Dataset Information

A comprehensive evaluation of single nucleotide polymorphisms associated with atrophic gastritis risk: A protocol for systematic review and network meta-analysis.

ABSTRACT:

Background

Single nucleotide polymorphisms (SNPs) have been inconsistently associated with atrophic gastritis (AG) risk. This meta-analysis aimed to synthesize relevant data on SNPs associated with AG.

Methods

To identify all associated studies of SNPs and AG published, databases had been searched through January 2020 from the databases of PubMed, China National Knowledge Infrastructure (CNKI), Web of Science, Embase, the Chinese Science and Technology Periodical Database (VIP), Cochrane Library, and Wanfang databases. With the help of network meta-analysis and Thakkinstian algorithm, the best genetic model with the strongest correlation with AG was selected, the final result - matching to the noteworthy correlation - was obtained by referring to the false positive reporting rate (false positive report probability, FPRP). Based on STREGA's stated criteria, the methodological quality of the data we collected was valued. Both Stata 14.0 and GeMTC will be used for a comprehensive review of the system and will be used in our meta-analysis.

Results

This study will provide a high-quality evidence to find the SNP most associated with AG susceptibility and the best genetic model.

Conclusions

This study will explore which SNP is most associated with AG susceptibility.

Registration

INPLASY202050016.

SUBMITTER: Tang ZY

PROVIDER: S-EPMC7373582 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A comprehensive evaluation of single nucleotide polymorphisms associated with atrophic gastritis risk: A protocol for systematic review and network meta-analysis.

Tang Zhen-Yu ZY Ye Zhuo-Miao ZM Zheng Jing-Hui JH Jiang Feng F Tang You-Ming YM

Medicine 20200701 29

<h4>Background</h4>Single nucleotide polymorphisms (SNPs) have been inconsistently associated with atrophic gastritis (AG) risk. This meta-analysis aimed to synthesize relevant data on SNPs associated with AG.<h4>Methods</h4>To identify all associated studies of SNPs and AG published, databases had been searched through January 2020 from the databases of PubMed, China National Knowledge Infrastructure (CNKI), Web of Science, Embase, the Chinese Science and Technology Periodical Database (VIP), C ...[more]

PMID: 32702817

Similar Datasets

Project description:Polymorphisms of NER genes could change NER ability, thereby altering individual susceptibility to GC. We systematically analyzed 39 SNPs of 8 key genes of NER pathway in 2686 subjects including 898 gastric cancer (GC), 851 atrophic gastritis (AG) and 937 controls (CON) in northern Chinese. SNP genotyping were performed using Sequenom MassARRAY platform. The results demonstrated that DDB2 rs830083 GG genotype was significantly associated with increased GC risk compared with wild-type CC (OR=2.32, P= 6.62 × 10-9); XPC rs2607775 CG genotype conferred a 1.73 increased odds of GC risk than non-cancer subjects compared with wild-type CC (OR=1.73, P= 3.04 × 10-4). The combined detection of these two polymorphisms demonstrated even higher GC risk (OR=3.05). Haplotype analysis suggested that DDB2 rs2029298-rs326222-rs3781619-rs830083 GTAG haplotype was significantly associated with disease risk in each step of CON→AG→GC development (AG vs. CON: OR=2.88, P= 7.51 × 10-7; GC vs. AG: OR=2.90, P=5.68 × 10-15; GC vs. CON: OR=8.42, P=2.22 × 10-15); DDB2 GTAC haplotype was associated with reduced risk of GC compared with CON (OR=0.63, P= 8.31 × 10-12). XPC rs1870134-rs2228000-rs2228001-rs2470352-rs2607775 GCAAG haplotype conferred increased risk of GC compared with AG (OR=1.88, P= 6.98 × 10-4). XPA rs2808668 and drinking, DDB2 rs326222, rs3781619, rs830083 and smoking demonstrated significant interactions in AG; XPC rs2607775 had significant interaction with smoking in GC. In conclusion, NER pathway polymorphisms especially in "damage incision" step were significantly associated with GC risk and had interactions with environment factors. The detection of NER pathway polymorphisms such as DDB2 and XPC might be applied in the prediction of GC risk and personalized prevention in the future. NER pathway polymorphisms especially in "damage incision" step were significantly associated with GC risk and had interactions with environment factors, which might be applied in the prediction of GC risk and personalized prevention in the future.

