Integrative analysis based on the cell cycle-related genes identifies TPX2 as a novel prognostic biomarker associated with tumor immunity in breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38643462", "kind": "science-record", "revision": 5, "content_hash": "sha256:f0f5e3fd56c72dfc25bfd185862cec57e403543b036c6e5b4b32e0ce8e0fbb82", "created_at": "2026-11-01T19:20:36Z", "updated_at": "2026-11-01T22:54:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analysis based on the cell cycle-related genes identifies TPX2 as a novel prognostic biomarker associated with tumor immunity in breast cancer.", "doi": "10.18632/aging.205752", "pmid": "38643462", "authors": ["Xinli Liu", "Wenyi Wang", "Bing Chen", "Shengjie Wang"], "journal": "Aging", "year": 2024, "abstract": "BACKGROUND: This study aims to identify the essential cell cycle-related genes associated with prognosis in breast cancer (BRCA), and to verify the relationship between the central gene and immune infiltration, so as to provide detailed and comprehensive information for the treatment of BRCA.\nMATERIALS AND METHODS: Gene expression profiles (GSE10780, GSE21422, GSE61304) and the Cancer Genome Atlas (TCGA) BRCA data were used to identify differentially expressed genes (DEGs) and further functional enrichment analysis. STRING and Cytoscape were employed for the protein-protein interaction (PPI) network construction. TPX2 was viewed as the crucial prognostic gene by the Survival and Cox analysis. Furthermore, the connection between TPX2 expression and immune infiltrating cells and immune checkpoints in BRCA was also performed by the TIMER online database and R software.\nRESULTS: A total of 18 cell cycle-related DEGs were identified in this study. Subsequently, an intersection analysis based on TCGA-BRCA prognostic genes and the above DEGs identified three genes (TPX2, UBE2C, CCNE2) as crucial prognostic candidate biomarkers. Moreover, we also demonstrated that TPX2 is closely associated with immune infiltration in BRCA and a positive relation between TPX2 and PD-L1 expression was firstly detected.\nCONCLUSIONS: These results revealed that TPX2 is a potential prognostic biomarker and closely correlated with immune infiltration in BRCA, which could provide powerful and efficient strategies for breast cancer immunotherapy.", "claims": [{"id": "claim-method", "statement": "The Kaplan-Meier method with the log-rank test was employed for analyzing the survival endpoint of these genes in the study. Multivariate and univariate Cox regression analyses including specific indicators, age, pathological stage, TNM stage, TPX2 expression, were performed in the study, and the nomogram analysis was depicted via “RMS” package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38643462", "locator": "sections[5] \"Identification of prognosis-related DEGs and survival analysis\" paragraph 2", "quote": "The Kaplan-Meier method with the log-rank test was employed for analyzing the survival endpoint of these genes in the study. Multivariate and univariate Cox regression analyses including specific indicators, age, pathological stage, TNM stage, TPX2 expression, were performed in the study, and the nomogram analysis was depicted via “RMS” package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used in this study are available from the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38643462", "locator": "sections[14] \"Availability of data and material\" paragraph 2", "quote": "The data used in this study are available from the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "These results revealed that TPX2 is a potential prognostic biomarker and closely correlated with immune infiltration in BRCA, which could provide powerful and efficient strategies for breast cancer immunotherapy.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38643462", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "These results revealed that TPX2 is a potential prognostic biomarker and closely correlated with immune infiltration in BRCA, which could provide powerful and efficient strategies for breast cancer immunotherapy."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "These results revealed that TPX2 is a potential prognostic biomarker and closely correlated with immune infiltration in BRCA, which could provide powerful and efficient strategies for breast cancer immunotherapy.", "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:38643462"], "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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