MicroRNA expression profiles in head and neck cancer cell lines

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Abstract

Non-coding RNA molecules such as microRNAs (miRNAs) may play an important role in human carcinogenesis. Their expression has been profiled in many human cancers but there are few published studies in head and neck cancer. In this study, the relative expression of 261 mature miRNA genes was determined in nine head and neck cancer cell lines using an oligonucleotide array platform. Thirty-three miRNAs in the array were found to be highly expressed and 22 showed low levels of expression in all cell lines. Notable was the high expression of miR-21 and miR-205. Expression of several miRNAs was validated using Northern blot analysis. Potential targets of validated miRNAs included tumor suppressor genes, kinesin family member 1B isoform alpha (KIF1B), and hypermethylated in cancer 2 (HIC2), and pleomorphic adenoma gene 1 (PLAG1). This study provides the largest genomewide survey of mature miRNA transcripts in head and neck cancer cell lines.

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Materials and methods

Cell lines and tissue culture. Investigations were carried out on nine mammalian cell lines. Details of the cell lines and their corresponding tissue culture techniques are presented in Table 1.

Detection of specific miRNA genes by RNA analysis. RNA was isolated from cell lines using Trizol (Invitrogen™, USA) as recommended by the manufacturer. Twenty micrograms of total RNA was electrophoresed in a 15% TBE–Urea gel using 1× RNA loading buffer (Ambion, USA). Following electrophoresis the RNA was

Relative expression of miRNA genes between head and neck cancer cell lines

The profiling data represented nine cell lines from four different anatomical head and neck sites. A reference set (Cy5-labelled) composed of oligonucleotides complementary to each miRNA probe on the array slide was used for the comparative analyses. Each array was co-hybridized with the reference set and sample (Cy3-labelled). In principle, the reference set acts as an internal hybridization control for every probe on the array. Expression of each miRNA was then calculated as a Cy3/Cy5 ratio

Acknowledgments

The study was funded by grants from The Sydney Cancer Foundation and The University of Sydney Cancer Fund.

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