Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35685832", "kind": "science-record", "revision": 5, "content_hash": "sha256:d4ce39092f812f131bd95e546318f27034832c1668fd88c8a66dfd76f0082f6f", "created_at": "2026-11-01T18:14:38Z", "updated_at": "2026-11-01T22:49:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer.", "doi": "10.1155/2022/5281846", "pmid": "35685832", "authors": ["Dengfa Peng", "Li Feng", "Huqing Li"], "journal": "International journal of genomics", "year": 2022, "abstract": "Objective: Evidence increasingly shows that circular RNAs (circRNAs) are closely associated with tumorigenesis and cancer progression. However, the roles of circRNAs and the underlying mechanism behind these circRNAs in gastric cancer (GC) remain to be elucidated. This study is aimed at conferring a better understanding of GC pathogenesis with a specific focus on circRNA-based ceRNA action.\nMethods: circRNA expression profiles were downloaded from two Gene Expression Omnibus (GEO) microarray datasets, GSE152309 and GSE121445. Expression profiles of miRNAs and mRNAs were collected from The Cancer Genome Atlas (TCGA) database. The ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs. Functional and pathway enrichment analyses were performed to evaluate functional pathways of differentially expressed mRNAs (DEmRNAs). The PPI network was constructed by mapping DEmRNAs into the STRING database to identify hub genes, and then the DEcircRNA-DEmiRNA-hub gene subnetwork was constructed. The expression levels of candidate differentially expressed circRNAs (DEcircRNAs) in cancerous and matched noncancerous gastric tissues surgically resected from 52 GC patients were determined by the RT-qPCR analysis.\nResults: Differential expression analysis with Venn diagram analysis showed 11 overlapped DEcircRNAs (7 upregulated circRNAs and 4 downregulated ones) between cancerous tissues and noncancerous gastric tissues. The DEcircRNA-DEmiRNA-DEmRNA network was constructed, consisting of 2 DEcircRNAs, 7 DEmiRNAs, and 104 DEmRNAs. GO and KEGG pathway analyses revealed that 104 DEmRNAs might be associated with GC development and progression. The PPI network was constructed, yielding 16 hub genes, TFDP1, KRAS, LMNB1, MET, MYBL2, CDC25A, E2F5, HMGA1, HMGA2, CBFB, CBX3, CDC7, IGF2BP3, KIF11, PDGFB, and SMC1A, which were all upregulated in GC tissues compared with adjacent tumor-free gastric tissues. Based on the above hub genes in GC, the DEcircRNA-DEmiRNA-hub gene subnetwork was reconstructed based on hsa_circ_0000384 and hsa_circ_0000043, including 22 pairs of the upcircRNA-downmiRNA-upmRNA network. The expression levels of hsa_circ_0000384 and hsa_circ_0000043 were remarkably higher in GC tissues than those in matched adjacent tumor-free gastric tissues (p < 0.001), concurring with the bioinformatics results.\nConclusion: Our study offers a better understanding of circRNA-related ceRNA regulatory mechanism in the pathogenesis of GC, highlighting two ceRNA networks based on hsa_circ_0000384 and hsa_circ_0000043.", "claims": [{"id": "claim-method", "statement": "The limma package loaded in the R/Bioconductor software was employed to analyze DEcircRNAs, DEmiRNAs, and DEmRNAs using (|log (fold change [FC])| > 1.5 and adjusted p < 0.05 as cutoff values, between cancerous tissues and noncancerous gastric tissues. Relative expression levels of hsa_circ_0000384 and hsa_circ_0000043 between cancerous and matched noncancerous gastric tissues were compared using the paired t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35685832", "locator": "sections[3] \"2.1. Acquisition of Raw Data\" paragraph 2", "quote": "The limma package loaded in the R/Bioconductor software was employed to analyze DEcircRNAs, DEmiRNAs, and DEmRNAs using (|log (fold change [FC])| > 1.5 and adjusted p < 0.05 as cutoff values, between cancerous tissues and noncancerous gastric tissues."}, {"asset": "source:pmid:35685832", "locator": "sections[10] \"2.8. Statistical Analysis\" paragraph 2", "quote": "Relative expression levels of hsa_circ_0000384 and hsa_circ_0000043 between cancerous and matched noncancerous gastric tissues were compared using the paired t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE152309 and GSE121445 microarray datasets and miRNA and mRNA profiles supporting the results displayed in the study could be downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/gds) and TCGA database (https://tcga-data.nci.nih.gov/), respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35685832", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The GSE152309 and GSE121445 microarray datasets and miRNA and mRNA profiles supporting the results displayed in the study could be downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/gds) and TCGA database (https://tcga-data.nci.nih.gov/), respectively."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 11 overlapping DEcircRNAs and showed that hsa_circ_0000384 and hsa_circ_0000043 were upregulated in GC tissues, with both circRNAs showing higher expression in GC tissues than in matched adjacent tumor-free tissues (p < 0.001).", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "The expression levels of hsa_circ_0000384 and hsa_circ_0000043 were remarkably higher in GC tissues than those in matched adjacent tumor-free gastric tissues (p < 0.001), concurring with the bioinformatics results."}, "evidence": [{"asset": "source:pmid:35685832", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Differential expression analysis with Venn diagram analysis showed 11 overlapped DEcircRNAs (7 upregulated circRNAs and 4 downregulated ones) between cancerous tissues and noncancerous gastric tissues."}, {"asset": "source:pmid:35685832", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The expression levels of hsa_circ_0000384 and hsa_circ_0000043 were remarkably higher in GC tissues than those in matched adjacent tumor-free gastric tissues (p < 0.001), concurring with the bioinformatics results."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 11 overlapping DEcircRNAs and showed that hsa_circ_0000384 and hsa_circ_0000043 were upregulated in GC tissues, with both circRNAs showing higher expression in GC tissues than in matched adjacent tumor-free tissues (p < 0.001).", "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:35685832"], "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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