Abstract 150: Long non-coding RNA are differentially expressed in breast cancer clinical subtypes

Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA A primary benefit of RNA-Seq over traditional DNA microarrays is the ability to interrogate expression in unannotated areas of the transcriptome. Methods for identifying novel genes in genomic DNA sequence can use features such as an open reading frame and conserved functional protein elements. Non-coding RNA structures are more difficult to detect, and most of our knowledge of them comes from expressed sequence tags (ESTs), which are large, sequenced contigs from transcriptome cDNA libraries. Carninci et al. showed that over half of these sequences appear to originate from non-coding sources, though very few are annotated. Moreover, many of these non-coding sources are poorly conserved over multiple species indicating that these transcripts may not be functional, but instead, may be the result of “random” transcription. As more studies focus on these “non-coding” regions of the genome evidence of conservation and functionality is emerging. To identifying possibly functional transcripts, we took the approach of identifying only non-coding transcripts which were differentially expressed between breast cancer tumor subtypes, and tumor versus non-tumor samples by RNAseq analysis. We reason that such ncRNA transcription is more likely to be functional because of its association with a specific disease phenotype and the possibility that they affect some regulatory pathway. We have identified known long-non coding tumor suppressors, such as H19 and MEG3, as expressed exclusively in non-tumor samples. In addition we have identified 59 intergenic regions representing a total of 132 300 bp which were differentially expressed between ER+/HER2- and ER-/HER2- breast tumor subtypes. This resulted in 4 potential non-coding regions associated with ER-/HER2- tumors, and 6 potential non-coding regions associated with ER+/HER2- tumors. These transcripts are of great interest, and should be studied in more detail to elucidate the function of these non-coding RNA molecules. Citation Format: Surendra Kumar, Michael Seiler, Sunniva Bjorklund, Anne-Lise Borresen-Dale, Vessela Kristensen, Gyan Bhanot, Shridar Ganesan. Long non-coding RNA are differentially expressed in breast cancer clinical subtypes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 150. doi:10.1158/1538-7445.AM2015-150