Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Network pharmacology dissection of multiscale mechanisms of herbal medicines in stage IV gastric adenocarcinoma treatment.

ABSTRACT: Increasing evidence has shown that Chinese Herbal Medicine (CHM) has efficient therapeutic effects for advanced gastric adenocarcinoma, while the therapeutic mechanisms underlying this treatment remain unclear.In this study, the Kaplan-Meier method and Cox regression analysis were used to evaluate the survival benefit of CHM treatment, and correlation analysis was applied to identify the most effective components in the formulas. A network pharmacological approach was developed to decipher the potential therapeutic mechanisms of CHM.CHM treatment was an independent protective factor. The hazard ratio was 0.364 (95% CI 0.245-0.540; P?

SUBMITTER: Gao L

PROVIDER: S-EPMC5008533 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Network pharmacology dissection of multiscale mechanisms of herbal medicines in stage IV gastric adenocarcinoma treatment.

Gao Li L Hao Jian J Niu Yang-Yang YY Tian Miao M Yang Xue X Zhu Cui-Hong CH Ding Xiu-Li XL Liu Xiao-Hui XH Zhang Hao-Ran HR Liu Chang C Qin Xue-Mei XM Wu Xiong-Zhi XZ

Medicine 20160801 35

Increasing evidence has shown that Chinese Herbal Medicine (CHM) has efficient therapeutic effects for advanced gastric adenocarcinoma, while the therapeutic mechanisms underlying this treatment remain unclear.In this study, the Kaplan-Meier method and Cox regression analysis were used to evaluate the survival benefit of CHM treatment, and correlation analysis was applied to identify the most effective components in the formulas. A network pharmacological approach was developed to decipher the p ...[more]

PMID: 27583849

Similar Datasets

Systems pharmacology dissection of multi-scale mechanisms of action for herbal medicines in stroke treatment and prevention.

Project description:Annually, tens of millions of first-ever strokes occur in the world; however, currently there is lack of effective and widely applicable pharmacological treatments for stroke patients. Herbal medicines, characterized as multi-constituent, multi-target and multi-effect, have been acknowledged with conspicuous effects in treating stroke, and attract extensive interest of researchers although the mechanism of action is yet unclear. In this work, we introduce an innovative systems-pharmacology method that combines pharmacokinetic prescreening, target fishing and network analysis to decipher the mechanisms of action of 10 herbal medicines like Salvia miltiorrhizae, Ginkgo biloba and Ephedrae herba which are efficient in stroke treatment and prevention. Our systematic analysis results display that, in these anti-stroke herbal medicines, 168 out of 1285 constituents with the favorable pharmacokinetic profiles might be implicated in stroke therapy, and the systematic use of these compounds probably acts through multiple mechanisms to synergistically benefit patients with stroke, which can roughly be classified as preventing ischemic inflammatory response, scavenging free radicals and inhibiting neuronal apoptosis against ischemic cerebral damage, as well as exhibiting lipid-lowering, anti-diabetic, anti-thrombotic and antiplatelet effects to decrease recurrent strokes. Relying on systems biology-based analysis, we speculate that herbal medicines, being characterized as the classical combination therapies, might be not only engaged in multiple mechanisms of action to synergistically improve the stroke outcomes, but also might be participated in reducing the risk factors for recurrent strokes.

| S-EPMC4122378 | biostudies-literature

Gene expression profiles in bone marrow of human gastric adenocarcinoma at stage III and stage IV

2013-10-22 | GSE41801 | GEO

The Effectiveness of Gastrectomy With Chemoradiotherapy Among Stage IV Gastric Adenocarcinoma: A Population-Based Analysis.

Project description:Objectives: The strategy for the treatment of stage IV gastric cancer remains controversial. The objective of this study was to assess whether tumor resection is beneficial to survival in gastric cancer patients with incurable stage IV disease. Methods: This is a retrospective cohort study of gastric cancer patients in the Surveillance, Epidemiology, and End Results (SEER) database between 2010 and 2015. Due to the baseline bias, 1:1 propensity score matching (PSM) was used in this cohort. Patients were grouped by treatment, (1) gastrectomy with chemoradiotherapy (CRT), or (2) CRT only, and a Cox proportional hazards regression model was used to identify predictors of survival. Overall survival was compared between the two groups using the Kaplan-Meier method. Result: After propensity score matching, 162 stage IV gastric cancer patients diagnosed from 2010 to 2015 were identified. Among these patients, half underwent gastrectomy with CRT, while the others received CRT only. The median overall survival rates were 22 months from the date of surgery for the gastrectomy with CRT group and 9.0 months for CRT only group. In the multivariable Cox regression analysis, surgery was associated with a significant improvement in overall survival [hazard ratio (HR) of death = 0.31, 95% confidence interval (CI) = 0.21-0.46, P < 0.0001]. Conclusion: In conclusion, stage IV gastric cancer is still a fatal disease. This population-based study found that compared with CRT alone, CRT with gastrectomy may be associated with a survival benefit in patients with metastatic GC. In selected patients' survival can be prolonged when the primary tumor is removed. Prospective, randomized trials are required to determine the best strategy for metastatic GC and to describe the characteristics of the selected patients.

