miRNA PCR Array and Assay Application Examples

The regulated expression of miRNA adds another layer to an already complex gene regulatory network. One miRNA can regulate multiple mRNA targets, and one target mRNA may be regulated by multiple miRNA sequences. Therefore, the role that any given miRNA sequence plays has yet to be completely defined. Correlating miRNA expression profiles to biological phenotypes adds to our understanding of miRNA-based gene regulation. Analyzing a representative set of sequences with the Genome array discovers novel functional roles for each miRNA. Focused miRNA panels, like those on the Cancer or the Cell Differentiation and Development arrays, screen known miRNA biomarkers for those most important to a model system. The representative results below will illustrate experiments that may be performed with the RT² miRNA PCR Array and Assay System.

Cancer Research: Identifying miRNA Cancer Biomarkers
The RT² Human Cancer miRNA PCR Array identifies potential colon cancer biomarkers. Many of the miRNA sequences are up-regulated in colon cancer.

Small RNA isolated from human colon tumor and matched adjacent normal tissue (Biochain) was characterized with PCR Arrays containing assays specific for 88 cancer-related human miRNA sequences. The fold-differences plotted for each miRNA are calculated from via the ΔΔC_t method and raw data normalized to a panel of housekeeping small nuclear RNA.

Development Research: Identifying Tissue-Specific miRNA Biomarkers
The RT² Human Cell Differentiaion & Development miRNA PCR Array identifies 26 brain- and 20 muscle-specific miRNA.

Small RNA enriched from human brain and muscle tissue total RNA (200 ng, Ambion) were characterized with PCR Arrays containing assays for 88 differentiation-related miRNA sequences. Normalized miRNA sequence expression levels for both tissues are calculated and plotted against each other. Symbols outside the red lines represent miRNA with at least a 2-fold expression difference in the respective tissues.

Signal Transduction Research: Screen the Genome for p53-Responsive miRNA
RT² Human Genome miRNA PCR Array identifies known and novel miRNA sequences responsive to p53 over-expression. The array identifies the well-known p53 targets, mir-34a and mir-34c, as well as a dozen new candidate targets including mir-203, mir-551a, mir-940, mir-614, and others.

PC3 cells were transduced with adenovirus either encoding p53 or containing an empty vector. After 48 h, small RNA was characterized with PCR Arrays containing 376 human miRNA-specific assays. The heat map visualizes the fold-differences in miRNA expression upon p53 over-expression (red, up-regulated miRNA; green, down-regulated miRNA; black, no difference).