Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network

Prediction of cold and heat patterns using anthropometric measures based on machine learning

OBJECTIVE

To examine the association of body shape with cold and heat patterns, to determine which anthropometric measure is the best indicator for discriminating between the two patterns, and to investigate whether using a combination of measures can improve the predictive power to diagnose these patterns.

METHODS

Based on a total of 4,859 subjects (3,000 women and 1,859 men), statistical analyses using binary logistic regression were performed to assess the significance of the difference and the predictive power of each anthropometric measure, and binary logistic regression and Naive Bayes with the variable selection technique were used to assess the improvement in the predictive power of the patterns using the combined measures.

RESULTS

In women, the strongest indicators for determining the cold and heat patterns among anthropometric measures were body mass index (BMI) and rib circumference; in men, the best indicator was BMI. In experiments using a combination of measures, the values of the area under the receiver operating characteristic curve in women were 0.776 by Naive Bayes and 0.772 by logistic regression, and the values in men were 0.788 by Naive Bayes and 0.779 by logistic regression.

CONCLUSIONS

Individuals with a higher BMI have a tendency toward a heat pattern in both women and men. The use of a combination of anthropometric measures can slightly improve the diagnostic accuracy. Our findings can provide fundamental information for the diagnosis of cold and heat patterns based on body shape for personalized medicine.

Network pharmacology-based identification of key pharmacological pathways of Yin-Huang-Qing-Fei capsule acting on chronic bronchitis

For decades in China, the Yin-Huang-Qing-Fei capsule (YHQFC) has been widely used in the treatment of chronic bronchitis, with good curative effects. Owing to the complexity of traditional Chinese herbal formulas, the pharmacological mechanism of YHQFC remains unclear. To address this problem, a network pharmacology-based strategy was proposed in this study. At first, the putative target profile of YHQFC was predicted using MedChem Studio, based on structural and functional similarities of all available YHQFC components to the known drugs obtained from the DrugBank database. Then, an interaction network was constructed using links between putative YHQFC targets and known therapeutic targets of chronic bronchitis. Following the calculation of four topological features (degree, betweenness, closeness, and coreness) of each node in the network, 475 major putative targets of YHQFC and their topological importance were identified. In addition, a pathway enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes pathway database indicated that the major putative targets of YHQFC are significantly associated with various pathways involved in anti-inflammation processes, immune responses, and pathological changes caused by asthma. More interestingly, eight major putative targets of YHQFC (interleukin [IL]-3, IL-4, IL-5, IL-10, IL-13, FCER1G, CCL11, and EPX) were demonstrated to be associated with the inflammatory process that occurs during the progression of asthma. Finally, a molecular docking simulation was performed and the results exhibited that 17 pairs of chemical components and candidate YHQFC targets involved in asthma pathway had strong binding efficiencies. In conclusion, this network pharmacology-based investigation revealed that YHQFC may attenuate the inflammatory reaction of chronic bronchitis by regulating its candidate targets, which may be implicated in the major pathological processes of the asthma pathway.

Douchi (fermented Glycine max Merr.) alleviates atopic dermatitis-like skin lesions in NC/Nga mice by regulation of PKC and IL-4

BACKGROUND

Douchi (fermented Glycine max Merr.) is produced from fermented soybeans, which is widely used in traditional herbal medicine. In this study, we investigated whether Douchi attenuates protein kinase C (PKC) and interleukin (IL)-4 response and cutaneous inflammation in Atopic dermatitis (AD)-like NC/Nga mice.

METHODS

To induce AD-like skin lesions, D. farinae antigen was applied to the dorsal skin of 3-week-old NC/Nga mice. After inducing AD, Douchi extract was administered 20 mg/kg daily for 3 weeks to the Douchi-treated mice group. We identified the changes of skin barrier and Th2 differentiation through PKC and IL-4 by immunohistochemistry.

RESULTS

Douchi treatment of NC/Nga mice significantly reduced clinical scores (p < 0.01) and histological features. The levels of PKC and IL-4 were significantly reduced in the Douchi-treated group (p < 0.01). The reduction of IL-4 and PKC led to decrease of inflammatory factors such as substance P, inducible nitric oxide synthase (iNOS) and Matrix metallopeptidase 9 (MMP-9) (all p < 0.01). Douchi also down-regulated Th1 markers (IL-12, TNF-α) as well as Th2 markers (IL-4, p-IκB) (p < 0.01).

CONCLUSION

Douchi alleviates AD-like skin lesions through suppressing of PKC and IL-4. These results also lead to diminish levels of substance P, iNOS and MMP-9 in skin lesions. Therefore, Douchi may have potential applications for the prevention and treatment of AD.

Efficacy and safety of Chinese herbal medicine for chronic prostatitis associated with damp-heat and blood-stasis syndromes: a meta-analysis and literature review

OBJECTIVE

The aim of this meta-analysis and systematic review is to evaluate the safety and efficacy of Chinese herbal medicine (CHM) for chronic prostatitis (CP) associated with damp-heat and blood-stasis syndromes.

METHODS

An electronic search of 13 databases up to May 2016 was screened to identify randomized controlled trials comparing the safety and efficacy of CHM for the treatment of CP associated with damp-heat and blood-stasis syndromes. Studies reporting on effective rates, adverse events, National Institutes of Health chronic prostatitis symptom index (NIH-CPSI) scores, and symptom index of Chinese medicine for chronic prostatitis (SI-CM) scores as outcomes were included in the analysis. Data were analyzed by fixed- or random-effect models using the Review Manager software.

RESULTS

Thirteen articles with the modified Jadad score ≥4 were identified. It was found that CHM was superior to placebo in increasing the efficacy (odds ratio: 6.72, 95% confidence interval [CI]: 2.78-9.48, P<0.00001) and reducing the SI-CM scores (standardized mean difference: -1.08, 95% CI: -1.35 to -0.81, P<0.00001). Oral CHMs were significantly more effective than placebo at reducing NIH-CPSI scores, with a mean difference of -1.39 (95% CI: -1.87 to -0.92, P<0.00001). Nevertheless, no significant differences were found between Prostant and placebo (standardized mean difference: -0.23, 95% CI: -0.46 to 0.01, P=0.06). The frequency of adverse events associated with oral CHM was similar to that associated with placebo (risk ratio: 1.36, 95% CI: 0.72-2.55, P=0.34) and less than that associated with Prostant (risk ratio: 1.63, 95% CI: 1.14-2.34, P=0.008).

CONCLUSION

Our novel analysis demonstrates that CHM ranks highest in terms of improvement of CP associated with damp-heat and blood-stasis syndromes. While Prostant showed some efficacy in this disorder, it was associated with a smaller reduction in NIH-CPSI scores. In conclusion, CHM monotherapy is safe and effective for the treatment of CP associated with damp-heat and blood-stasis syndromes.

Proteomics of hot-wet and cold-dry temperaments proposed in Iranian traditional medicine: a Network-based Study

Lack of molecular biology evidence has led clinical success of alternative and complementary medicine (CAM) to be marginalized. In turn, a large portion of life Science researchers could not communicate and help to develop therapeutic potential laid in these therapeutic approaches. In this study, we began to quantify descriptive classification theory in one of the CAM branches i.e. Iranian traditional medicine (ITM). Using proteomic tools and network analysis, the expressed proteins and their relationships were studied in mitochondrial lysate isolated from PBMCs from two different temperaments i.e. Hot-wet (HW) and Cold-dry (CD). The 82% of the identified proteins are over- or under-represented in distinct temperaments. Also, our result showed the different protein-protein interaction networks (PPIN) represented in these two temperaments using centrality and module finding analysis. Following the gene ontology and pathway enrichment analysis, we have found enriched biological terms in each group which are in conformity with the physiologically known evidence in ITM. In conclusion, we argued that the network biology which naturally consider life at the system level along with the different omics data will pave the way toward explicit delineation of the CAM activities.

