Identification of key genes in HER2-positive breast cancer with brain metastasis via bioinformatics methods

Brain metastasis (BM) represents one of the most common advanced disease states in breast cancer (BC), especially in human epidermal growth factor receptor 2 (HER2)-positive BC, and is associated with poor survival outcomes.

In this study, in-depth analysis of the microarray data from the GSE43837 dataset with 19 BM samples of HER2-positive BC patients and 19 HER2-positive nonmetastatic primary BC samples was conducted. The differentially expressed genes (DEGs) between BM and primary BC samples were identified and function enrichment analysis of the DEGs was conducted to identify potential biological functions. The hub genes were identified by constructing the protein-protein interaction (PPI) network using STRING and Cytoscape. UALCAN and Kaplan-Meier plotter online tools were used to verify the clinical roles of the hub DEGs in HER2-positive BC with BM (BCBM).

A total of 1,056 DEGs including 767 downregulated and 289 upregulated genes were identified by comparing the microarray data of the HER2-positive BM and primary BC samples. Functional enrichment analysis demonstrated that the DEGs were mainly enriched in pathways related to extracellular matrix (ECM) organization, cell adhesion, and collagen fibril organization. PPI network analysis identified 14 hub genes. Among these, CD44, COL1A2, MMP14, POSTN, and SOX9 were associated with the survival outcomes of HER2-positive patients.

In summary, 5 BM-specific hub genes were identified in the study; those are potential prognostic biomarkers and therapeutic targets for HER2-positive BCBM patients. However, further investigations are necessary to unravel the mechanisms by which these 5 hub genes regulate BM in HER2-positive BC.