| S-EPMC7198747 | biostudies-literature

Gene expression profiles in bone marrow of human gastric adenocarcinoma at stage III and stage IV

Project description:A secreted factor in bone marrow associated with metastatic gastric cancer was indentified through expression profiling in bone marrow of stage III and stage IV gastric adenocarcinoma. In the study presented here, bone marrow samples from patients with stage III or stage IV gastric adenocarcinoma were used to acquire expression profiles.

2013-10-22 | E-GEOD-41801 | biostudies-arrayexpress

Conversion Surgery for Stage IV Gastric Cancer.

Project description:The prognosis of stage IV gastric cancer (GC) is poor, with palliative chemotherapy remaining the main therapeutic option. Studies increasingly indicate that patients with unresectable stage IV GC, who undergo gastrectomy with radical intention after responding to several regimens of combined chemotherapy, can achieve good survival outcomes. Thus, surgery aiming at radical resection for unresectable stage IV GC after combined chemotherapy has received increasing attention in recent years. This novel therapeutic strategy was defined as conversion surgery in patients with unresectable stage IV GC and it can associate with significant improved survival when R0 resection can be achieved. Despite the recent advances in conversion surgery for patients with unresectable stage IV GC, selection criteria for combination chemotherapy regimens, indications for conversion surgery, optimal timing to surgery, and postoperative chemotherapy all remain controversial. This article reviews the current state of conversion surgery for unresectable stage IV GC.

| S-EPMC6854003 | biostudies-literature

Systems pharmacology: network analysis to identify multiscale mechanisms of drug action.

Project description:Systems approaches have long been used in pharmacology to understand drug action at the organ and organismal levels. The application of computational and experimental systems biology approaches to pharmacology allows us to expand the definition of systems pharmacology to include network analyses at multiple scales of biological organization and to explain both therapeutic and adverse effects of drugs. Systems pharmacology analyses rely on experimental "omics" technologies that are capable of measuring changes in large numbers of variables, often at a genome-wide level, to build networks for analyzing drug action. A major use of omics technologies is to relate the genomic status of an individual to the therapeutic efficacy of a drug of interest. Combining pathway and network analyses, pharmacokinetic and pharmacodynamic models, and a knowledge of polymorphisms in the genome will enable the development of predictive models of therapeutic efficacy. Network analyses based on publicly available databases such as the U.S. Food and Drug Administration's Adverse Event Reporting System allow us to develop an initial understanding of the context within which molecular-level drug-target interactions can lead to distal effectors in a process that results in adverse phenotypes at the organ and organismal levels. The current state of systems pharmacology allows us to formulate a set of questions that could drive future research in the field. The long-term goal of such research is to develop polypharmacology for complex diseases and predict therapeutic efficacy and adverse event risk for individuals prior to commencement of therapy.

| S-EPMC3619403 | biostudies-literature

Pharmacokinetic Interactions between Herbal Medicines and Drugs: Their Mechanisms and Clinical Relevance.

Project description:The therapeutic efficacy of a drug or its unexpected unwanted side effects may depend on the concurrent use of a medicinal plant. In particular, constituents in the medicinal plant extracts may influence drug bioavailability, metabolism and half-life, leading to drug toxicity or failure to obtain a therapeutic response. This narrative review focuses on clinical studies improving knowledge on the ability of selected herbal medicines to influence the pharmacokinetics of co-administered drugs. Moreover, in vitro studies are useful to anticipate potential herbal medicine-drug interactions. In particular, they help to elucidate the cellular target (metabolic or transporter protein) and the mechanism (induction or inhibition) by which a single constituent of the herbal medicine acts. The authors highlight the difficulties in predicting herbal-drug interactions from in vitro data where high concentrations of extracts or their constituents are used and pharmacokinetics are missed. Moreover, the difficulty to compare results from human studies where different kinds of herbal extracts are used is discussed. The herbal medicines discussed are among the best sellers and they are reported in the "Herbal Medicines for Human Use" section of the European Medicinal Agency (EMA).

| S-EPMC7400069 | biostudies-literature

Endoscopic Submucosal Dissection of Papillary Gastric Adenocarcinoma; Systematic Review.