Guizhi-Shaoyao-Zhimu decoction attenuates rheumatoid arthritis partially by reversing inflammation-immune system imbalance

BACKGROUND

Guizhi-Shaoyao-Zhimu decoction (GSZD) has been extensively used for rheumatoid arthritis (RA) therapy. Marked therapeutic efficacy of GSZD acting on RA has been demonstrated in several long-term clinical trials without any significant side effects. However, its pharmacological mechanisms remain unclear due to a lack of appropriate scientific methodology.

METHODS

GSZD's mechanisms of action were investigated using an integrative approach that combined drug target prediction, network analysis, and experimental validation.

RESULTS

A total of 77 putative targets were identified for 165 assessed chemical components of GSZD. After calculating the topological features of the nodes and edges in the created drug-target network, we identified a candidate GSZD-targeted signal axis that contained interactions between two putative GSZD targets [histone deacetylase 1 (HDAC1) and heat shock protein 90 kDa alpha, class A member 1 (HSP90AA1)] and three known RA-related targets [NFKB2; inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta (IKBKB); and tumor necrosis factor-alpha (TNF-α)]. This signal axis could connect different functional modules that are significantly associated with various RA-related signaling pathways, including T/B cell receptor, Toll-like receptor, NF-kappa B and TNF pathways, as well as osteoclast differentiation. Furthermore, the therapeutic effects and putative molecular mechanisms of GSZD's actions on RA were experimentally validated in vitro and in vivo.

CONCLUSIONS

GSZD may partially attenuate RA by reversing inflammation-immune system imbalance and regulating the HDAC1-HSP90AA1-NFKB2-IKBKB-TNF-α signaling axis.

Susceptible gene polymorphisms for blood stasis syndrome of coronary heart disease

Coronary heart disease (CHD) is a typically polygenic and multi-factorial disease. Recent advances have proposed the hypothesis that multiple polymorphisms in the presence of environmental factors could act synergistically in the pathogenesis of CHD. Lots of gene polymorphisms related with CHD have been discovered by genome-wide linkage (in families) and association (in populations) studies. A key issue now is to move from mapping gene polymorphisms to pinpointing causal genes and variants, and to develop a molecular understanding of how these genes lead to CHD. New thinking needs to be brought in for resolving this problem. The benefifit of Chinese medicine (CM) in CHD has been proven by more and more clinical evidences. More importantly, linking CM syndrome differentiation and biomedical diagnosis might help further accurate stratifification of CHD patients for intervention selection. The epidemiological investigation has demonstrated that blood stasis syndrome (BSS) is the major CM syndrome type of CHD. BSS is a kind of pathological state caused by disturbance of blood circulation. Clinical studies indicate that the severity of BSS is related with the severity of CHD and BSS of CHD may be "one involved in multiple genes" with hereditary tendency. If BSS of CHD is polygenic and hereditary, gene polymorphisms may be one of the pathogens. There are some pilot researches to explore the association between gene polymorphisms and BSS of CHD. In this review, the current status of gene polymorphisms related with BSS of CHD and future perspectives are discussed.

Revealing the Effects of the Herbal Pair of Euphorbia kansui and Glycyrrhiza on Hepatocellular Carcinoma Ascites with Integrating Network Target Analysis and Experimental Validation

Although the herbal pair of Euphorbia kansui (GS) and Glycyrrhiza (GC) is one of the so-called "eighteen antagonistic medicaments" in Chinese medicinal literature, it is prescribed in a classic Traditional Chinese Medicine (TCM) formula Gansui-Banxia-Tang for cancerous ascites, suggesting that GS and GC may exhibit synergistic or antagonistic effects in different combination designs. Here, we modeled the effects of GS/GC combination with a target interaction network and clarified the associations between the network topologies involving the drug targets and the drug combination effects. Moreover, the "edge-betweenness" values, which is defined as the frequency with which edges are placed on the shortest paths between all pairs of modules in network, were calculated, and the ADRB1-PIK3CG interaction exhibited the greatest edge-betweenness value, suggesting its crucial role in connecting the other edges in the network. Because ADRB1 and PIK3CG were putative targets of GS and GC, respectively, and both had functional interactions with AVPR2 approved as known therapeutic target for ascites, we proposed that the ADRB1-PIK3CG-AVPR2 signal axis might be involved in the effects of the GS-GC combination on ascites. This proposal was further experimentally validated in a H22 hepatocellular carcinoma (HCC) ascites model. Collectively, this systems-level investigation integrated drug target prediction and network analysis to reveal the combination principles of the herbal pair of GS and GC. Experimental validation in an in vivo system provided convincing evidence that different combination designs of GS and GC might result in synergistic or antagonistic effects on HCC ascites that might be partially related to their regulation of the ADRB1-PIK3CG-AVPR2 signal axis.

Therapeutic Efficacy and Safety of Paeoniae Radix Rubra Formulae in Relieving Hyperbilirubinemia Induced by Viral Hepatitis: A Meta-Analysis

Objective: Hyperbilirubinemia is one of the most devastating pathologies induced by various liver diseases. Formulae related to Paeoniae Radix Rubra (PRR) at high doses have been applied to treat hyperbilirubinemia in traditional Chinese medicine (TCM). The aim of this systematic review and meta-analysis is to assess the efficacy and safety of formulae relevant to high-dose PRR in patients suffering from hyperbilirubinemia induced by viral hepatitis.

Methods: We performed a meta-analysis of randomized-controlled clinical trials to evaluate the efficacy and safety of formulae that apply a high dose of PRR for hyperbilirubinemia. Seven databases were searched until April, 2015. All studies were included according to detailed criteria and assessed for methodological quality. The outcome measurements were recorded for further analysis using the RevMan 5.2.11 software.

Results: Fifteen articles involving 1323 patients with hyperbilirubinemia were included. Formulae with high-dose PRR might promote the efficacy of either a combined application ([OR: 3.98, 95% CI (2.91, 5.43)]; P < 0.01) or a single application ([OR: 4.00, 95% CI (1.50, 10.68)]; P < 0.01) for hyperbilirubinemia. The indices of TBIL, ALT, and AST significantly decreased ([MD: –75.57, 95% CI (−94.88, −56.26)], [MD: −26.54, 95% CI (−36.19, −16.88)], and ([MD: −28.94, 95% CI (−46.26, −11.61)]; P < 0.01), respectively. In addition, formulae with high-dose PRR could enhance the treatment efficacy of hyperbilirubinemia triggered by hepatitis B ([OR: 2.98, 95% CI (1.75, 5.05)]; P < 0.01). Furthermore, the efficacy was enhanced with an increasing dosage of PRR. Two articles reported that no side effects occurred in clinical trials, and three studies noted that patients presented light digestive tract symptoms.

Conclusion: Formulae relevant to high-dose PRR ameliorate hyperbilirubinemia and might constitute a promising therapeutic approach. For widespread acceptance by practitioners, more rigorously designed multicenter, double-blind, randomized, and large-scale controlled trials are required.

