Abstract 1842: Identifying long noncoding RNAs in breast cancer microarrays.

Abstract Long noncoding RNAs (lncRNA) are powerful regulators of gene expression. The emerging role of long noncoding RNAs (lncRNA) is facilitated by the development of new technologies such as tilling array and next generation sequencing. In this study, our research focused on lncRNA's regulatory mechanisms in breast cancer. Methods: The Gencode v7 lncRNA and FANTOM5 lncRNA datasets were integrated as our lncRNA transcriptome. The expression profile was from four publications of microarray analysis in breast cancer. First, we checked the Affymetrix probe dataset U133 plus with our lncRNA transcriptome. If a probe was on the same strand and 100% fell into the exonic region of one lncRNA transcript, then the probe could this lncRNA. We integrated all lncRNAs from our transcriptome which matched the probes from the supplementary data of four papers and selected those occurred more than once. Results: There were 23 nonredundant lncRNA candidates identified. Among those 23 candidates, PTENP1 was identified. PTENP1 is the pseudogene of tumor suppressor gene PTEN. The 3’UTR can bind the same miRNAs as the related protein-coding gene, PTEN. This suggests that pseudogenes may have a biological function as ‘decoys’, sequestering miRNAs and thereby affecting their regulation of expressed genes. Another candidate identified was ENST00000415285.1, which is the antisense gene of FGF14. FGF14 is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including tumor growth and invasion. ENST00000415285.1 is up-regulated in breast cancer, while the expression level of FGF14 is unknown, so further research is necessary to predict the possible mechanism of regulation to FGF14. Conclusion: LncRNAs are identified in datasets for breast cancer that may elucidate further regulatory mechanisms driving the pathogenesis of breast cancer. Citation Format: Hui Jia, Leonard Lipovich, Donghong Ju, Mary A. Kosir. Identifying long noncoding RNAs in breast cancer microarrays. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1842. doi:10.1158/1538-7445.AM2013-1842