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Identification of key genes related to bone metastasis of breast cancer using bioinformatics methods and construction of a prognostic model.

Zheng Fu·Li Zhu·Chongyong Guo·Hongjian Yu·Jingtian Li·Mingming Wang·Bin Zhao
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Abstract

Breast cancer (BC) ranks among the most prevalent cancers in females, with bone metastasis significantly compromising patients' quality of life and survival rates. Enhancing our comprehension of BC bone metastasis mechanisms at the molecular level holds promise for improving BC treatment and prognosis. Leveraging bioinformatics tools, we integrated multiple datasets, conducted comprehensive analyses across various databases, identified biomarkers associated with BC bone metastasis, and constructed a prognostic model. Firstly, 3 BC bone metastasis-related datasets were downloaded from gene expression omnibus, the data were merged, and batch effects were removed, followed by identification of differentially expressed genes (DEGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DEGs. A protein-protein interaction network was constructed using the STRING database to screen hub genes. Then, survival analysis of hub genes was performed using the Cancer Genome Atlas (TCGA) database. A prognostic model was constructed using key genes with survival differences, and the model was evaluated. Two hundred ninety-two DEGs were identified. Gene ontology and KEGG pathway enrichment analysis yielded 769 biological processes (BPs), 78 cellular components, 43 molecular functions, and 50 KEGG pathways. Fifteen hub genes were selected from the protein-protein interaction network. Survival analysis revealed 6 genes related to BC survival. The prognostic model identified 4 genes with important predictive value for BC prognosis. Our study utilized bioinformatics analysis to identify a series of DEGs related to BC bone metastasis. Based on further selection of hub genes, we constructed a relatively ideal prognostic model for BC, and identified 4 genes (DLGAP5, TPX2, PLK1, and CENPN) with valuable predictive value for BC prognosis.

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HumansBreast NeoplasmsBone NeoplasmsFemaleComputational BiologyPrognosisProtein Interaction MapsBiomarkers, TumorGene OntologyGene Expression Regulation, NeoplasticGene Expression ProfilingDatabases, GeneticSurvival AnalysisGO and KEGG pathway enrichment analysisPPI networkbioinformaticsbreast cancer bone metastasisdifferential analysisprognostic modelsurvival analysisJournal Article

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Zheng Fu, Li Zhu, Chongyong Guo, Hongjian Yu, Jingtian Li, Mingming Wang, Bin Zhao. 2025-10-17. Identification of key genes related to bone metastasis of breast cancer using bioinformatics methods and construction of a prognostic model.. https://doi.org/10.1097/md.0000000000045273

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