A network pharmacology approach to discover active compounds and action mechanisms of San-Cao Granule for treatment of liver fibrosis

Ethnopharmacological relevance

San-Cao Granule (SCG) has been used in patients with liver fibrosis for many years and has shown good effect. However, its mechanism of therapeutic action is not clear because of its complex chemical system. The purpose of our study is to establish a comprehensive and systemic method that can predict the mechanism of action of SCG in antihepatic fibrosis.

Materials and methods

In this study, a “compound–target–disease” network was constructed by combining the SCG-specific and liver fibrosis–specific target proteins with protein–protein interactions, and network pharmacology was used to screen out the underlying targets and mechanisms of SCG for treatment of liver fibrosis. Then, some key molecules of the enriched pathway were chosen to verify the effects of SCG on liver fibrosis induced by thioacetamide (TAA).

Results

This systematic approach had successfully revealed that 16 targets related to 11 SCG compounds were closely associated with liver fibrosis therapy. The pathway-enrichment analysis of them showed that the TGF-β1/Smad signaling pathway is relatively important. Animal experiments also proved that SCG could significantly ameliorate liver fibrosis by inhibiting the TGF-β1/Smad pathway.

Conclusion

SCG could alleviate liver fibrosis through the molecular mechanisms predicted by network pharmacology. Furthermore, network pharmacology could provide deep insight into the pharmacological mechanisms of Chinese herbal formulas.

UHPLC/Q-TOFMS-based metabolomics for the characterization of cold and hot properties of Chinese materia medica

ETHNOPHARMACOLOGICAL RELEVANCE

The cold/hot property of Chinese materia medica (CMM) and the application of its corresponding knowledge in the diagnosis, differentiation and treatment of diseases have been considered to be the extremely important part of traditional Chinese medicine (TCM). As highly abstracted TCM theory, the cold/hot property of CMMs is still not fully understood and remains to be elucidated by systems biology approach. The cold and hot properties of CMM are mainly defined by the response of the body to a given CMM. Metabolomics is a promising systems biology method to profile entire endogenous metabolites and monitor their fluctuations related to an exogenous stimulus. Thus, a metabolomics approach was applied to characterize the cold and hot properties of CMMs.

MATERIAL AND METHODS

Mice were intragastrically administered three selected cold property CMMs (i.e., Rheum palmatum L., radix et rhizoma; Coptis chinensis Franch, rhizome and Scutellaria baicalensis Georgi, radix) and three hot property CMMs (i.e., Cinnamomum cassia (L.) J. Presl, cortex; Zingiber officinale Roscoe, rhizoma and Evodia rutaecarpa (Juss.) Benth., fructus) once daily for one week. The comprehensive metabolome changes in the plasma of mice after treatment with cold or hot property CMMs were characterized by ultra-high performance liquid chromatography/time of flight mass spectrometry (UHPLC/Q-TOF-MS), and the potential biomarkers related to cold and hot properties of CMM were explored.

RESULTS

Metabolites perturbation in plasma occurs after treatment with cold CMMs and hot CMMs in mice, and 15 and 16 differential biomarkers were identified to be associated with the cold and hot properties of CMMs, respectively. Among them, LPC (18:0), LPC (18:1), LPC (20:4) and LPC (20:5) showed decreased trends in the cold property CMM treated groups, but increased in the hot property CMM treated groups.

CONCLUSIONS

There is a strong connection between the cold/hot property of CMMs and lysophosphatidylcholines metabolism. This study offers new insight into CMM properties and their clinical application.

Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Cholestasis and Intervention Effect of Paeonia lactiflora Pall

Background: The dried root of Paeonia lactiflora Pall. (PLP) is a classical Chinese herbal medicine that has been used to treat hepatic disease for 1000s of years. Our previous work suggested that PLP can be used to treat hepatitis with severe cholestasis. This study explored the mechanism by which PLP affects ANIT-induced cholestasis in rats using a metabolomics approach.

Methods: The effects of PLP on serum indices (TBIL, DBIL, AST, ALT, ALP, and TBA) and the histopathology of the liver were analyzed. Moreover, UHPLC-Q-TOF was performed to identify the possible effect of PLP on metabolites. The pathway analysis was conducted to illustrate the pathways and network by which PLP treats cholestasis.

Result: High-dose PLP remarkably down-regulated the serum indices and alleviated histological damage to the liver. Metabolomics analyses showed that the therapeutic effect of high-dose PLP is mainly associated with the regulation of several metabolites, such as glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, L(D)-arginine, and L-tryptophan. A pathway analysis showed that the metabolites were related to bile acid secretion and amino acid metabolism. In addition, the significant changes in bile acid transporters also indicated that bile acid metabolism might be involved in the therapeutic effect of PLP on cholestasis. Moreover, a principal component analysis indicated that the metabolites in the high-dose PLP group were closer to those of the control, whereas those of the moderate dose or low-dose PLP group were closer to those of the ANIT group. This finding indicated that metabolites may be responsible for the differences between the effects of low-dose and moderate-dose PLP.

Conclusion: The therapeutic effect of high-dose PLP on cholestasis is possibly related to regulation of bile acid secretion and amino acid metabolism. Moreover, these findings may help better understand the mechanisms of disease and provide a potential therapy for cholestasis.

Using Bioinformatics Approach to Explore the Pharmacological Mechanisms of Multiple Ingredients in Shuang-Huang-Lian

Due to the proved clinical efficacy, Shuang-Huang-Lian (SHL) has developed a variety of dosage forms. However, the in-depth research on targets and pharmacological mechanisms of SHL preparations was scarce. In the presented study, the bioinformatics approaches were adopted to integrate relevant data and biological information. As a result, a PPI network was built and the common topological parameters were characterized. The results suggested that the PPI network of SHL exhibited a scale-free property and modular architecture. The drug target network of SHL was structured with 21 functional modules. According to certain modules and pharmacological effects distribution, an antitumor effect and potential drug targets were predicted. A biological network which contained 26 subnetworks was constructed to elucidate the antipneumonia mechanism of SHL. We also extracted the subnetwork to explicitly display the pathway where one effective component acts on the pneumonia related targets. In conclusions, a bioinformatics approach was established for exploring the drug targets, pharmacological activity distribution, effective components of SHL, and its mechanism of antipneumonia. Above all, we identified the effective components and disclosed the mechanism of SHL from the view of system.

Systems Biology - A Pivotal Research Methodology for Understanding the Mechanisms of Traditional Medicine

Objectives:

Systems biology is a novel subject in the field of life science that aims at a systems’ level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era.

Methods:

The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network analysis and inference, and modeling and systems prediction.

Results:

The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted.

Conclusion:

Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.

Effect of serum from postmenopausal women with osteoporosis exhibiting the Kidney-Yang deficiency pattern on bone formation in an hFOB 1.19 human osteoblastic cell line

The aim of the present study was to investigate the underlying mechanism of the Kidney-Yang deficiency (KYD) pattern of osteoporosis in postmenopausal women of a certain age range by comparing the effect of serum from postmenopausal women with osteoporosis exhibiting the KYD pattern with that of serum from postmenopausal women without osteoporosis on bone formation in an hFOB 1.19 human osteoblastic cell line. A random selection of 30 female, postmenopausal volunteers aged 60-70 years, including 15 cases without osteoporosis and 15 cases with the KYD pattern of osteoporosis, were enrolled at the Physical Examination Center of the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine. Venous blood was extracted and the serum was separated. The hFOB 1.19 cells were treated with 10% KYD pattern-serum or control serum from postmenopausal women of the same age range without osteoporosis. It was found that the KYD pattern-serum significantly decreased the cell viability, activity of alkaline phosphatase and number of calcified nodules, as well as downregulated the expression of osteocalcin and osteoprotegerin (OPG) and upregulated that of receptor activator of nuclear factor κB ligand (RANKL) in the hFOB 1.19 cells. In addition, the present results showed that the concentrations of estradiol (E₂), OPG and insulin-like factor-1 (IGF-1) in the KYD pattern-serum were lower than those in the control serum. In combination, these findings suggest that the downregulation of E₂, OPG and IGF-1 in the KYD pattern-serum inhibits the OPG/RANKL system, leading to a decrease in bone formation in the hFOB 1.19 cells. This indicates that the alterations in E₂, OPG and IGF-1 may account for the susceptibility of certain postmenopausal women to the KYD pattern of osteoporosis.

