RNA-seq analysis of breast cancer

Background: We searched triple negative breast cancer (TNBC) specifically expressing candidates for target therapy. Methods: High expressing genes in three TNBC cell lines compared to three non-TNBC cell lines were evaluated by using RNA sequencing (log2 ratio>5, q<0.05). By integrating the shRNA library screening and public gene expression databases, we identifyied candidates for therapeutic targets. The expression significance of the candidates was examined by using immunohistochemistry of 248 clinical breast cancer patients. Results: One hundred seventy one genes were detected as highly expressed genes in TNBC cell lines than non-TNBC cell lines, and 13 genes were picked up as candidates not expressing in non-cancerous tissues. Integrated analysis with shRNA screening identified three candidates as TBNC specific molecular targets. Protein staining were stronger in breast cancer tissues, especially TNBC, than in the normal tissues. Overall design: Gene expression profiles of 6 breast cancer cell lines were generated by RNA-seq using Illumina NextSeq 500 system.