DNA methylation biomarkers for nasopharyngeal carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32271791", "kind": "science-record", "revision": 8, "content_hash": "sha256:9fa0cd6ee83d1205392d3d596c9092d12e76a9ecf767c7921a8f88b423d44633", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T22:01:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DNA methylation biomarkers for nasopharyngeal carcinoma.", "doi": "10.1371/journal.pone.0230524", "pmid": "32271791", "authors": ["Baoai Han", "Xiuping Yang", "Po Zhang", "Ya Zhang", "Yaqin Tu", "Zuhong He", "Yongqin Li", "Jie Yuan", "Yaodong Dong", "Davood K Hosseini", "Tao Zhou", "Haiying Sun"], "journal": "PloS one", "year": 2020, "abstract": "BACKGROUND: Aberrant methylation of DNA plays an important role in the pathogenesis of nasopharyngeal carcinoma (NPC). In the current study, we aimed to integrate three cohorts profile datasets to identify abnormally methylated-differentially expressed genes and pathways associated with NPC.\nMETHODS: Data of gene expression microarrays (GSE53819, GSE412452) and gene methylation microarrays (GSE52068) obtained from the GEO database. Aberrantly methylated differentially expressed genes (DEGs) were obtained by GEO2R. The David database was utilized to perform enrichment and functional analysis regarding selected genes. To create a protein-protein interaction (PPI), STRING and Cytoscape software were utilized. The MCODE was used for module analysis of the PPI network.\nRESULTS: In total, 181 hypomethylation-high expression genes were identified, which were enriched in the biological mechanisms involved in the differentiation of endodermal cell, mitotic nuclear division, mitotic cell cycle process, chromosome segregation and cell cycle phase transition, etc. Pathway enrichment showed ECM-receptor interaction, PI3K-Akt signaling pathway, Focal adhesion, Protein digestion and absorption and Amoebiasis, etc. The top 3 hub genes of PPI network were FANCI, POSTN, and IFIH1. Additionally, 210 hypermethylation-low expression genes were identified, and our data revealed enrichment in biological processes including axoneme assembly, micro tubular formation, assembly of axonemal dynein complex, cilium movement and cilium organization, etc. Pathway analysis indicated enrichment in B cell receptor signaling pathway, Hematopoietic cell lineage, Leukocyte transendothelial migration, Complement and coagulation cascades and Fc gamma R-mediated phagocytosis, etc. The ZMYND10, PACRG and POU2AF1 were identified as the top three hub genes of PPI network. After validation in TCGA and GEPIA database, most hub genes remained significant. Patients with high expression of POSTN found to have shorter overall survival, while in patients with high expression of ZMYND10 and POU2AF1 longer overall survival was identified.\nCONCLUSIONS: The data revealed novel aberrantly methylated-differentially expressed genes and pathways in NPC by bioinformatics analysis, potentially providing novel insights for the molecular mechanisms governing NPC progression. Hub genes including FANCI, POSTN, IFIH1, ZMYND10, PACRG and POU2AF1 might serve as novel biomarkers for precision diagnosis and providing medical treatment for patient with NPC.", "claims": [{"id": "claim-data-access", "statement": "Totally 18NPC and 18 normal specimens were obtained in GSE53819 while 31NPC and 10 normal samples were obtained in GSE12452. Both expression microarrays used the platform GPL570 (Affymetrix Human Genome U133 plus 2.0 Array, Thermo Fisher scientific, USA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32271791", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "Totally 18NPC and 18 normal specimens were obtained in GSE53819 while 31NPC and 10 normal samples were obtained in GSE12452. Both expression microarrays used the platform GPL570 (Affymetrix Human Genome U133 plus 2.0 Array, Thermo Fisher scientific, USA)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32271791"], "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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