Prognostic biomarkers and molecular pathways mediating Helicobacter pylori-induced gastric cancer: a network-biology approach.

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Helicobacter pylori in the stomach is closely associated with the progression of GC. We identified the genes associated with poor/favorable prognosis in H. pylori-induced GC. Multivariate statistical analysis was applied on the Gene Expression Omnibus (GEO) dataset GSE54397 to identify differentially expressed miRNAs (DEMs) in gastric tissues with H. pylori-induced cancer compared with the H. pylori-positive with non-cancerous tissue. A protein interaction map (PIM) was built and subjected to DEMs targets. The enriched pathways and biological processes within the PIM were identified based on substantial clusters. Thereafter, the most critical genes in the PIM were illustrated, and their prognostic impact in GC was investigated. Considering p-value less than 0.01 and |Log2 fold change| as >1, five microRNAs demonstrated significant changes among the two groups. Gene functional analysis revealed that the ubiquitination system, neddylation pathway, and ciliary process are primarily involved in H. pylori-induced GC. Survival analysis illustrated that the overexpression of DOCK4, GNAS, CTGF, TGF-b1, ESR1, SELE, TIMP3, SMARCE1, and TXNIP was associated with poor prognosis, while increased MRPS5 expression was related to a favorable prognosis in GC patients. DOCK4, GNAS, CTGF, TGF-b1, ESR1, SELE, TIMP3, SMARCE1, TXNIP, and MRPS5 may be considered prognostic biomarkers for H. pylori-induced GC. However, experimental validation is necessary in the future.", "claims": [{"id": "claim-method", "statement": "The OPLS-DA identified the DEMs between two groups using the R version 4.0.2 programming language [71].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37037466", "locator": "sections[3] \"Microarray expression data acquisition and analysis\" paragraph 2", "quote": "The OPLS-DA identified the DEMs between two groups using the R version 4.0.2 programming language [71]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE54397 contained 32 observations containing eight H. pylori–induced gastric cancerous tissues, eight non-tumor tissues collected from H. pylori–positive patients, eight gastric cancerous tissues obtained from H. pylori–negative patients, and eight non-tumor tissues collected from H. pylori–negative patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37037466", "locator": "sections[3] \"Microarray expression data acquisition and analysis\" paragraph 2", "quote": "GSE54397 contained 32 observations containing eight H. pylori–induced gastric cancerous tissues, eight non-tumor tissues collected from H. pylori–positive patients, eight gastric cancerous tissues obtained from H. pylori–negative patients, and eight non-tumor tissues collected from H. pylori–negative patients."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Considering p-value less than 0.01 and |Log2 fold change| as >1, five microRNAs demonstrated significant changes among the two groups.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Considering p-value less than 0.01 and |Log2 fold change| as >1, five microRNAs demonstrated significant changes among the two groups."}, "evidence": [{"asset": "source:pmid:37037466", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Considering p-value less than 0.01 and |Log2 fold change| as >1, five microRNAs demonstrated significant changes among the two groups."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Considering p-value less than 0.01 and |Log2 fold change| as >1, five microRNAs demonstrated significant changes among the two groups.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37037466"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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