Association of TP53 gene codon 72 polymorphism with Helicobacter pylori-positive non-cardia gastric cancer in Vietnam

Ha, Thi Minh Thi; Le, Thanh Nha Uyen; Nguyen, Viet Nhan; Tran, Van Huy

doi:10.3855/jidc.11488

Cited by 6 publications

(5 citation statements)

References 39 publications

(44 reference statements)

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“…We established a protein-protein interaction (PPI) network consisting of 165 nodes and 170 edges and identified 18 hub genes by using the MCODE plugin in Cytoscape. The 18 hub genes have been reported to be associated with gastric cancer, which are CCND2 [ 28 ], STAT3 [ 29 ], TP53 [ 30 ], MCL1 [ 31 ], MYC [ 32 ], FOXO1 [ 33 ], FOXO3 [ 34 ], BCL2L11 [ 35 ], GSK3B [ 36 ], CDKN1A [ 37 ], CDH1 [ 38 ], PTEN [ 39 ], MTOR [ 40 ], MAPK1 [ 41 ], CASP3, CDC42 [ 42 ], SMAD4 [ 43 ], and IL6 [ 44 ]. All of them were predicted target genes for hsa-miR-197-3p, hsa-miR-451a, hsa-miR-136-5p, hsa-miR-337-3p, hsa-miR-654-3p, hsa-miR-182-5p, hsa-miR-1228-3p, hsa-miR-942-5p, hsa-miR-488-3p, and hsa-miR-876-3p, and all 10 miRNAs were predicted miRNAs for hsa_circ_0001013.…”

Section: Discussionmentioning

confidence: 99%

Construction of a circRNA-miRNA-mRNA network based on differentially co-expressed circular RNA in gastric cancer tissue and plasma by bioinformatics analysis

Gong

Jiao

et al. 2022

World J Surg Onc

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Background Increasing evidence implicates circular RNAs (circRNAs) have been involved in human cancer progression. However, the mechanism remains unclear. In this study, we identified novel circRNAs related to gastric cancer and constructed a circRNA-miRNA-mRNA network. Methods Microarray datasets GSE83521 and GSE93541 were obtained from the Gene Expression Omnibus (GEO). Then, we used computational biology to identify circRNAs that were differentially expressed in both GC tissue and plasma compared to normal controls; then, we detected the expression of the selected circRNAs in gastric cell lines by quantitative real-time polymerase chain reaction (qRT-PCR). We also identified circRNA-related candidate miRNAs and their target genes with online tools. Combining the predicted miRNAs and target mRNAs, a competing endogenous RNA regulatory network was established. Functional and pathway enrichment analyses were performed, and interactions between proteins were predicted by using String and Cytoscape. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the possible functions of these differentially expressed circRNAs. The regulatory network constructed using the microarray datasets (GSE83521 and GSE93541) contained three differentially co-expressed circRNAs (DECs). A circRNA-miRNA-mRNA network was constructed based on 3 circRNAs, 43 miRNAs and 119 mRNAs. Results GO and KEGG analysis showed that the regulation of apoptotic signaling pathway and PI3K−Akt signaling pathway were highest degrees of enrichment respectively. We established a protein-protein interaction (PPI) network consisting of 165 nodes and 170 edges and identified hub genes by using MCODE plugin in Cytoscape. Furthermore, a core circRNA-miRNA-mRNA network was constructed based on hub genes. Hsa_circ_0001013 was finally determined to play an important role in the pathogenesis of GC according to the core circRNA-miRNA-mRNA network. Conclusions We propose a new circRNA-miRNA-mRNA network that is associated with the pathogenesis of GC. The network may become a new molecular biomarker and could be used to develop potential therapeutic strategies for gastric cancer.

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Section: Discussionmentioning

confidence: 99%

Construction of a circRNA-miRNA-mRNA network based on differentially co-expressed circular RNA in gastric cancer tissue and plasma by bioinformatics analysis

Gong

Jiao

et al. 2022

World J Surg Onc

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“…81 The study by Ha et al found that the synergistic effect between H. pylori infection and TP53 may play an important role in the pathogenesis of gastric cancer in the Vietnamese population. 82 IL-6, as a PIC, plays an important role in the process of inflammatory reaction. The expression of IL-6 and its receptor was significantly increased in patients infected with H. pylori , especially in those with gastric cancer.…”

Section: Discussionmentioning

confidence: 99%

Basic Traditional Chinese Medicinal Compound for Adjuvant Treatment of Helicobacter pylori-Related Gastritis: Implication for Anti-H. pylori-Related Gastritis Drug Discovery