Yinchenhao decoction in the treatment of cholestasis: A systematic review and meta-analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Yinchenhao decoction, a well-known Chinese herbal formula, has been widely used in Chinese Medicine for thousands of years. However, no systematic review of Yinchenhao decoction in treating cholestasis has been completed. This study aims to evaluate the efficacy and safety of the Yinchenhao decoction in treating cholestasis.

MATERIALS AND METHODS

The major databases (PubMed, Embase, Cochrane Library, Chinese Biomedical Database, Wanfang database, VIP medicine information system and China National Knowledge Infrastructure) were searched from the databases' inception through November 2014. Randomized controlled trials (RCTs) of Yinchenhao decoction reported in publications for treatment of cholestasis were extracted by two reviewers. The RCTs examined included total efficacy rate and biochemical indices including alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL) and direct bilirubin (DBIL). The Cochrane tool was applied to assess the risk of bias of the trials. The main outcomes of the trials were analyzed using Review Manager 5.3 software. The odds ratio (OR) or mean difference (MD) with a 95% confidence interval (CI) was used to measure the effect.

RESULTS

Among the 698 studies identified in the literature search, 15 studies involving 1405 subjects with cholestasis were included in the analysis. Yinchenhao decoction demonstrated efficacy in cholestasis treatment whether in a combined application or not. Additionally, the decoction significantly reduced the elevated levels of cholestasis serum markers, such as ALT, AST, TBIL and DBIL, with a significant difference observed in short and long curative time periods. Remarkably, Yinchenhao decoction displayed a significant efficacy in treating the long-term disease.

CONCLUSION

No serious adverse event was reported. This meta-analysis provides evidence that Yinchenhao decoction is an effective and safe treatment for cholestasis.

Deciphering the pharmacological mechanism of the Chinese formula huanglian-jie-du decoction in the treatment of ischemic stroke using a systems biology-based strategy

AIM

Huanglian-jie-du decoction (HLJDD) is an important multiherb remedy in TCM, which is recently demonstrated to be effective to treat ischemic stroke. Here, we aimed to investigate the pharmacological mechanisms of HLJDD in the treatment of ischemic stroke using systems biology approaches.

METHODS

Putative targets of HLJDD were predicted using MetaDrug. An interaction network of putative HLJDD targets and known therapeutic targets for the treatment of ischemic stroke was then constructed, and candidate HLJDD targets were identified by calculating topological features, including 'Degree', 'Node-betweenness', 'Closeness', and 'K-coreness'. The binding efficiencies of the candidate HLJDD targets with the corresponding compositive compounds were further validated by a molecular docking simulation.

RESULTS

A total of 809 putative targets were obtained for 168 compositive compounds in HLJDD. Additionally, 39 putative targets were common to all four herbs of HLJDD. Next, 49 major nodes were identified as candidate HLJDD targets due to their network topological importance. The enrichment analysis based on the Gene Ontology (GO) annotation system and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway demonstrated that candidate HLJDD targets were more frequently involved in G-protein-coupled receptor signaling pathways, neuroactive ligand-receptor interactions and gap junctions, which all played important roles in the progression of ischemic stroke. Finally, the molecular docking simulation showed that 170 pairs of chemical components and candidate HLJDD targets had strong binding efficiencies.

CONCLUSION

This study has developed for the first time a comprehensive systems approach integrating drug target prediction, network analysis and molecular docking simulation to reveal the relationships between the herbs contained in HLJDD and their putative targets and ischemic stroke-related pathways.

Multiscale Modeling of Drug-induced Effects of ReDuNing Injection on Human Disease: From Drug Molecules to Clinical Symptoms of Disease

ReDuNing injection (RDN) is a patented traditional Chinese medicine, and the components of it were proven to have antiviral and important anti-inflammatory activities. Several reports showed that RDN had potential effects in the treatment of influenza and pneumonia. Though there were several experimental reports about RDN, the experimental results were not enough and complete due to that it was difficult to predict and verify the effect of RDN for a large number of human diseases. Here we employed multiscale model by integrating molecular docking, network pharmacology and the clinical symptoms information of diseases and explored the interaction mechanism of RDN on human diseases. Meanwhile, we analyzed the relation among the drug molecules, target proteins, biological pathways, human diseases and the clinical symptoms about it. Then we predicted potential active ingredients of RDN, the potential target proteins, the key pathways and related diseases. These attempts may offer several new insights to understand the pharmacological properties of RDN and provide benefit for its new clinical applications and research.

Herb Network Analysis for a Famous TCM Doctor's Prescriptions on Treatment of Rheumatoid Arthritis

Traditional Chinese Medicine (TCM) doctors always prescribe various herbal formulae tailored to individual patients. However, there is still a lack of appropriate methods to study the rule and potential biological basis underlying the numerous prescriptions. Here we developed an Herb-Compound-Target-Disease coherent network approach to analyze 871 herbal prescriptions from a TCM master, Mr. Ji-Ren Li, in his clinical practice on treatment of rheumatoid arthritis (RA). The core herb networks were extracted from Mr. Li's prescriptions. Then, we predicted target profiles of compounds in core herb networks and calculated potential synergistic activities among them. We further found that the target sets of core herbs overlapped significantly with the RA related biological processes and pathways. Moreover, we detected a possible connection between the prescribed herbs with different properties such as Cold and Hot and the Western drugs with different actions such as immunomodulatory and hormone regulation on treatment of RA. In summary, we explored a new application of TCM network pharmacology on the analysis of TCM prescriptions and detected the networked core herbs, their potential synergistic and biological activities, and possible connections with drugs. This work offers a novel way to understand TCM prescriptions in clinical practice.

Cardioprotective effects of fucoidan against hypoxia-induced apoptosis in H9c2 cardiomyoblast cells

CONTEXT

Cardiomyocyte apoptosis plays a critical role in the progress of heart diseases. Fucoidan, a complex-sulfated polysaccharide, has been reported to possess potential cardioprotective efficacy in vivo.

OBJECTIVE

The present study determines whether fucoidan could provide cardioprotection on hypoxia-induced cardiomyocyte apoptosis.

MATERIALS AND METHODS

H9c2 cardiomyoblast cells were incubated with various concentrations (15, 30, and 60 μg/ml) of fucoidan in a humidified incubator at 37 °C with 95% O2 and 5% CO2. After 6 h, hypoxia was processed and the cardioprotective effects of fucoidan were evaluated by applying MTT, ELISA, Hoechst 33258 nucleus staining, and western blot.

