MicroRNA Expression Profiling by Bead Array Technology in Human Tumor Cell Lines Treated with Interferon-Alpha-2a

The gene expression patterns of tumor-derived cell lines differ greatly, as do their responses to antiproliferative effects of interferons (IFNs). The cause of this variation has been under investigation for more than 40 years, but only basic regulatory mechanisms of interferon signaling are understood today. Small regulatory genome encoded RNAs, such as microRNAs, have recently attracted attention in genomic research. New methods to analyze the levels of these regulatory elements are now commercially available, but the power of these techniques is still discussed extensively. Our study was designed to compare two methods for microRNA detection with respect to usefulness in defined cell culture assays. The experimental design assesses variation between the two cell lines and the treatment effects of IFNα.

A hallmark of the therapeutic activity of type I interferons is the induction of antiproliferative activity mediated by the upregulation of several hundred response genes with pleiotropic functions (1). These genes can be divided into two major classes based on the kinetic properties of induction (2). Primary response genes (PRGs) are upregulated within 24 h after the cytokine signal and the secondary response genes (SRGs) are induced following day 1 when the activity of the PRGs decays. In contrast to SRGs, all PRGs studied to date contain bona fide interferon response elements in the promoter region, which are required for binding of the interferon-stimulated gene factor 3 (ISGF3) complex and for janus kinase/signal transducer of transcription (JAK/STAT)-pathway-mediated signaling.

Expression of PRGs is turned off by proteins termed suppressors of cytokine signaling (SOCS) (3). As the nomenclature indicates, this class of polypeptides has the capacity to interfere and silence other cytokine-induced signaling cascades (for review see (4)). SOCS1 for instance is part of the early inducible PRG cluster and down modulation occurs together with the other genes before onset of SRG expression. It is believed that feedback inhibition of JAK/STAT signaling by SOCS1 represses transcriptome modulation of IFNα signaling (5). Regulation of SOCS protein translation by interferon-regulated microRNAs (IRmiRs) would enhance the potential of cytokine fine regulation. It has been reported that miR-19 antagonists lead to higher SOCS1 levels and miR-19 mimics can repress SOCS1 reporter constructs, thus obviously supporting the bioinformatic predictions that SOCS1 is a direct target of miR-19 (6). Inhibition of SOCS activity could for instance prolong the duration of cytokine activity, which has obvious clinical implications.

Following the discovery of microRNAs in virtually all higher eukaryotic organisms significant research efforts were initiated to address the function of these catalytic oligonucleotides which are the natural counterparts of synthetic small inhibitory RNAs (siRNAs) used for experimental gene silencing (for review see (7)). MicroRNAs are positive and negative modulators of the expression of entire gene clusters that contain complementary microRNA recognition sequence motifs in the 3′-UTR. Today, prediction of microRNA target genes by homology-based algorithms is still ambiguous (8). The activity of one or several microRNAs could explain suppression of the entire PRG cluster provided that microRNA abundance is regulated by IFNα. Alternatively, microRNA-mediated degradation of transcripts encoding negative