Splice Variants In Aggressive Human Breast Cancer Subtypes

Alternative splicing happens in all types of cells including benign or normal cells. However, the expression levels of the non-canonical variants in the normal cells are low that there is no notable effect by them. Studies have shown that altered cellular mechanisms in tumor cells can affect the transcription and splicing processes. If a variant is able to fold into a stable structure similar to that of the canonical variant, it may mimic the structural features and interact with interaction partners without processing them further. Thus, alternative splicing could provide a mechanism for turning an activator into an effective inhibitor. Moreover, the ratio of the expression of the splice isoforms plays a significant role in the normal functioning of a biological system. We hypothesize that due to the altered mechanisms in tumor environment, some non-canonical variants are expressed at higher levels that they have distinct functions compared to their corresponding canonical proteins or may even be drivers of certain pathological processes. In this study, we propose to analyze the alternative splice variants that are expressed in ERBB2+ (ERBB2+, ER-, PR-) subtypes of breast cancer. ERBB2+ subtypes are known to be aggressive with poor prognosis and account for 15-20% of breast cancers in US. Breast cancer cell lines have been used widely to investigate breast cancer mechanisms and to develop new therapeutic approaches. SKBR3, which is ER –, PR - with ERBB2/HER2 amplification has been used successfully as a preclinical model to screen for therapeutic agents targeting ERBB2 and to delineate mechanisms of resistance to ERBB2-based therapies. SUM190 and SUM149 serve as models for inflammatory breast cancer, the most lethal form of breast cancer. Both these cell lines are ER –, PR – and clinically very aggressive, but ERBB2 is amplified in SUM190 and expressed at low levels in SUM149. The contrasting ERBB2 expression observed in the similar clinical IBC phenotype represented by SUM149 and SUM190 and over-expression of ERBB2 in SKBR3, representing a non IBC epithelial adenocarcinoma tumor type, makes this group of cell lines ideal for the comparisons that we set out to produce. By integrating the proteomics and RNA-Seq data from SKBR3, SUM190 and SUM149, we studied the splice variants that are expressed in the Her2+ breast cancer subtypes. We identified more than one splice variant for 1904 genes expressed in at least one of the three cancer cell lines. Multiple variants of genes that are key players in the downstream ERBB signaling pathways along with variants specific to one cancer cell line compared to the other two cancer cell lines and normal mammary cells were found. The top-ranking Gene Ontology and BioCarta pathways for these specific variants pointed to distinct mechanisms; aminoglycan metabolism for SKBR3, lipid biosynthesis and metabolism in SUM190 and cell adhesion in SUM149. The transcript profiles for mRNA splicing mechanism show similarities between the inflammatory models SUM190 and SUM149, which was further supported by the identification of a novel peptide from the intronic region of 17-beta dehydrogenase 4 from both of these cell lines. The overall transcript profile and some key ERBB downstream pathways show a more robust clustering between SKBR3 and SUM190. Detailed experimental studies on the distinct variants identified from each of these three breast cancer cell lines may unveil their roles in the underlying cancer progression and metastasis. Citation Format: Rajasree Menon, Hogune Im, Michael Snyder, Emma (Yue) Zhang, Rui Chen, Shiaw-Lin Wu, William S. Hancock, Gilbert S. Omenn. Splice variants in aggressive human breast cancer subtypes. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr B38.