RESULTS

Following a 6 h exposure of H9c2 to hypoxic condition, significant reduction was found in cell survival (0.57-fold) and superoxide dismutase (SOD) activity (0.56-fold), which were associated with the increase of malondialdehyde (MDA) level (2.58-fold), creatine phosphokinase (CK, 3.57-fold), and lactate dehydrogenase (LDH) activities (2.39-fold). Moreover, hypoxia-induced apoptosis was confirmed by Hoechst 33258 nuclear staining, and these changes were accompanied by the increase of Bcl-2 (1.27-fold) and Bax expression (2.6-fold). However, preincubation of the cells with fucoidan prior to hypoxia exposure elevated the cell viability (30 μg/ml, 1.18-fold; 60 μg/ml, 1.32-fold) and SOD activity (30 μg/ml, 1.12-fold; 60 μg/ml, 1.25-fold), but decreased the MDA level (30 μg/ml, 0.70-fold; 60 μg/ml, 0.80-fold), CK (30 μg/ml, 0.69-fold; 60 μg/ml, 0.76-fold), and LDH (30 μg/ml, 0.67-fold; 60 μg/ml, 0.86-fold) leakages. Hoechst 33258 nuclear staining observations demonstrated the same protective effect of fucoidan on hypoxia-induced myocardial injury. Also, cardioprotective effects of fucoidan were reflected by increasing Bcl-2 (60 μg/ml, 1.84-fold), as well as decreasing Bax (60 μg/ml, 0.6-fold).

CONCLUSION

Fucoidan had protective effect against hypoxia-induced cardiomyocytes apoptosis, and the mechanism might involve protections of the cell from oxidative injury.

Uncovering pharmacological mechanisms of Wu-tou decoction acting on rheumatoid arthritis through systems approaches: drug-target prediction, network analysis and experimental validation

Wu-tou decoction (WTD) has been extensively used for the treatment of rheumatoid arthritis (RA). Due to lack of appropriate methods, pharmacological mechanisms of WTD acting on RA have not been fully elucidated. In this study, a list of putative targets for compositive compounds containing in WTD were predicted by drugCIPHER-CS. Then, the interaction network of the putative targets of WTD and known RA-related targets was constructed and hub nodes were identified. After constructing the interaction network of hubs, four topological features of each hub, including degree, node betweenness, closeness and k-coreness, were calculated and 79 major hubs were identified as candidate targets of WTD, which were implicated into the imbalance of the nervous, endocrine and immune (NEI) systems, leading to the main pathological changes during the RA progression. Further experimental validation also demonstrated the preventive effects of WTD on inflammation and joint destruction in collagen-induced arthritis (CIA) rats and its regulatory effects on candidate targets both in vitro and in vivo systems. In conclusion, we performed an integrative analysis to offer the convincing evidence that WTD may attenuate RA partially by restoring the balance of NEI system and subsequently reversing the pathological events during RA progression.

The th17/treg immune balance in ulcerative colitis patients with two different chinese syndromes: dampness-heat in large intestine and spleen and kidney yang deficiency syndrome

Objective. To investigate the Th17/Treg immune balance in the ulcerative colitis (UC) patients with two Chinese syndrome: dampness-heat in large intestine (DHLI) and spleen and kidney Yang deficiency (SKYD). Methods. Ninety UC patients (45 were diagnosed with DHLI and 45 with SKYD syndrome) and 23 healthy people were recruited. The serumIL-17 and TGF-β1 levels of these participants were measured with ELISA; the expression of IL-17 and TGF-β 1 in colonic mucosa tissue was determined with immunohistochemistry and the percentage of Th17 and Treg in peripheral blood with flow cytometry. Results. The levels of IL-17 and Th17 were significantly higher in both DHLI and SKYD groups than in healthy control group and higher in DHLI than in SKYD group (P < 0.05). The levels of TGF-β1 and Treg were significantly lower in the two UC patients groups than in healthy control group; and lower in SKYD group than in DHLI group (P < 0.05). Conclusions. UC with DHLI syndrome could be characterized by the elevation of Th17 and IL-17 levels, which indicated an accentuation of inflammatory reaction; UC with SKYD syndrome could be characterized by the reduction of serum Treg and TGF-β1 levels, which represented a depression of immune tolerance.

Phenomics research on coronary heart disease based on human phenotype ontology

The characteristics of holistic, dynamics, complexity, and spatial and temporal features enable "Omics" and theories of TCM to interlink with each other. HPO, namely, "characterization," can be understood as a sorting and generalization of the manifestations shown by people with diseases on the basis of the phenomics. Syndrome is the overall "manifestation" of human body pathological and physiological changes expressed by four diagnostic methods' information. The four diagnostic methods' data could be the most objective and direct manifestations of human body under morbid conditions. In this aspect, it is consistent with the connation of "characterization." Meanwhile, the four diagnostic methods' data also equip us with features of characterization in HPO. In our study, we compared 107 pieces of four diagnostic methods' information with the "characterization database" to further analyze data of four diagnostic methods' characterization in accordance with the common characteristics of four diagnostic methods' information and characterization and integrated 107 pieces of four diagnostic methods' data to relevant items in HPO and finished the expansion of characterization information in HPO.

Standardization and future directions in pattern identification research: International brainstorming session

An international brainstorming session on standardizing pattern identification (PI) was held at the Korea Institute of Oriental Medicine on October 1, 2013 in Daejeon, South Korea. This brainstorming session was convened to gather insights from international traditional East Asian medicine specialists regarding PI standardization. With eight presentations and discussion sessions, the meeting allowed participants to discuss research methods and diagnostic systems used in traditional medicine for PI. One speaker presented a talk titled "The diagnostic criteria for blood stasis syndrome: implications for standardization of PI". Four speakers presented on future strategies and objective measurement tools that could be used in PI research. Later, participants shared information and methodology for accurate diagnosis and PI. They also discussed the necessity for standardizing PI and methods for international collaborations in pattern research.

Applications of data mining methods in the integrative medical studies of coronary heart disease: progress and prospect

A large amount of studies show that real-world study has strong external validity than the traditional randomized controlled trials and can evaluate the effect of interventions in a real clinical setting, which open up a new path for researches of integrative medicine in coronary heart disease. However, clinical data of integrative medicine in coronary heart disease are large in amount and complex in data types, making exploring the appropriate methodology a hot topic. Data mining techniques are to analyze and dig out useful information and knowledge from the mass data to guide people's practices. The present review provides insights for the main features of data mining and their applications of integrative medical studies in coronary heart disease, aiming to analyze the progress and prospect in this field.

Comprehensive analysis of microRNA-regulated protein interaction network reveals the tumor suppressive role of microRNA-149 in human hepatocellular carcinoma via targeting AKT-mTOR pathway

BACKGROUND

Our previous study identified AKT1, AKT2 and AKT3 as unfavorable prognostic factors for patients with hepatocellular carcinoma (HCC). However, limited data are available on their exact mechanisms in HCC. Since microRNAs (miRNAs) are implicated in various human cancers including HCC, we aimed to screen miRNAs targeting AKTs and investigate their underlying mechanisms in HCC by integrating bioinformatics prediction, network analysis, functional assay and clinical validation.

METHODS

Five online programs of miRNA target prediction and RNAhybrid which calculate the minimum free energy (MFE) of the duplex miRNA:mRNA were used to screen optimized miRNA-AKT interactions. Then, miRNA-regulated protein interaction network was constructed and 5 topological features ('Degree', 'Node-betweenness', 'Edge-betweenness', 'Closeness' and 'Modularity') were analyzed to link candidate miRNA-AKT interactions to oncogenesis and cancer hallmarks. Further systematic experiments were performed to validate the prediction results.

