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. 2011 Feb;116(3):459-66.
doi: 10.1111/j.1471-4159.2010.07126.x. Epub 2010 Dec 22.

Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers

Sharon K Michelhaugh  1 , Leonard Lipovich, Jason Blythe, Hui Jia, Gregory Kapatos, Michael J Bannon
Affiliations

Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers

Sharon K Michelhaugh et al. J Neurochem. 2011 Feb.

Abstract

Although recent data suggest that some long non-coding RNAs (lncRNAs) exert widespread effects on gene expression and organelle formation, lncRNAs as a group constitute a sizable but poorly characterized fraction of the human transcriptome. We investigated whether some human lncRNA sequences were fortuitously represented on commonly used microarrays, then used this annotation to assess lncRNA expression in human brain. A computational and annotation pipeline was developed to identify lncRNA transcripts represented on Affymetrix U133 arrays. A previously published dataset derived from human nucleus accumbens was then examined for potential lncRNA expression. Twenty-three lncRNAs were determined to be represented on U133 arrays. Of these, dataset analysis revealed that five lncRNAs were consistently detected in samples of human nucleus accumbens. Strikingly, the abundance of these lncRNAs was up-regulated in human heroin abusers compared to matched drug-free control subjects, a finding confirmed by quantitative PCR. This study presents a paradigm for examining existing Affymetrix datasets for the detection and potential regulation of lncRNA expression, including changes associated with human disease. The finding that all detected lncRNAs were up-regulated in heroin abusers is consonant with the proposed role of lncRNAs as mediators of widespread changes in gene expression as occur in drug abuse.

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Figures

Figure 1
Figure 1
An overview of the long noncoding RNA computational pipeline developed to analyze Affymetrix U133 datasets.
Figure 2
Figure 2
qRT-PCR validation of four long noncoding RNAs differentially expressed between heroin abusers and matched controls. LncRNA abundances were corrected for actin transcript levels in the same sample and RT reaction. Black bars- control subjects, white bars- heroin subjects. For all four target genes, p<0.05 by paired t-test. AU-arbitrary units.
Figure 3
Figure 3
Significant correlation between lncRNA transcript abundance as seen in Affymetrix microarray data and by qRT-PCR. □-control subjects, ■-heroin subjects. Log2fold change shown is calculated from the ChipInspector group-wise analysis. Microarray data for probes 223940_x_at, 224566_at, 210794_s_at, 227168_at were used for NEAT2, NEAT1, MEG3 and MIAT, respectively. For all correlations, p<0.03.
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