HNF4A-Bridging the Gap Between Intestinal Metaplasia and Gastric Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38680615", "kind": "science-record", "revision": 4, "content_hash": "sha256:d864efdc7f7620c59eea5a3fe730036168eede27098802bcb0c9824aede8afdb", "created_at": "2026-11-01T19:20:38Z", "updated_at": "2026-11-01T22:54:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "HNF4A-Bridging the Gap Between Intestinal Metaplasia and Gastric Cancer.", "doi": "10.1177/11769343241249017", "pmid": "38680615", "authors": ["Yihang Zhao", "Hong Tang", "Jianhua Xu", "Feifei Sun", "Yuanyuan Zhao", "Yang Li"], "journal": "Evolutionary bioinformatics online", "year": 2024, "abstract": "Background: Intestinal metaplasia (IM) of gastric epithelium has traditionally been regarded as an irreversible stage in the process of the Correa cascade. Exploring the potential molecular mechanism of IM is significant for effective gastric cancer prevention.\nMethods: The GSE78523 dataset, obtained from the Gene Expression Omnibus (GEO) database, was analyzed using RStudio software to identify the differently expressed genes (DEGs) between IM tissues and normal gastric epithelial tissues. Subsequently, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Gene Set Enrichment Analysis (GESA), and protein-protein interaction (PPI) analysis were used to find potential genes. Additionally, the screened genes were analyzed for clinical, immunological, and genetic correlation aspects using single gene clinical correlation analysis (UALCAN), Tumor-Immune System Interactions Database (TISIDB), and validated through western blot experiments.\nResults: Enrichment analysis showed that the lipid metabolic pathway was significantly associated with IM tissues and the apolipoprotein B (APOB) gene was identified in the subsequent analysis. Experiment results and correlation analysis showed that the expression of APOB was higher in IM tissues than in normal tissues. This elevated expression of APOB was also found to be associated with the expression levels of hepatocyte nuclear factor 4A (HNF4A) gene. HNF4A was also found to be associated with immune cell infiltration to gastric cancer and was linked to the prognosis of gastric cancer patients. Moreover, HNF4A was also highly expressed in both IM tissues and gastric cancer cells.\nConclusion: Our findings indicate that HNF4A regulates the microenvironment of lipid metabolism in IM tissues by targeting APOB. Higher expression of HNF4A tends to lead to a worse prognosis in gastric cancer patients implying it may serve as a predictive indicator for the progression from IM to gastric cancer.", "claims": [{"id": "claim-method", "statement": "The limma package of RStudio software was used to normalize the data, and subsequently the differently expressed genes (DEGs) between IM tissues and normal tissues were obtained (|logFC| > 4, P value < .01, the base of |logFC| is two).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38680615", "locator": "sections[2] \"Materials and Methods\" paragraph 3", "quote": "The limma package of RStudio software was used to normalize the data, and subsequently the differently expressed genes (DEGs) between IM tissues and normal tissues were obtained (|logFC| > 4, P value < .01, the base of |logFC| is two)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/gds/?term=,GSE78523."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our findings indicate that HNF4A regulates the microenvironment of lipid metabolism in IM tissues by targeting APOB.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38680615", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our findings indicate that HNF4A regulates the microenvironment of lipid metabolism in IM tissues by targeting APOB."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our findings indicate that HNF4A regulates the microenvironment of lipid metabolism in IM tissues by targeting APOB.", "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:38680615"], "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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Results: Enrichment analysis sh", "e considered statistically significant.26,27 Western blot: Western/IP cell lysate (biosharp, BL509A) w", "levels in GES-1, HGC27, and MGC803 cells by western blot (left) and quantified(right) and All samples", "No.:180-506W/506B) was used to visualize the immunoblot bands using the Tanon Chemiluminescent Image"], "order_basis": "paper_text_order:994", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["dence interval as the dotted line. The ID of affymetrix that was used is 208429_x_at. Analysis of ge", "HNF4A expression (Log-rank P = 9.6 × 10−7). Affymetrix ID is 208429_x_at. 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