RESULTS

Six optimized miRNA-AKT interactions (miR-149-AKT1, miR-302d-AKT1, miR-184-AKT2, miR-708-AKT2, miR-122-AKT3 and miR-124-AKT3) were obtained by combining the miRNA target prediction and MFE calculation. Then, 103 validated targets for the 6 candidate miRNAs were collected from miRTarBase. According to the enrichment analysis on GO items and KEGG pathways, these validated targets were significantly enriched in many known oncogenic pathways for HCC. In addition, miRNA-regulated protein interaction network were divided into 5 functional modules. Importantly, AKT1 and its interaction with mTOR respectively had the highest node-betweenness and edge-betweenness, implying their bottleneck roles in the network. Further experiments confirmed that miRNA-149 directly targeted AKT1 in HCC by a miRNA luciferase reporter approach. Then, re-expression of miR-149 significantly inhibited HCC cell proliferation and tumorigenicity by regulating AKT1/mTOR pathway. Notably, miR-149 down-regulation in clinical HCC tissues was correlated with tumor aggressiveness and poor prognosis of patients.

CONCLUSION

This comprehensive analysis identified a list of miRNAs targeting AKTs and revealed their critical roles in HCC malignant progression. Especially, miR-149 may function as a tumor suppressive miRNA and play an important role in inhibiting the HCC tumorigenesis by modulating the AKT/mTOR pathway. Our clinical evidence also highlight the prognostic potential of miR-149 in HCC. The newly identified miR-149/AKT/mTOR axis might be a promising therapeutic target in the prevention and treatment of HCC.

Curcumin protects against CCl4-induced liver fibrosis in rats by inhibiting HIF-1α through an ERK-dependent pathway

The ERK/HIF-1α signaling pathway is believed to play an important role in the genesis of progressive fibrosis. An increasing expression of HIF-1α and ERK accompanies CCl₄-induced liver fibrosis in rats. Curcumin is verified to have antifibrotic effects in several kinds of liver fibrosis models. There is no specific evidence illustrating a connection between curcumin and the HIF-1α/ERK pathway in rat liver fibrosis induced by CCl₄. In this study, liver fibrosis was induced by CCl₄ in treated rats. The data demonstrated that curcumin was able to attenuate liver fibrosis and inhibit the proliferation of HSC. Moreover, curcumin could remarkably elevate the hepatic function by decreasing serum levels of ALT, AST and ALP, and increasing levels of ALB, TP and α-SMA, Col III mRNA expression. Meanwhile, ECM status could also be reflected by curcumin treatment. The alleviation with curcumin treatment was associated with inhibition of HIF-1α and phosphor-ERK. This study indicates that curcumin alleviates fibrosis by reducing the expression of HIF-1α partly through the ERK pathway.

System analysis of LWDH related genes based on text mining in biological networks

Liuwei-dihuang (LWDH) is widely used in traditional Chinese medicine (TCM), but its molecular mechanism about gene interactions is unclear. LWDH genes were extracted from the existing literatures based on text mining technology. To simulate the complex molecular interactions that occur in the whole body, protein-protein interaction networks (PPINs) were constructed and the topological properties of LWDH genes were analyzed. LWDH genes have higher centrality properties and may play important roles in the complex biological network environment. It was also found that the distances within LWDH genes are smaller than expected, which means that the communication of LWDH genes during the biological process is rapid and effectual. At last, a comprehensive network of LWDH genes, including the related drugs and regulatory pathways at both the transcriptional and posttranscriptional levels, was constructed and analyzed. The biological network analysis strategy used in this study may be helpful for the understanding of molecular mechanism of TCM.

Identification of AKT kinases as unfavorable prognostic factors for hepatocellular carcinoma by a combination of expression profile, interaction network analysis and clinical validation

BACKGROUND & AIM

identification of key markers that differentiate occurrence and progression of hepatocellular carcinoma (HCC) is of great significance to develop novel prognostic factors and improve therapeutic strategies. The aim of this study was to screen novel markers for HCC by combining expression profile, interaction network analysis and clinical validation.

METHODS & RESULTS

HCC significant molecules which were differentially expressed in HCC tissues were obtained from five existing HCC related databases (OncoDB.HCC, HCC.net, dbHCCvar, EHCO and Liverome). The protein-protein interaction network of HCC significant proteins was constructed and 331 candidate HCC markers were identified by calculating four topological features of the network ('Degree', 'Betweenness', 'Closeness' and 'K-coreness'). According to the enrichment analysis on Gene ontology items and KEGG pathways, these candidate HCC markers were more frequently involved in cellular protein metabolic processes, translational elongation and intracellular signaling cascade, which are associated with cancer development and metastasis. Among 331 candidate HCC markers, the three AKT kinase family members (AKT1-AKT3) were selected for clinical validation by immunohistochemistry analysis using 130 HCC specimens and matched adjacent non-neoplastic liver tissues. Interestingly, the upregulation of AKT1, AKT2 and AKT3 proteins were all significantly associated with tumor aggressiveness and poor prognosis in patients with HCC.

CONCLUSION

this study provided an integrated analysis by combining expression profile and interaction network analysis to identify a list of biologically significant HCC related markers and pathways. Further experimental validation also indicated that AKT1, AKT2 and AKT3 proteins may all be novel unfavorable prognostic factors for patients with HCC.

Traditional Chinese herbs as chemical resource library for drug discovery of anti-infective and anti-inflammatory

ETHNOPHARMACOLOGICAL RELEVANCE

Infection is a major group of diseases which caused significant mortality and morbidity worldwide. Traditional Chinese herbs have been used to treat infective diseases for thousands years. The numerous clinical practices in disease therapy make it a large chemical resource library for drug discovery.

MATERIALS AND METHODS

In this study, we collected 1156 kinds of herbs and 22,172 traditional Chinese medicinal compounds (Tcmcs). The chemical informatics and network pharmacology were employed to analyze the anti-infective effects of herbs and Tcmcs. In order to evaluate the drug likeness of Tcmcs, the molecular descriptors of Tcmcs and FDA-approved drugs were calculated and the chemical space was constructed on the basis of principal component analysis in the eight descriptors. On purpose to estimate the effects of Tcmcs to the targets of FDA-approved anti-infective or anti-inflammatory drugs, the molecular docking was employed. After that, docking score weighted predictive models were used to predict the anti-infective or anti-inflammatory efficacy of herbs.

RESULTS

The distribution of herbs in the phylogenetic tree showed that most herbs were distributed in family of Asteraceae, Fabaceae and Lamiaceae. Tcmcs were well coincide with drugs in chemical space, which indicated that most Tcmcs had good drug-likeness. The predictive models obtained good specificity and sensitivity with the AUC values above 0.8. At last, 389 kinds of herbs were obtained which were distributed in 100 families, by using the optimal cutoff values in ROC curves. These 389 herbs were widely used in China for treatment of infection and inflammation.

CONCLUSION

Traditional Chinese herbs have a considerable number of drug-like natural products and predicted activities to the targets of approved drugs, which would give us an opportunity to use these herbs as a chemical resource library for drug discovery of anti-infective and anti-inflammatory.

A systems biology-based approach to uncovering the molecular mechanisms underlying the effects of dragon's blood tablet in colitis, involving the integration of chemical analysis, ADME prediction, and network pharmacology

Traditional Chinese medicine (TCM) is one of the oldest East Asian medical systems. The present study adopted a systems biology-based approach to provide new insights relating to the active constituents and molecular mechanisms underlying the effects of dragon's blood (DB) tablets for the treatment of colitis. This study integrated chemical analysis, prediction of absorption, distribution, metabolism, and excretion (ADME), and network pharmacology. Firstly, a rapid, reliable, and accurate ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry method was employed to identify 48 components of DB tablets. In silico prediction of the passive absorption of these compounds, based on Caco-2 cell permeability, and their P450 metabolism enabled the identification of 22 potentially absorbed components and 8 metabolites. Finally, networks were constructed to analyze interactions between these DB components/metabolites absorbed and their putative targets, and between the putative DB targets and known therapeutic targets for colitis. This study provided a great opportunity to deepen the understanding of the complex pharmacological mechanisms underlying the effects of DB in colitis treatment.

