Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in <i>H. pylori-</i>CagA transfected gastric cancer cells

Chen, Dingyu; Li, Chao; Zhao, Yan; Zhou, Jing; Wang, Qinrong; Xie, Yuan

doi:10.7717/peerj.11203

Cited by 3 publications

(1 citation statement)

References 38 publications

(34 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In previous research by our group, Hp-CagA transfected gastric cancer cells were used for transcriptome sequencing and it was found that the expression of FTO mRNA was increased (38). It was speculated that Hp may play a role in the development and progression of gastric cancer by increasing FTO expression.…”

Section: Discussionmentioning

confidence: 99%

Effects of Helicobacter pylori on the expression of the FTO gene and its biological role in gastric cancer

et al. 2023

View full text Add to dashboard Cite

Helicobacter pylori (Hp) is a primary risk factor for gastric cancer. The fat mass and obesity-associated (FTO) gene is associated with the development and progression of various cancer types such as glioma, leukemia, breast cancer and colorectal cancer. The aim of the present study was to investigate the effect of Hp infection on the expression of FTO and its roles in gastric cancer. It was found that the expression levels of both FTO mRNA and protein were significantly increased in Hp-infected human gastric mucosal epithelial cells and Mongolian gerbil gastric tissues. The expression of FTO in gastric cancer tissues was higher than that in para-cancer tissues. Data from The Cancer Genome Atlas demonstrated that FTO expression in gastric cancer tissues was significantly higher than that in normal tissues. Patient survival rate was significantly decreased in patients with high expression levels of FTO. It was also demonstrated that FTO expression was associated with several pathological parameters, such as tumor stage, metastasis stage and the American Joint Committee on Cancer stage. The FTO gene was positively correlated with 16,601 genes in gastric cancer and negatively correlated with 3,623 genes. Gene Ontology enrichment analysis demonstrated that FTO was significantly enriched in the regulation of gene expression and oxidative RNA demethylase activity, and it was associated with components such as the RNA N6-methyladenosine methyltransferase complex and nuclear speckle. In addition, knockdown of the FTO gene inhibited the migration and invasion of Hp-infected cells. In conclusion, the data suggests that Hp infection leads to upregulation of the FTO gene, which may be related to patient survival rate, tumor staging and other pathological parameters of patients with gastric cancer. It also suggests that FTO promotes proliferation and migration of gastric cancer cells, which may be involved in the pathogenesis of Hp-induced gastric cancer.

show abstract

Section: Discussionmentioning

confidence: 99%

Effects of Helicobacter pylori on the expression of the FTO gene and its biological role in gastric cancer

et al. 2023

View full text Add to dashboard Cite

show abstract

Identification of Vital Hub Genes and Potential Molecular Pathways of Dermatomyositis by Bioinformatics Analysis

Ouyang

Zeng

Jiang

et al. 2021

BioMed Research International

View full text Add to dashboard Cite

Dermatomyositis is an autoimmune disease characterized by severe symmetrical muscle dysfunction and pain. This study was aimed at discovering vital hub genes and potential molecular pathways of DM through bioinformatics analysis, which contributes to identifying potential diagnostic or therapeutic biomarkers and targets. In this study, a total of 915 DEGs in DM samples including 167 upregulated genes and 748 downregulated genes were screened out by the limma package based on the GSE142807 dataset from the Gene Expression Omnibus (GEO) database. Furthermore, the results of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that these downregulated genes were highly associated with the immune-related biological processes and pathways. Therefore, 41 genes closely related to DM were extracted for further study based on the subcluster analysis through the Molecular Complex Detection (MCODE) software plugin in Cytoscape. Ultimately, 10 hub genes (including ISG15, DDX58, IFIT3, CXCL10, and STAT1) were identified as the potential candidate biomarkers and targets. Besides, we found that the identified hub genes directly or indirectly communicated with each other via molecular signaling pathways on the protein and transcription level. In general, under the guidance of bioinformatics analysis, 10 vital hub genes and molecular mechanisms in DM were identified and the expression of proinflammatory factors and interferon family proteins and genes showed high association with DM, which might help provide a theoretical foundation for the development of point-to-point targeted therapy in the future treatment of DM.

show abstract

Assessing Clinical Relevance of Gastric Cancer Cell Lines as Tumor Models by Identifying Key Genes and miRNAs involved in EMT Metastasis Pathway

Taluja,

Sharma,

Nayyar

et al. 2023

Microsphere

View full text Add to dashboard Cite

Cancer cell lines are in-vitro cancer cell models that continue to divide and proliferate under controlled laboratory conditions. They are used in medical research to study tumor pathology and for testing therapeutics efficacy. Despite their extensive application, significant differences in genetic and transcriptomic expression exist between cell lines and tumor cells. The purpose of this study was to identify the relevance of gastric cancer cell lines as suitable models for gastric tumor research. Using a two-tiered bioinformatics approach- a comparison between the gastric tumor and the gastric cancer cell line was performed using functional genomics data available in the literature to identify the common Differentially Expressed Genes (DEGs). The study revealed differential expression of a total 380 genes common in both gastric cancer cell lines and tumor samples. Interestingly, four of these genes were identified as the Epithelial Mesenchymal Transition (EMT) markers, involved in the accelerated metastasis, of which two genes with discrete over-expression patterns, namely- ITGB1 and TGFB1 were selected for further analysis. Their survival analysis revealed their key role in gastric cancer severity, evident by the regressed survival rate of gastric cancer patients upon their overexpression. A total of nine tumor-suppressor miRNAs relevant to ITGB1 and TGFB1 were also identified. In conclusion, our findings indicate that inspite of various genetic and transcriptomic deviations, the tumor and cell line exhibit comparable expression patterns. The data obtained would be useful to implore the druggability of these targets with a goal of improved translational rates.

show abstract

Bioinformatics analysis for the identification of differentially expressed genes and related signaling pathways in H. pylori-CagA transfected gastric cancer cells

Cited by 3 publications

References 38 publications

Effects of Helicobacter pylori on the expression of the FTO gene and its biological role in gastric cancer

Effects of Helicobacter pylori on the expression of the FTO gene and its biological role in gastric cancer

Identification of Vital Hub Genes and Potential Molecular Pathways of Dermatomyositis by Bioinformatics Analysis

Assessing Clinical Relevance of Gastric Cancer Cell Lines as Tumor Models by Identifying Key Genes and miRNAs involved in EMT Metastasis Pathway

Contact Info

Product

Resources

About