Abstract A19: Profiling long noncoding RNA expression in cancer cells by real-time PCR arrays

Abstract

Abstract Long noncoding RNAs (lncRNAs), as a new class of transcripts, have been recently shown to be pervasively transcribed in the genomes of human and mouse. In particular, accumulating evidence link the expression of lncRNAs to diverse human diseases, highlighting their potential as biomarkers and therapeutic targets. However, there are still many missing dots in our current understanding of lncRNA function. Thus, investigation of the expression patterns of lncRNAs is a crucial step to understanding of their roles in many model systems. To this end, we developed a qPCR based disease-related human lncRNA profiler, which allows for the quantification of differential expression of 83 individual lncRNAs among various experimental RNA samples. All 83 lncRNAs chosen for the array are based on publications and they are implicated in diseases ranging from neurodegeneration to cancer. The array plate also includes the house keeping genes and small RNA transcripts for normalization purposes. To determine the utility of this lncRNA profiler, we profiled their expression in breast cancer specimens compared to matched normal tissue and identified several lncRNAs are dysregulated, suggesting that lncRNAs may function as oncogenes or tumor suppressors. Gene expression profiling with this lncRNA profiler in a series of breast cell lines such as MCF10A, MCF7 and MDA-MB-231 cells identified differential expression patterns unique to each cell line, which may provide a basis for future analysis of these differentially expressed lncRNAs. Furthermore, we determined the effect of p53 on lncRNA expression in HCT-116 and MCF-7 cells. Initial testing indicated that at least three lncRNAs are induced by p53 in both cell lines. Experiments are underway to further characterize these p53 inducible lncRNAs. Together, these results suggest that disease-related human lncRNA profiler is a valuable research tool that can be tailored for specific needs in different research laboratories. The features of this profiler are easy, convenient, sensitive and specific. Accordingly it serves the first step toward the understanding of the role of lncRNAs in human diseases. Citation Format: Fangting Wu, Yin-Yuan Mo. Profiling long noncoding RNA expression in cancer cells by real-time PCR arrays [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A19.