Real-time expression profiling of microRNA precursors in human cancer cell lines

Abstract

Our previous study described a real-time PCR method to quantify microRNA (miRNA) precursors using SYBR green detection [T. D. Schmittgen, J. Jiang, Q. Liu and L. Yang (2004) Nucleic Acids Res., 32, e43]. The present study adapted the assay to a 384-well format and expanded it to include primers to 222 human miRNA precursors. TaqMan minor groove binder probes were used to discriminate nearly identical members of the let-7 family of miRNA isoforms. The miRNA precursor expression was profiled in 32 human cell lines from lung, breast, colorectal, hematologic, prostate, pancreatic, and head and neck cancers. Some miRNA precursors were expressed at similar levels in many of the cell lines, while others were differentially expressed. Clustering analysis of the miRNA precursor expression data revealed that most of the cell lines clustered into their respective tissues from which each cell line was ostensibly derived. miRNA precursor expression by PCR paralleled the mature miRNA expression by northern blotting for most of the conditions studied. Our study provides PCR primer sequences to all of the known human miRNA precursors as of December 2004 and provides a database of the miRNA precursor expression in many commonly used human cancer cell lines.

miR-449a targets HDAC-1 and induces growth arrest in prostate cancer

“…Microarray studies have characterized the modulation of miRNA expression in prostate cancer as compared with normal prostate tissue and identified a number of miRNAs that are up-or downregulated in prostate tumors (Jiang et al, 2005;Mattie et al, 2006;Volinia et al, 2006;Gaur et al, 2007;Porkka et al, 2007;Ozen et al, 2008). In all of these studies, miRNA expression profiles were based on the current databases of miRNAs known at the time (Volinia et al, 2006).…”

MicroRNA involvement in mammary gland development and breast cancer

“…Expression of 222 pre-miRNA was studied by real-time PCR in 32 commonly used cell lines, including 5 breast cancer ones (T47D, SKBR3, MDA361, MCF7 and MDA231) [25]. This study revealed that let-7f-1 is increased by 7-fold in the epithelial-derived breast, lung and colorectal cancer cells.…”

“…MicroRNA (miRNA) represent a class of naturally occurring small non-coding RNA molecules (19)(20)(21)(22)(23)(24)(25) nucleotides in length) whose functions are generally unknown, but believed to be important in development. miRNA originate from genes that are transcribed by RNA polymerase II [1].…”

“…We also compared our results with those of the pre-miRNA profiles found in human breast cancer cell lines [25] (Tab. II).…”

mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

“…In general, to further validate the quantity of miRNAs from NGS, one of three methods are typically used, cloned small RNA library technologies [22], northern blot analysis [23], and qPCR [24]. Among these, qPCR is widely used to validate the quantification of gene expression of mRNAs or miRNAs.…”