Tan

2022

Natural Product Communications

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This study was aimed at evaluating the efficacy of traditional Chinese medicine (TCM) in the adjuvant treatment of Helicobacter pylori-associated gastritis (HPAG) and exploring the molecular mechanism underlying the action of the basic TCM compounds against HPAG. Eight representative Chinese and British databases were combed for pertinent literature. In light of the basic principle of evidence-based medicine, this work rigorously stuck to the inclusion and exclusion of criteria so as to plump for qualified articles. Also, the data mining method was adopted to help determine the basic TCM compound for HPAG treatment. Furthermore, a network pharmacology-based strategy was used to uncover the underlying mechanisms of the basic TCM compound against HPAG. Ultimately, molecular docking was used for preliminary verification. TCM combined with triple or quadruple therapy against HPAG possessed more advantages in improving the total effective rate and H. pylori eradication rate than triple or quadruple therapy alone. The basic TCM plant materials against HPAG consisted of Citrus reticulata Blanco, Glycyrrhiza uralensis Fisch, Pinellia ternata (Thunb.) Breit, Coptis chinensis Franch, and Poria cocos (Schw.) Wolf. Quercetin, kaempferol, naringenin, baicalein, nobiletin, and hederagenin were determined as the key active ingredients of the basic TCM preparation against HPAG. Moreover, these ingredients played a therapeutic role by acting on AKT1, TP53, interleukin (IL)-6, VEGFA, CASP3, MAPK3, JUN, TNF, and MAPK8 via Pathways in cancer, PI3K-Akt signaling pathway, TNF signaling pathway, and MAPK signaling pathway. The results of molecular docking indicated that the key ingredients could bind stably with the core targets. The efficacy of the TCM in the adjuvant treatment of HPAG is worthy of affirmation. Compatible use of the key ingredients of the basic TCM compound is a novel idea of drug research with profound clinical significance and research value in the development of anti- H. pylori drugs.

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“…We established a protein-protein interaction (PPI) network consisting of 165 nodes and 170 edges and identified 18 hub genes by MCODE plugin in Cytoscape. The 18 hub genes have been reported to be associated with gastric cancer, which are CCND2 [27] STAT3 [28], TP53 [29], MCL1 [30], MYC [31], FOXO1 [32], FOXO3 [33], BCL2L11 [34], GSK3B [35], CDKN1A [36], CDH1 [37], PTEN [38], MTOR [39], MAPK1 [40], CASP3, CDC42[41], SMAD4 [42] and IL6 [43]. All of them were predicted target genes for hsa-miR-197-3p, hsa-miR-451a, hsa-miR-136-5p, hsa-miR-337-3p, hsa-miR-654-3p, hsa-miR-182-5p, hsa-miR-1228-3p, hsa-miR-942-5p, hsa-miR-488-3p and hsa-miR-876-3p, and all these 10 miRNAs were predicted miRNAs for hsa_circ_0001013.…”

Section: Discussionmentioning

confidence: 99%

Construction of a circRNA-miRNA-mRNA network based on differentially co-expressed circular RNA in gastric cancer tissue and plasma by bioinformatics analysis

Gong¹,

Qi²,

Fu³

et al. 2020

Preprint

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Background: Increasing evidence implicates circular RNAs (circRNAs) have been involved in human cancer progression. However, the mechanism remains unclear. In this study, we identified novel circRNAs related to gastric cancer and constructed a circRNA-miRNA-mRNA network.Methods: Microarray dataset GSE83521 and GSE93541 were obtained from Gene Expression Omnibus (GEO). Then, we used computational biology to select differentially co-expressed circRNAs in GC tissue and plasma and detected the expression of selected circRNAs in gastric cell lines by quantitative real‑time polymerase chain reaction (qRT‑PCR). We also chose the candidate miRNAs and their target genes for circRNAs through online tools. Combining the predictions of miRNAs and target mRNAs, a competing endogenous RNA regulatory network was established. Functional and pathway enrichment analyses were performed, and interactions between proteins were predicted by using String and Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the possible functions of these differentially expressed circRNAs.Results: The regulatory network constructed using the microarray datasets (GSE83521 and GSE93541) contained three differentially co-expressed circRNAs (DECs). A circRNA-miRNA-mRNA network was constructed based on 3 circRNAs, 43 miRNAs and 119 mRNAs. GO and KEGG analysis showed that regulation of apoptotic signaling pathway and PI3K−Akt signaling pathway were highest degrees of enrichment respectively. We established a protein-protein interaction (PPI) network consisting of 165 nodes and 170 edges and identified hub genes by MCODE plugin in Cytoscape. Furthermore, a core circRNA-miRNA-mRNA network was constructed base on hub genes. Hsa_circ_0001013 was finally determined to play an important role in the pathogenesis of GC according to the core circRNA-miRNA-mRNA network.Conclusions: We propose a new circRNA-miRNA-mRNA network associated with the pathogenesis of GC. The network may become a new molecular biomarker and be used to develop potential therapeutic strategies for gastric cancer.

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Association of TP53 gene codon 72 polymorphism with Helicobacter pylori-positive non-cardia gastric cancer in Vietnam

Cited by 6 publications

References 39 publications

Construction of a circRNA-miRNA-mRNA network based on differentially co-expressed circular RNA in gastric cancer tissue and plasma by bioinformatics analysis

Construction of a circRNA-miRNA-mRNA network based on differentially co-expressed circular RNA in gastric cancer tissue and plasma by bioinformatics analysis

Basic Traditional Chinese Medicinal Compound for Adjuvant Treatment of Helicobacter pylori-Related Gastritis: Implication for Anti-H. pylori-Related Gastritis Drug Discovery

Construction of a circRNA-miRNA-mRNA network based on differentially co-expressed circular RNA in gastric cancer tissue and plasma by bioinformatics analysis

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