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Global miRNA and pre-miRNA expression profiling of the NCI-60 cancer cell lines using novel LNA enhanced microarrays

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Abstract:

The aberrant expression of microRNAs (miRNAs) in tumor tissue suggests that these small ∼22-nucleotide molecules play a role in the initiation and progression of cancer, and therefore, may comprise a novel class of diagnostic and prognostic signatures.

Here, we are studying the global expression profiles of miRNAs end their precursors in the NCI-60 cancer cell lines in order to identify both cell-type specific patterns as well as signatures for prediction of drug sensitivity. In the current study, an experimental microarray platform was used, which takes advantage of the locked nucleic acid (LNA) technology to provide specific and sensitive probes for mature miRNAs, pre-miRNAs as well as novel miRNAs identified by high-throughput pyrosequencing.

In our data analysis, we applied various methods for background correction, normalization and quality assessment. The normalized, quality-checked expression data were then used to:

1) determine the miRNA expression pattern shared between the NCI-60 cell lines by means of bootstrapping aided, hierarchical clustering,

2) identify differentially expressed miRNAs, specific for various NCI-60 cell lines and tissue types,

3) discover possible predictive biomarkers based on the correlation between miRNA expression and the drug resistance profiles of the NCI-60 cell lines.

Document Type: Abstract

DOI: http://dx.doi.org/10.1111/j.1600-0463.2008.001165_37.x

Affiliations: 1: Exiqon A/S, Bygstubben 16, DK-2950 Vedbæk, Denmark 2: University of Copenhagen, Department of Basic Animal and Veterinary Sciences, Grønnegårdsvej 3, 1870 Frederiksberg C

Publication date: May 1, 2008

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