Use of gene expression and alternative splicing signatures to discriminate breast cancer stem cells from fibroblasts.

1057 Background: Tumors frequently contain cancer stem cells (CSCs) or tumor-initiating subpopulations, with an ability to self-renew and regenerate all cell types within the tumor. Basal-like breast cancers exhibit features of CSCs, including expression of surface markers, even though these cells are rare. Given the role of CSCs in the recurrence and spread of cancer, there is an urgent need to develop new therapeutic agents that target CSCs. Development of CSC-targeted drugs will be greatly facilitated by biomarkers that can identify CSCs to aid in patient selection and determination of drug response. Defining the CSCs in tumors is complicated by the high mesenchymal nature of fibroblasts. Analysis of gene expression and alternative splicing patterns in CSCs that are not observed in fibroblasts may provide valuable new CSC-specific markers. Methods: Alternative splicing and gene expression microarray strategies were used to identify selected exons and differentially expressed genes between 10 Basal human breast cancer cell lines and a combination of 12 Luminal and 3 fibroblast cell lines. Q-PCR analysis was conducted to determine candidate CSC gene differential expression between Basal, Luminal, and Fibroblast cells lines. Results: Expression levels of 11 genes were higher and 24 genes were lower in the Basal cell lines versus Luminal or fibroblastic cell lines. Comparison of Basal cell lines to the Luminal/Fibroblast cell lines identified 36 cassette exons that were included, and 26 that were excluded in Basal cell lines. Also, 19 genes were upregulated in Basal cell lines compared to the other groups as detected by Q-PCR. Interestingly, the 19-multigene model defined the Triple Negative Breast Cancer patients that were Likely to Recur under standard chemotherapy with a p = 1.90e-03 and AUC 0.723. Conclusions: Gene and exon marker sets distinguish CSC versus fibroblasts and may be instructive in identifying patients that recur early in Triple Negative Breast Cancer. The CSC-associated RNA signatures identified here will be further refined to develop new CSC-specific diagnostic markers to stratify breast cancer patients and monitor response to novel CSC-targeted therapies.