Comprehensive Analysis of a circRNA-miRNA-mRNA Network to Reveal Potential Inflammation-Related Targets for Gastric Adenocarcinoma.

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This study was aimed at elucidating the regulatory network of circRNA-miRNA-mRNA and identifying the precise inflammation-related targets in GC. The expression profiles of GSE83521, GSE78091, and GSE33651 were obtained from the GEO database. Interactions between miRNAs and circRNAs were investigated by the Circular RNA Interactome, and targets of miRNAs were predicted with miRTarBase. Then, a circRNA/miRNA/mRNA regulatory network was constructed. Also, functional enrichment analysis of selected differentially expressed genes (DEGs) was performed. The inflammation-/GC-related targets were collected in the GeneCards and GenLiP3 database, respectively. And a protein-protein interaction (PPI) network of DE mRNAs was constructed with STRING and Cytoscape to identify hub genes. The genetic alterations, neighboring gene networks, expression levels, and the poor prognosis of hub genes were investigated in cBioPortal, Oncomine, and Human Protein Atlas databases and Kaplan-Meier plotter, respectively. A total of 10 DE miRNAs and 33 DEGs were identified. The regulatory network contained 26 circRNAs, 10 miRNAs, and 1459 mRNAs. Functional enrichment analysis revealed that the selected 33 DEGs were involved in negative regulation of fat cell differentiation, response to wounding, extracellular matrix- (ECM-) receptor interaction, and regulation of cell growth pathways. THBS1, FN1, CALM1, COL4A1, CTGF, and IGFBP5 were selected as inflammation-related hub genes of GC in the PPI network. The genetic alterations in these hub genes were related to amplification and missense mutations. Furthermore, the genes RYR2, ERBB2, PI3KCA, and HELZ2 were connected to hub genes in this study. The hub gene levels in clinical specimens were markedly upregulated in GC tissues and correlated with poor overall survival (OS). Our results suggest that THBS1, FN1, CALM1, COL4A1, CTGF, and IGFBP5 were associated with the pathogenesis of gastric carcinogenesis and may serve as biomarkers and inflammation-related targets for GC.", "claims": [{"id": "claim-method", "statement": "The prognostic value of hub gene mRNA transcription level was measured using the Kaplan-Meier plotter (http://www.kmplot.com), an online open database that consists of gene expression profiles and survival information for 5,143 breast cancer, 1,816 ovarian cancer, 2,437 lung cancer, and 1,065 GC patients with mean follow-ups of 69, 40, 49, and 33 months, respectively. To evaluate the overall survival (OS) of patients with GC, we separated individuals into two groups based on median gene expression (high vs. low) and then validated their Kaplan-Meier survival curves. Hazard ratios (HRs) with 95% confidence intervals (CIs) and log-rank P values were calculated to evaluate the associations of gene expression with survival, and the number-at-risk values were displayed below the curves.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32801999", "locator": "sections[11] \"2.9. Kaplan-Meier Plotter\" paragraph 2", "quote": "The prognostic value of hub gene mRNA transcription level was measured using the Kaplan-Meier plotter (http://www.kmplot.com), an online open database that consists of gene expression profiles and survival information for 5,143 breast cancer, 1,816 ovarian cancer, 2,437 lung cancer, and 1,065 GC patients with mean follow-ups of 69, 40, 49, and 33 months, respectively. To evaluate the overall survival (OS) of patients with GC, we separated individuals into two groups based on median gene expression (high vs. low) and then validated their Kaplan-Meier survival curves. 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