Figure 3 Supervised hierarchical clustering analysis of miRNA expression. 17 miRNAs expression profile (from SAM result) of 6 samples were clustered using Cluster 3.0. 6 samples were successfully separated into 2 discrete groups. Stem-loop
qRT-PCR for miRNAs Our miRNA microarray detection platform was constructed by CapitalBio, and several previous comparative studies between microarray platforms and analysis procedures had indicated the very high sensitivity, reproducibility, and specificity using their recommended methods [28]. To confirm the microarray findings, we determined the hsa-miR-21 and hsa-miR-16 expression levels by Stem-loop qRT-PCR in all samples. The miRNAs were found to have the same expression levels as seen by microarray analysis (Figure 4). Figure 4 qRT-PCR analysis of miR-21 and miR-16 in three cancer selleck chemical and three normal
tissues. A: The expression level of miR-21 in all samples. B: The expression level of miR-16 in all samples. C: The electrophoresis result of PCR products. U 6 expression was used as a loading control. Discussion Since Sally first established the DMBA-induced oral carcinogenesis model in the cheek pouch of Syrian hamster in 1954, it has become a classic animal model of OSCC [29]. In BMN 673 mw this study, we successfully constructed this animal model of OSCC using tri-weekly applications of a 5% solution of DMBA in acetone onto the cheek pouch of Syrian hamsters over about a 12-week period. For models like the hamster model for OSCC, microarray assay provides a powerful tool for analyzing both miRNA expression patterns and quantitative expression levels, as it profiles thousands of genes simultaneously. This technology is much more efficient than the now outmoded and time-consuming methods used in earlier work, and is becoming the broadest miRNA research tool available [30]. We used a newly designed microarray platform specific for the analysis of the expression of some 924
mammalian miRNAs. The platform and assay are similar in many respects to other spotted oligonucleotide microarray designs, but have several important differences in application [24]. First, a modified spotting buffer and an advanced hybridization system were used PAK5 in this study. These measures have both previously shown to result in large improvements in the local signal intensity and global signal Selleckchem EPZ015938 uniformity, as well as in the elimination of the doughnut spots commonly seen on spotted oligonucleotide arrays. These improvements are believed to be due to better blocking of the slide surface chemistry [31]. A detailed assessment of the quality control and reproducibility of this new miRNA microarray platform has been published [32]. Using miRNA microarray analysis, we evaluated miRNA expression profiles of OSCC and normal cheek mucosa tissues, and identified seventeen miRNAs that were up-regulated and down-regulated in cancer tissues compared with normal tissues.