Identification of Altered Transcripts and Pathways in Triple Negative Breast Cancer

Abstract Triple negative breast cancer (TNBC) is a breast cancer subtype characterised by lack of oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor, and by worse prognosis than other cancer types. The aim of this study was to identify hub genes and molecular pathways for possible prognostic markers for TNBC. Nineteen breast cancer transcriptomes were sequenced using Illumina platform and analysed to identify differentially expressed genes in the TNBC subtype. Gene ontology enrichment analysis was conducted using the ToppGene tool. Then, the STRING online database was used for protein-protein interaction (PPI) network construction. Cytohubba and the MCODE plug-in were used to screen functional modules and hub genes. In total, 229 DEGs were identified by differential gene expression analysis in the TNBC group. Eight genes were screened out from the PPI network — FOXA1, ESR1, TFF1, GATA3, TFF3, AR, SLC39A6, COL9A1. In conclusion, this study indicates that the molecular subtype specific gene expression pattern provides useful information for targeted, biomarker-driven treatment options.