Integrated Bioinformatics and Experimental Analysis of Long Noncoding RNA Associated-ceRNA as Prognostic Biomarkers in Advanced Stomach Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38370380", "kind": "science-record", "revision": 4, "content_hash": "sha256:cd7298568f17f71a17dd5037466928b7c8ca898c147443c9c943d439c8ef1ffb", "created_at": "2026-11-01T19:20:18Z", "updated_at": "2026-11-01T22:53:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics and Experimental Analysis of Long Noncoding RNA Associated-ceRNA as Prognostic Biomarkers in Advanced Stomach Adenocarcinoma.", "doi": "10.7150/jca.89526", "pmid": "38370380", "authors": ["Yixin Chen", "Xin Gao", "Xinyang Dai", "Yuwei Xia", "Xinran Zhang", "Leitao Sun", "Ying Zhu"], "journal": "Journal of Cancer", "year": 2024, "abstract": "BACKGROUND: Advanced stomach adenocarcinoma (ASTAD) is a highly malignant and prognostically poor stage of gastric cancer. Recently, long noncoding RNA (lncRNA) was found to play a crucial role, including as competing endogenous RNA (ceRNA) in cancer. However, studies on large-scale sample in ASTAD are still lacking, thus we constructed the ceRNA network of ASTAD to explore its molecular mechanism.\nMETHODS: We compared the expression of mRNAs, lncRNAs and miRNAs between ASTAD and normal tissues utilizing RNA-Seq and miRNA-seq Data from The Cancer Genome Atlas (TCGA). GO and KEGG enrichment analysis were executed for annotating the functions of differentially expressed mRNAs. Subsequently, we investigated the expression correlations between the differentially expressed lncRNAs and their respective mRNAs by constructing a ceRNA network. Kaplan-Meier survival analysis was used to assess the relationship between high/low risk scores based on this network with patient prognosis in TCGA training cohort and GSE15459 validation cohort. In vitro functional assays were employed to verify the cancer-promoting effects of key lncRNAs in the ceRNA network and their possible mechanisms.\nRESULTS: In ASTAD tissues, a total of 176 lncRNAs, 124 miRNAs, and 2205 mRNAs were identified as differentially expressed. Our constructed ceRNA network consisted 6 differentially expressed lncRNAs (PVT1, MAGI2-AS3, KCNQ1OT1, LINC02086, AC125807.2 and LINC02535), 25 miRNAs and 130 mRNAs, and the risk score derived from these lincRNAs could predict ASTAD patient outcomes. Key lncRNA LINC02086 was experimentally verified to enhance proliferation and migration of gastric cancer cells by competitively binding to miR-93a-5p with MMP3.\nCONCLUSION: Our comprehensive ceRNA network for ASTAD provides valuable insights into its molecular mechanisms, and LINC02086 may be used as an innovative target for clinical treatment.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier survival analysis was used to assess the relationship between high/low risk scores based on this network with patient prognosis in TCGA training cohort and GSE15459 validation cohort.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38370380", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Kaplan-Meier survival analysis was used to assess the relationship between high/low risk scores based on this network with patient prognosis in TCGA training cohort and GSE15459 validation cohort."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38370380", "locator": "sections[32] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our constructed ceRNA network consisted 6 differentially expressed lncRNAs (PVT1, MAGI2-AS3, KCNQ1OT1, LINC02086, AC125807.2 and LINC02535), 25 miRNAs and 130 mRNAs, and the risk score derived from these lincRNAs could predict ASTAD patient outcomes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38370380", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our constructed ceRNA network consisted 6 differentially expressed lncRNAs (PVT1, MAGI2-AS3, KCNQ1OT1, LINC02086, AC125807.2 and LINC02535), 25 miRNAs and 130 mRNAs, and the risk score derived from these lincRNAs could predict ASTAD patient outcomes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our constructed ceRNA network consisted 6 differentially expressed lncRNAs (PVT1, MAGI2-AS3, KCNQ1OT1, LINC02086, AC125807.2 and LINC02535), 25 miRNAs and 130 mRNAs, and the risk score derived from these lincRNAs could predict ASTAD patient outcomes.", "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:38370380"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE15459"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE15459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38370380", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.89526", "sha256": 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The above cell lines were cultured in Roswell Park Memorial Institute (RPMI) 16", "ided upon request. 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