Abstract 4236: Evaluating alterations in mRNA biogenesis with TCGA breast cancer sequencing data

Abstract

Abstract Alternative splicing leads to the production of multiple mRNA isoforms of a gene transcript with distinct functional characteristics. These events are frequently observed in rapidly dividing cancer cells and are broadly recognized as important signatures for oncogenesis pathways and treatment options. In this study, we utilized data from The Cancer Genome Atlas (TCGA) to identify differences in isoform expression between estrogen receptor-positive and estrogen receptor-negative breast cancer cell lines. RNA sequencing analysis combined with clinical annotation data revealed alterations in isoform expression that were associated with patient survival. These global changes in isoform expression occurred independently of total gene expression in both estrogen receptor-positive and -negative breast cancer. Furthermore, we identified multiple underrepresented isoforms including CDKAL1 and CSTF3 that were associated with favorable prognostic outcomes despite a lack of association observed with their traditional transcripts. These data suggest an underlying role mediated by alternative spliced isoforms in driving clinical outcome in breast cancer, warranting further investigation in delineating isoform expression profiles in previously established cancer pathways. Citation Format: Thomas J. Yan, Matthew E. Burow, Elizabeth C. Martin. Evaluating alterations in mRNA biogenesis with TCGA breast cancer sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4236.