Project description:This study evaluated the possibility of endoscopic submucosal dissection (ESD) for early gastric cancer with papillary adenocarcinoma (EGC-PAC). PAC, an uncommon pathologic type of stomach cancer, is classified into differentiated-type histology. However, aggressive features, including a high rate of submucosal invasion, lymphovascular invasion (LVI), and lymph node metastasis (LNM), have been reported in studies with surgical specimens. Treatment outcomes of ESD for EGC-PAC have not been precisely demonstrated. Core databases were sought for the following inclusion criteria: studies of endoscopic resection or surgery of EGC-PAC presenting the following therapeutic indicators; en bloc resection, complete resection, curative resection, recurrence, complications associated with procedures, LVI, or LNM that enabled an analysis of ESD possibility. Overall, 15 studies were included for systematic review. Frequent submucosal invasion and high LVI were noted in EGC-PAC. However, PAC was not significantly associated with LNM. Pooled en bloc resection, complete resection, and curative resection rates were 89.7% (95% confidence interval: 55.3%-98.4%), 85.3% (67.7%-94.2%), and 67% (43%-84.5%), respectively. No LNM was observed if EGC-PAC satisfied the curative resection criteria. ESD seems technically feasible, although a high LVI rate results in a lower rate of curative resection.

| S-EPMC7290846 | biostudies-literature

Tumor microenvironment characterization in stage IV gastric cancer.

Project description:Immunotherapy is remarkably affected by the immune environment of the principal tumor. Nonetheless, the immune environment's clinical relevance in stage IV gastric cancer (GC) is largely unknown. The gene expression profiles of 403 stage IV GC patients in the three cohorts: GEO (Gene Expression Omnibus, GSE84437 (n=292) and GSE62254 (n=77), and TCGA (The Cancer Genome Atlas, n=34) were used in the present study. Using four publicly available stage IV GC expression datasets, 29 immune signatures were expression profiled, and on this basis, we classified stage IV GC. The classification was conducted using the hierarchical clustering method. Three stage IV GC subtypes L, M, and H were identified representing low, medium, and high immunity, respectively. Immune correlation analysis of these three types revealed that Immune H exhibited a better prognostic outcome as well as a higher immune score compared with other subtypes. There was a noticeable difference in the three subgroups of HLA genes. Further, on comparing with other subtypes, CD86, CD80, CD274, CTLA4, PDCD1, and PDCD1LG2 had higher expression in the Immunity H subtype. In stage IV GC, potentially positive associations between immune and pathway activities were displayed, due to the enrichment of pathways including TNF signaling, Th-17 cell differentiation, and JAK-STAT signaling pathways in Immunity H vs Immunity L subtypes. External cohorts from TCGA cohort ratified these results. The identification of stage IV GC subtypes has potential clinical implications in stage IV GC treatment.

| S-EPMC7796192 | biostudies-literature

Systems pharmacology dissection of action mechanisms for herbs in osteoporosis treatment.

Project description:ObjectiveOsteoporosis has become the biggest cause of non-fatal health issue. Currently, the limitations of traditional anti-osteoporosis drugs such as long-term ill-effects and drug resistance, have raised concerns toward complementary and alternative therapies, particularly herbal medicines and their natural active compounds. Thus, this study aimed to provide an integrative analysis of active chemicals, drug targets and interacting pathways of the herbs for osteoporosis treatment.MethodsHere, we introduced a systematic pharmacology model, combining the absorption, distribution, metabolism, and excretion (ADME) screening model, drug targeting and network pharmacology, to probe into the therapeutic mechanisms of herbs in osteoporosis.ResultsWe obtained 86 natural compounds with favorable pharmacokinetic profiles and their 58 targets from seven osteoporosis-related herbs. Network analysis revealed that they probably synergistically work through multiple mechanisms, such as suppressing inflammatory response, maintaining bone metabolism or improving organism immunity, to benefit patients with osteoporosis. Furthermore, experimental results showed that all the five compounds (calycosin, asperosaponin VI, hederagenin, betulinic acid and luteolin) enhanced osteoblast proliferation and differentiation in vitro, which corroborated the validity of this system pharmacology approach. Notably, gentisin and aureusidin among the identified compounds were first predicted to be associated with osteoporosis.ConclusionHerbs and their natural compounds, being characterized as the classical combination therapies, might be engaged in multiple mechanisms to coordinately improve the osteoporosis symptoms. This work may contribute to offer novel strategies and clues for the therapy and drug discovery of osteoporosis and other complex diseases.

| S-EPMC9476722 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data