Large dosage of chishao in formulae for cholestatic hepatitis: a systematic review and meta-analysis

Objective. To evaluate the efficacy and safety of large dosage of Chishao in formulae for treatment of cholestatic hepatitis. Methods. The major databases (PubMed, Embase, Cochrane Library, Chinese Biomedical Database Wanfang, VIP medicine information system, and China National Knowledge Infrastructure) were searched until January 2014. Randomized controlled trials (RCTs) of large dosage of Chishao in formulae that reported on publications in treatment of cholestatic hepatitis with total efficacy rate, together with the biochemical indices including alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), and direct bilirubin (DBIL), were extracted by two reviewers. The Cochrane tool was used for the assessment of risk of bias included trials. Data were analyzed with RevMan 5.2.7 software. Results. 11 RCTs involving 1275 subjects with cholestatic hepatitis were included. Compared with essential therapy, large dosage of Chishao in formulae demonstrated more efficiently with down regulation of serum ALT, AST, TBIL, DBIL. Meanwhile, there were no obvious adverse events. Conclusion. As a promising novel treatment approach, widely using large dosage of Chishao in formulae may enhance the curative efficacy for cholestatic hepatitis. Considering being accepted by more and more practitioners, further rigorously designed clinical studies are required.

ZHENG May Contribute to Obesity Phenotypes Based on Body Composition: A Pilot Study on the Traditional Chinese Medicine Approach

Objective. Obesity therapy needs new approaches to complement current phenotyping systems. This study aims to assess associations between the Traditional Chinese Medicine (TCM) ZHENG and obesity phenotypes. Methods. We assessed medical history and habitual physical activity and measured body composition, fasting plasma glucose and insulin, and lipids. We collected TCM data through face-to-face interview. ZHENG elements (essentials and locations) were identified by TCM practitioner. Primary ZHENG was assessed by cluster analysis. Results. In 140 consecutive subjects enrolled in a university clinic (body mass index (BMI): 39.9 ± 5.8 kg/m2), ZHENG essentials were identified as “QiXu,” “Re,” “YinXu,” and “TanShi” (totally 86.8%). Locations were “Shen,” “Wei,” “Pi,” and “Gan” (totally 91.8%). Four types of primary ZHENG were identified: A (37.1% of subjects), B (16.5%), C (35.7%), and D (10.7%). Subjects in type D showed elevated BMI, total fat mass (FM), FM index, trunk FM, and less physical activity, as compared with others. Subjects in type B changed regional body composition (reduced trunk FM% and elevated appendicular FM%). Biological parameters did not differ across primary ZHENG clusters. Conclusions. Obesity phenotypes based on body composition differ according to ZHENG in obese patients. This study is a first step toward understanding the contribution of TCM to obesity phenotyping.

Study on qi deficiency syndrome identification modes of coronary heart disease based on metabolomic biomarkers

Coronary heart disease (CHD) is one of the most important types of heart disease because of its high incidence and mortality. With the era of systems biology bursting into reality, the analysis of the whole biological systems whether they are cells, tissues, organs, or the whole organisms has now become the norm of biological researches. Metabolomics is the branch of science concerned with the quantitative understandings of the metabolite complement of integrated living systems and their dynamic responses to the changes of both endogenous and exogenous factors. The aim of this study is to discuss the characteristics of plasma metabolites in CHD patients and CHD Qi deficiency syndrome patients and explore the composition and concentration changes of the plasma metabolomic biomarkers. The results show that 25 characteristic metabolites related to the CHD patients comparing with the healthy people, and 4 identifiable variables had significant differences between Qi deficiency and non-Qi deficiency patients. On the basis of identifying the different plasma endogenous metabolites between CHD patients and healthy people, we further prompted the metabolic rules, pathogenesis, and biological essence in Qi deficiency syndrome patients.

A systems biology-based investigation into the therapeutic effects of Gansui Banxia Tang on reversing the imbalanced network of hepatocellular carcinoma

Several complex molecular events are involved in tumorigenesis of hepatocellular carcinoma (HCC). The interactions of these molecules may constitute the HCC imbalanced network. Gansui Banxia Tang (GSBXT), as a classic Chinese herbal formula, is a popular complementary and alternative medicine modality for treating HCC. In order to investigate the therapeutic effects and the pharmacological mechanisms of GSBXT on reversing HCC imbalanced network, we in the current study developed a comprehensive systems approach of integrating disease-specific and drug-specific networks, and successfully revealed the relationships of the ingredients in GSBXT with their putative targets, and with HCC significant molecules and HCC related pathway systems for the first time. Meanwhile, further experimental validation also demonstrated the preventive effects of GSBXT on tumor growth in mice and its regulatory effects on potential targets.

A network pharmacology approach to determine active compounds and action mechanisms of ge-gen-qin-lian decoction for treatment of type 2 diabetes

Traditional Chinese medicine (TCM) herbal formulae can be valuable therapeutic strategies and drug discovery resources. However, the active ingredients and action mechanisms of most TCM formulae remain unclear. Therefore, the identification of potent ingredients and their actions is a major challenge in TCM research. In this study, we used a network pharmacology approach we previously developed to help determine the potential antidiabetic ingredients from the traditional Ge-Gen-Qin-Lian decoction (GGQLD) formula. We predicted the target profiles of all available GGQLD ingredients to infer the active ingredients by clustering the target profile of ingredients with FDA-approved antidiabetic drugs. We also applied network target analysis to evaluate the links between herbal ingredients and pharmacological actions to help explain the action mechanisms of GGQLD. According to the predicted results, we confirmed that a novel antidiabetic ingredient from Puerariae Lobatae radix (Ge-Gen), 4-Hydroxymephenytoin, increased the insulin secretion in RIN-5F cells and improved insulin resistance in 3T3-L1 adipocytes. The network pharmacology strategy used here provided a powerful means for identifying bioactive ingredients and mechanisms of action for TCM herbal formulae, including Ge-Gen-Qin-Lian decoction.

Traditional Chinese medicine network pharmacology: theory, methodology and application

Traditional Chinese medicine (TCM) has a long history of viewing an individual or patient as a system with different statuses, and has accumulated numerous herbal formulae. The holistic philosophy of TCM shares much with the key ideas of emerging network pharmacology and network biology, and meets the requirements of overcoming complex diseases, such as cancer, in a systematic manner. To discover TCM from a systems perspective and at the molecular level, a novel TCM network pharmacology approach was established by updating the research paradigm from the current "one target, one drug" mode to a new "network target, multi-components" mode. Subsequently, a set of TCM network pharmacology methods were created to prioritize disease-associated genes, to predict the target profiles and pharmacological actions of herbal compounds, to reveal drug-gene-disease co-module associations, to screen synergistic multi-compounds from herbal formulae in a high-throughput manner, and to interpret the combinatorial rules and network regulation effects of herbal formulae. The effectiveness of the network-based methods was demonstrated for the discovery of bioactive compounds and for the elucidation of the mechanisms of action of herbal formulae, such as Qing-Luo-Yin and the Liu-Wei-Di-Huang pill. The studies suggest that the TCM network pharmacology approach provides a new research paradigm for translating TCM from an experience-based medicine to an evidence-based medicine system, which will accelerate TCM drug discovery, and also improve current drug discovery strategies.

