Abstract 1256: Profiling protein-coding RNA and thousands of large non-coding RNAs from nanogram amounts of total RNA using a single microarray design

Abstract

Abstract Large intergenic non-coding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes, yet determining the function of individual lincRNAs remains challenging. Recently, more than 8,000 human lincRNAs were annotated and cataloged from more than 4 billion RNA-Seq reads across 24 tissues and cell types by scientists at the Broad Institute of MIT and Harvard. Data from this project indicates that lincRNA expression is highly tissue-specific as compared to protein coding gene expression. As researchers continue to investigate the function of lincRNAs, there is a need for tools that can rapidly and accurately measure the expression of the recently annotated lincRNAs along with mRNA expression. We have previously developed and recently updated the content of the human SurePrint G3 microarrays so that they are comprised of all known protein-coding mRNAs and lincRNAs, to enable systematic profiling and simultaneous detection of coding and non-coding gene expression from a single sample. To demonstrate the utility of the new microarray design we used low nanogram amounts RNA from matched tumor and adjacent normal tissues to produce cyanine-labeled cRNA. The labeled cRNA was applied to the microarrays to detect differences in coding and non-coding gene expression profiles. Using the GeneSpring GX software we are able to identify differentially expressed lincRNAs and protein-coding RNAs in the tumor and normal samples in less than two days. Comparisons of probe signals from technical replicate samples demonstrated high reproducibility with wide dynamic ranges and high sensitivity. Data from the microarrays correlates well with whole transcriptome sequencing of the same matched tumor/normal samples. Using this approach we show that lincRNA expression coincides with key genes known to regulate biological processes involved in cancer progression and this work demonstrates how profiling mRNA and lincRNA from matched tumor and adjacent normal samples can enable researchers to further define the role of lincRNAs in gene regulation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1256. doi:1538-7445.AM2012-1256