Project description:PurposeThe aim of this study is to determine the effectiveness and reliability of adding traditional Chinese medicine (TCM) in the clinical intervention and explore mechanisms of action for chronic atrophic gastritis (CAG) through meta- and network pharmacology analysis (NPAs).MethodsA predefined search strategy was used to retrieve literature from PubMed, Embase database, Cochrane Library, China National Knowledge Infrastructure (CNKI), Chinese BioMedical Literature Database (CBM), Wan Fang Data and China Science and Technology Journal Database (VIP). After applying inclusion and exclusion criteria, a total of 12 randomized controlled trials (RCTs) were included for meta-analysis to provide clinical evidence of the intervention effects. A network meta-analysis using Bayesian networks was conducted to observe the relative effects of different intervention measures and possible ranking of effects. The composition of the TCM formulation in the experimental group was analysed, and association rule mining was performed to identify hub herbal medicines. Target genes for CAG were searched in GeneCards, Online Mendelian Inheritance in Man, PharmGKB, Therapeutic Target Database and DrugBank. A regulatory network was constructed to connect the target genes with active ingredients of the hub herbal medicines. Enrichment analyses were performed using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to examine the central targets from a comprehensive viewpoint. Protein-protein interaction networks (PPINs) were constructed to identify hub genes and conduct molecular docking with differentially expressed genes (DEGs) and corresponding active molecules.ResultsA total of 1140 participants from 12 RCTs were included in the statistical analysis, confirming that the experimental group receiving the addition of TCM intervention had better clinical efficacy. Seven hub TCMs (Paeonia lactiflora, Atractylodes macrocephala, Pinellia ternata, Citrus reticulata, Codonopsis pilosula, Salvia miltiorrhiza and Coptis chinensis) were identified through association rule analysis of all included TCMs. Thirteen hub genes (CDKN1A, CASP3, STAT1, TP53, JUN, MAPK1, STAT3, MAPK3, MYC, HIF1A, FOS, MAPK14 and AKT1) were obtained from 90 gene PPINs. Differential gene expression analysis between the disease and normal gastric tissue identified MAPK1 and MAPK3 as the significant genes. Molecular docking analysis revealed that naringenin, luteolin and quercetin were the main active compounds with good binding activities to the two hub targets. GO analysis demonstrated the function of the targets in protein binding, while KEGG analysis indicated their involvement in important pathways related to cancer.ConclusionsThe results of a meta-analysis of 12 RCTs indicate that TCM intervention can improve the clinical treatment efficacy of CAG. NPAs identified seven hub TCM and 13 target genes associated with their actions, while bioinformatics analysis identified two DEGs between normal and CAG gastric tissues. Finally, molecular docking was employed to reveal the mechanism of action of the active molecules in TCM on the DEGs. These findings not only reveal the mechanisms of action of the active components of the TCMs, but also provide support for the development of new drugs, ultimately blocking the progression from chronic gastritis to gastric cancer.

Project description:BackgroundThe study aimed to conduct a network meta-analysis of randomized controlled trials (RCTs) to examine the effectiveness and safety of traditional Chinese patent medicine (TCPM), either used alone or combined with conventional treatment (CT) of chemical drugs, for treating chronic atrophic gastritis (CAG).MethodsWe searched the literature from database creation to December 2023; our primary endpoint was clinical response rate. Secondary outcome measures were the inhibition rate of Helicobacter pylori and clinical symptom score, including pain and noisy scores for the stomach, score for belch and acid reflux, score for the bitter taste and the dry throat, and safety according to total adverse events. Data analyzed using RevMan 5.3, R (v4.0.2), and Stata SE 15.0. Mean differences (MDs) for continuous outcomes and odds ratios (ORs) for dichotomous outcomes and drug ranking by P-score. Network meta-analysis presented as forest plot and league table. Results reported as MDs/ORs with 95% confidence interval (CI).ResultsOur analysis comprised 49 RCTs with 5218 patients. Compared to using CT alone, all TCPMs + CT performed better in improving clinical response rate. The Weifuchun tablet (WFCT) inhibition rate (OR = 9.05; 95% CI = 1.89-43.34; P-score = .92) was relatively high, but only 1 RCT supported this result. WFCT + CT (OR = 2.94; 95% CI = 1.97-4.39; P-score = .57), Qizhiweitong granule (QZWTG) + CT (OR = 2.91; 95% CI = 1.07-7.89; P-score = .55), and Moluodan (MLD) + CT (OR = 2.44; 95% CI = 1.37-4.36; P-score = .43) had certain advantages in inhibiting H pylori compared to using CT alone. Compared with CT, Weisu tablet (WST) + CT (OR = 0.21; 95% CI = 0.05-0.89; P-score = .24) and Xiangshayangwei pill (XSYWP) + CT (OR = 0.41; 95% CI = 0.18-0.92; P-score = .44) were drugs that were less likely to cause adverse reactions.ConclusionOur results demonstrate that, compared to using CT alone, TCPMs combined with CT can improve the clinical response rate in the treatment of CAG. Additionally, some TCPMs combined with CT can enhance the H pylori inhibition rate. WST + CT and XSYWP + CT can even reduce the occurrence of adverse reactions.

Dataset Information

A comprehensive evaluation of single nucleotide polymorphisms associated with atrophic gastritis risk: A protocol for systematic review and network meta-analysis.

Background

Methods

Results

Conclusions

Registration

Publications

A comprehensive evaluation of single nucleotide polymorphisms associated with atrophic gastritis risk: A protocol for systematic review and network meta-analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets