd, 4th, and 10th week after permanent occlusion was conducted. In an effort to identify a more reliable potential metabolic marker, common metabolic markers of the 2nd, 4th, and 10th week were selected through multivariate data analysis. Furthermore, MALDI-MS was applied to identify metabolic biomarkers in the blood at apoptotic positions of heart tissues. Results: The results showed that HF appeared at the fourth week after permanent occlusion based on echocardiographic assessment. Clear separations were observed between the sham and model group by loading plots of orthogonal projection to latent structure discrimination analysis (OPLS-DA) at different time points after permanent occlusion. Potential markers of interest were extracted from the combining S-plots, variable importance for the projections values (VIP > 1), and t-test (p < 0.05). Twenty-one common metabolic markers over the course of the development and progression of HF after permanent occlusion were identified. These were determined to be mainly related to disturbances in fatty acids, phosphatidylcholine, bile acids, amino acid metabolism, and pyruvate metabolism. Of the metabolic markers, 16 metabolites such as palmitoleic acid, arachidonic acid, and lactic acid showed obvious changes (p < 0.05) and a tendency for returning to baseline values in YXSC-treated HF rats at the 10th week. Moreover, four biomarkers, including palmitoleic acid, palmitic acid, arachidonic, acid and lactic acid, were further validated at the apoptotic position of heart tissue using MALDI-MS, consistent to the variation trends in the plasma. Conclusions: Taken in concert, our proposed strategy may contribute to the understanding of the complex pathogenesis of ischemia-induced HF and the potential mechanism of YXSC.

Serum proteomics analysis based on label-free revealed the protective effect of Chinese herbal formula Gu-Ben-Fang-Xiao

Gubenfangxiao decoction (GBFXD) is a traditional Chinese medicine formula derived from Yupingfengsan, an ancient formula widely used to treat respiratory diseases. In recent years, GBFXD has been applied to efficaciously and safely treat asthma. However, the mechanism of GBFXD is still not fully elucidated. The aim of this study was to employ the label-free proteomic method to explore the protective mechanism of GBFXD in respiratory syncytial virus (RSV)-ovalbumin (OVA) induced chronic persistent asthmatic mice. After RSV-OVA challenge, mice were orally administered GBFXD at a dose of 36 g/kg accompanied with OVA nasal spray once every 3 days for 28 days. The label-free proteomics-based liquid chromatography-tandem mass spectrometry method was used to explore the differentially abundant proteins (DAPs) in the serum from model mice compared with that in control mice (M:C), and in GBFXD-treated mice compared with that in model mice (G:M). The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD013244. A total of 69 significant DAPs were identified including 39 in M:C, 46 in G:M, and 16 common differential proteins. Bioinformatics analysis revealed that the DAPs of M:C were mainly involved in inflammatory response and were related to lipid metabolism. However, the DAPs of G:M mostly participated in stress response, inflammatory response, and epithelial cell proliferation. Serum levels of Apoa-1, Apoc-1, Cfd, and Lrg1, EGFR and Lrg1 in the lungs were consistent with the results of proteomic analysis. Apoa-1 and Apoc-1 were closely related to cholesterol transport, lipid metabolism balance, and airway epithelial integrity; Cfd participated in immune response, affecting the occurrence and development of inflammation; EGFR and Lrg1 were involved in epithelial cell proliferation, influencing the process of airway remodeling. In summary, these results indicated that GBFXD may affect inflammatory and immune response of asthma by regulating cholesterol transport and complement factor activation. Furthermore, it could repair damaged airway epithelium and avoid airway remodeling to prevent and treat asthma.

Yixinshu capsule combined with conventional treatment for chronic heart failure: Protocol for a systematic review and trial sequential analysis

BACKGROUND

Yixinshu Capsule is widely utilized in Asia for the treatment of chronic heart failure (CHF) as a conventional drug, but a comprehensive conclusion is lacking. Here, we will provide a protocol to perform a meta-analysis and trial sequential analysis to evaluate the efficacy of Yixinshu Capsule combined with conventional treatment for chronic heart failure.

METHODS

We will conduct a thorough search in six databases, PubMed, EMBASE, Cochrane Library Database, Chinese National Knowledge Infrastructure (CNKI), Chinese Science Journal Database (VIP), and Chinese Biomedical and Medical Database (CBM). Inclusion criteria will be randomized control trials (RCTs) with one group receiving Yixinshu Capsule based on conventional treatment and another group receiving conventional treatment alone. Modified Jadad scale and Cochrane's risk of bias assessment will be used to assess methodological quality. Only studies with modified Jadad scale score ≥3 will be included in meta-analysis for efficacy, which will be defined as moderate methodological quality. The total effective rate will be considered as the primary outcome and the secondary outcome will include mortality, rehospitalized rate, left ventricular ejection fraction (LVEF), 6-minute walking distance, E/A, left ventricular end-diastolic diameter (LVEDD), BNP, and NT-proBNP. We will conduct trial sequential analysis to evaluate the reliability of the primary outcome.

RESULTS

This study will provide a rational synthesis of current evidences for Yixinshu Capsule on chronic heart failure.

CONCLUSION

The conclusion of this study will provide evidence for judging the efficacy of Yixinshu Capsule on chronic heart failure.

REGISTRATION

PROS-PERO CRD42019119612.