Abstract 3008: PNA based microarray for cancer & stem cell related miRNAs profiling from low total RNA with on-chip labeling

MicroRNAs(miRNAs) are short non-coding RNAs that play a critical role in many important biological processes. MiRNA expression profiling is important to understand the biological mechanisms, develop drugs, and diagnose. However, analyzed method of expression profiling is limited for short base of miRNA. Microarray which is hybridization based technique is the best for detection tool on miRNA characteristic. So, we have developed a PNA-based microarray that is highly sensitive, specific and reproducible to analyze miRNA expression profiles with direct miRNA labeling on chip after hybridization. PNA probes are well known to have stronger binding affinity, specificity to its complementary DNA or RNA strand and stability to biological enzymes. Unlabeled total RNA is hybridized to the PNA-based microarray for 4 hours and then only hybridized miRNA labeling is performed by using enzymatic ligation with pCp-Cy3. Labeling method of only hybridized miRNAs is an important technique for reproducibility and reliable results of microarray. Our data showed very low cross hybridization for miRNAs differing by single nucleotide such as human let7 family and miR-181 family. We used this microarray to determine the profile of microRNAs expressed in the developing cancer cell lines and Tissue. Array results have been validated by subsequent confirmation of miRNA expression using TaqMan qRT-PCR analysis. The results from the TaqMan qRT-PCR and PNA based microarray are shown that the range of correlation were 0.904-0.989. PNA-based microarray platform can detect small amounts of individual miRNAs from TM miRNA can be a powerful tool to analyze miRNA expression profiling in cancer diagnosis and prognosis for high throughput screening with high accuracy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3008.