Hydroxysafflor yellow A attenuates left ventricular remodeling after pressure overload-induced cardiac hypertrophy in rats

CONTEXT

Hydroxysafflor yellow A (HSYA), the main chemical component of the safflower yellow pigments, is used extensively in traditional Chinese medicine for the treatment of cerebrovascular and cardiovascular diseases.

OBJECTIVE

The present study determined the effects of HSYA on left ventricular hypertrophy after pressure overload and investigated the underlying mechanisms.

MATERIALS AND METHODS

Cardiac hypertrophy was induced by the ligation of abdominal aorta in male Wistar rats. The rats were then divided into five groups and treated with captopril (100 mg/kg) or HSYA at different doses (0, 10, 20 and 40 mg/kg). Six weeks after treatment, the weight of left ventricle, LVMI (left ventricular mass index) and pathological changes were measured. MMP-2 (metalloproteinase 2) and MMP-9 (metalloproteinase 9) levels were determined by ELISA. Protein expressions of Bcl-2 and Bax were evaluated by immunohistochemistry.

RESULTS

HSYA (20, 40 mg/kg) significantly attenuated the increase of LVMI (ventricular weight/body weight) by 13.04 and 30.43% respectively, when compared with the model group. This was associated with the amelioration of pathological lesion, such as cardiac muscle fibers were smaller and the nuclei of cardiomyocytes were lightly stained in animals treated with HSYA (20, 40 mg/kg). In addition, the administration of HSYA at doses of 20 and 40 mg/kg increased the Bcl-2/Bax ratio (1.17 ± 0.08 and 1.39 ± 0.07 versus 0.71 ± 0.06). In addition, the serum MMP-2 and MMP-9 levels were blocked by the treatment at doses of 20 and 40 mg/kg HSYA (MMP-2, 76.1 ± 9.2 and 65.6 ± 6.8 versus 82.9 ± 6.2, ng/ml; MMP-9, 66.6 ± 4.8 and 57.5 ± 5.0 versus 83.5 ± 6.0, ng/ml).

CONCLUSION

These findings indicated that HSYA has beneficial effects on hypertensive ventricular remodeling, which may involve mechanisms of inhibiting cell apoptosis and suppressing metalloproteinases expression.

Identification of GRB2 and GAB1 coexpression as an unfavorable prognostic factor for hepatocellular carcinoma by a combination of expression profile and network analysis

Aim

To screen novel markers for hepatocellular carcinoma (HCC) by a combination of expression profile, interaction network analysis and clinical validation.

Methods

HCC significant molecules which are differentially expressed or had genetic variations in HCC tissues were obtained from five existing HCC related databases (OncoDB.HCC, HCC.net, dbHCCvar, EHCO and Liverome). Then, the protein-protein interaction (PPI) network of these molecules was constructed. Three topological features of the network ('Degree', 'Betweenness', and 'Closeness') and the k-core algorithm were used to screen candidate HCC markers which play crucial roles in tumorigenesis of HCC. Furthermore, the clinical significance of two candidate HCC markers growth factor receptor-bound 2 (GRB2) and GRB2-associated-binding protein 1 (GAB1) was validated.

Results

In total, 6179 HCC significant genes and 977 HCC significant proteins were collected from existing HCC related databases. After network analysis, 331 candidate HCC markers were identified. Especially, GAB1 has the highest k-coreness suggesting its central localization in HCC related network, and the interaction between GRB2 and GAB1 has the largest edge-betweenness implying it may be biologically important to the function of HCC related network. As the results of clinical validation, the expression levels of both GRB2 and GAB1 proteins were significantly higher in HCC tissues than those in their adjacent nonneoplastic tissues. More importantly, the combined GRB2 and GAB1 protein expression was significantly associated with aggressive tumor progression and poor prognosis in patients with HCC.

Conclusion

This study provided an integrative analysis by combining expression profile and interaction network analysis to identify a list of biologically significant HCC related markers and pathways. Further experimental validation indicated that the aberrant expression of GRB2 and GAB1 proteins may be strongly related to tumor progression and prognosis in patients with HCC. The overexpression of GRB2 in combination with upregulation of GAB1 may be an unfavorable prognostic factor for HCC.

Study on incompatibility of traditional chinese medicine: evidence from formula network, chemical space, and metabolism room

A traditional Chinese medicine (TCM) formula network including 362 TCM formulas was built by using complex network methodologies. The properties of this network were analyzed including network diameter, average distance, clustering coefficient, and average degree. Meanwhile, we built a TCM chemical space and a TCM metabolism room under the theory of chemical space. The properties of chemical space and metabolism room were calculated and analyzed. The properties of the medicine pairs in “eighteen antagonisms and nineteen mutual inhibitors,” an ancient rule for TCM incompatibility, were studied based on the TCM formula network, chemical space, and metabolism room. The results showed that the properties of these incompatible medicine pairs are different from those of the other TCM based on the analysis of the TCM formula network, chemical space, and metabolism room. The lines of evidence derived from our work demonstrated that the ancient rule of TCM incompatibility, “eighteen antagonisms and nineteen mutual inhibitors,” is probably scientifically based.

Understanding Acupuncture Based on ZHENG Classification from System Perspective

Acupuncture is an efficient therapy method originated in ancient China, the study of which based on ZHENG classification is a systematic research on understanding its complexity. The system perspective is contributed to understand the essence of phenomena, and, as the coming of the system biology era, broader technology platforms such as omics technologies were established for the objective study of traditional chinese medicine (TCM). Omics technologies could dynamically determine molecular components of various levels, which could achieve a systematic understanding of acupuncture by finding out the relationships of various response parts. After reviewing the literature of acupuncture studied by omics approaches, the following points were found. Firstly, with the help of omics approaches, acupuncture was found to be able to treat diseases by regulating the neuroendocrine immune (NEI) network and the change of which could reflect the global effect of acupuncture. Secondly, the global effect of acupuncture could reflect ZHENG information at certain structure and function levels, which might reveal the mechanism of Meridian and Acupoint Specificity. Furthermore, based on comprehensive ZHENG classification, omics researches could help us understand the action characteristics of acupoints and the molecular mechanisms of their synergistic effect.

Bioinformatics analysis for the antirheumatic effects of huang-lian-jie-du-tang from a network perspective

Huang-Lian-Jie-Du-Tang (HLJDT) is a classic TCM formula to clear “heat” and “poison” that exhibits antirheumatic activity. Here we investigated the therapeutic mechanisms of HLJDT at protein network level using bioinformatics approach. It was found that HLJDT shares 5 target proteins with 3 types of anti-RA drugs, and several pathways in immune system and bone formation are significantly regulated by HLJDT's components, suggesting the therapeutic effect of HLJDT on RA. By defining an antirheumatic effect score to quantitatively measure the therapeutic effect, we found that the score of each HLJDT's component is very low, while the whole HLJDT achieves a much higher effect score, suggesting a synergistic effect of HLJDT achieved by its multiple components acting on multiple targets. At last, topological analysis on the RA-associated PPI network was conducted to illustrate key roles of HLJDT's target proteins on this network. Integrating our findings with TCM theory suggests that HLJDT targets on hub nodes and main pathway in the Hot ZENG network, and thus it could be applied as adjuvant treatment for Hot-ZENG-related RA. This study may facilitate our understanding of antirheumatic effect of HLJDT and it may suggest new approach for the study of TCM pharmacology.