Integrated analysis of anti-tumor roles of BAP1 in osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36003792", "kind": "science-record", "revision": 5, "content_hash": "sha256:34d2d5a9210bcd241df8e192546d0eca5388126c256455ad72c42403180e8a13", "created_at": "2026-11-01T18:15:10Z", "updated_at": "2026-11-01T22:49:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated analysis of anti-tumor roles of BAP1 in osteosarcoma.", "doi": "10.3389/fonc.2022.973914", "pmid": "36003792", "authors": ["Dong Hu", "Yongbin Zheng", "Xuehai Ou", "Lijun Zhang", "Xiaolong Du", "Shaoyan Shi"], "journal": "Frontiers in oncology", "year": 2022, "abstract": "Background: This study aims to screen out differentially expressed genes (DEGs) regulated by BRCA1-associated protein 1 (BAP1) in osteosarcoma cells, and to analyze their biological functions.\nMethods: The microarray dataset GSE23035 of BAP1-knockdown osteosarcoma cells was obtained from Gene Expression Omnibus (GEO) database, consisting of shControl, shBAP1#1 and shBAP1#2 samples. The DEGs between the BAP1-knockdown osteosarcoma cells and the untreated osteosarcoma cells were screened with limma package, and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Gene Set Enrichment Analysis (GSEA) was also performed for the three groups of samples. Hub genes in a protein-protein interaction (PPI) network of DEGs was filtered, and then subjected to prognostic analysis and correlation analysis with BAP1 in Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Besides, the correlation between BAP1 and biological processes/pathways was analyzed by Gene Set Variation Analysis (GSVA) method and the correlation between BAP1 and immune infiltration by CIBERSORT and ESTIMATE methods. The roles of BAP1 in regulating proliferation and epithelial-mesenchymal transition (EMT) were validated by CCK-8 and western blot.\nResults: 58 upregulated DEGs and 81 downregulated DEGs were obtained with |logFC| ≥ 1 and adj.p < 0.05. Cell cycle, DNA repair, and focal adhesion were associated with BAP1 in datasets. Further, BAP1 was negatively correlated with naïve CD4 T cells infiltration. In vitro, BAP1 inhibited proliferation and EMT.\nConclusion: BAP1 might be a tumor suppressor in osteosarcoma and a promising therapeutic target.", "claims": [{"id": "claim-method", "statement": "The mean between two groups was compared by independent sample t-test, and the mean between multiple groups was compared by one-way ANOVA analysis or two-way ANOVA analysis, and the difference was considered statistically significant at p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36003792", "locator": "sections[15] \"Statistical analysis\" paragraph 2", "quote": "The mean between two groups was compared by independent sample t-test, and the mean between multiple groups was compared by one-way ANOVA analysis or two-way ANOVA analysis, and the difference was considered statistically significant at p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . 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