Molecular therapy in the microRNA era

The Pharmacogenomics Journal (2007) 7, 297–304 & 2007 Nature Publishing Group All rights reserved 1470-269X/07 $30.00 www.nature.com/tpj REVIEW Molecular therapy in the microRNA era T Wurdinger1,2 and FF Costa1,3 1 Molecular Neurogenetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston/Charlestown, MA, USA; 2Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Boston/Charlestown, MA, USA and 3Cancer Biology and Epigenomics Program, Children’s Memorial Research Center and Northwestern University’s Feinberg School of Medicine, 2300 Children’s Plaza, Chicago, IL, USA Correspondence: Dr FF Costa, Cancer Biology and Epigenomics Program, Children’s Memorial Research Center and Northwestern University’s Feinberg School of Medicine, 2300 Children’s Plaza, Box 220, Chicago, IL, USA. E-mail: or T Wurdinger, E-mail: MicroRNAs (miRNAs) consist of a growing class of non-coding RNAs (ncRNAs) that negatively regulate the expression of genes involved in development, differentiation, proliferation, apoptosis and other important cellular processes. miRNAs are usually 18–25 nt long and are each able to regulate several mRNAs by mechanisms such as incomplete base pairing and Post-Transcriptional Gene Silencing (PTGS). A growing number of reports have shown that aberrant miRNA expression is a common feature of human diseases including cancer, which has sparked interest in targeting these regulators of gene expression as a means of ameliorating these diseases. Here, we review important aspects of miRNA function in normal and pathological states and discuss new modalities of epigenetic intervention strategies that could be used to amend defects in miRNA/mRNA interactions. The Pharmacogenomics Journal (2007) 7, 297–304; doi:10.1038/sj.tpj.6500429; published online 26 December 2006 Keywords: non-coding RNAs; miRNAs; mRNA targets; multigenic diseases; cancer; ’epigenetic’ therapy Introduction Received 10 April 2006; accepted 10 December 2006; published online 26 December 2006 Non-coding RNAs (ncRNAs) are genes that are able to function as RNA transcripts (reviewed in Eddy1 and Costa2). microRNAs (miRNAs) are part of the group of ncRNAs that can block mRNA translation and affect mRNA stability (reviewed in Ambros3 and Kim and Nam4). miRNAs are generally 18–25 nt long and were first described in the early 1990s in the worm Caenorhabditis elegans as regulators of development and differentiation.5,6 Since then, several miRNAs have been identified in animals, plants and viruses. In the human genome, recent estimates point to at least thousands of miRNAs.7 So far, more than 462 different miRNAs have been described in humans.8,9 miRNA genes are usually transcribed by RNA polymerase II into longer transcripts, referred to as primary transcripts or primiRNAs,10 and then processed into pre-miRNAs.11 Several important steps of miRNA biogenesis have been recently identified (reviewed in Bartel12), although the exact mechanisms by which specific miRNAs act still remains largely unclear. One therapeutically relevant concept is that one miRNA can downregulate multiple target proteins by interacting with different target mRNAs (‘one hitmultiple targets’ concept).13 There have been several reports implicating miRNAs in post-transcriptional regulation of proteins with diverse roles, from cell proliferation and differentiation to fat metabolism (reviewed in Filipowicz et al.14). Recently, miRNA deregulated expression has been extensively described in a variety of diseases, especially cancer (reviewed in Hwang and Mendell15). Some lines of evidence have already shown that up or downregulation of miRNAs correlates with many human cancers indicating that miRNAs can function as classical tumor suppressors or oncogenes.15,16 The aim of this article is to review important aspects of miRNA biogenesis and function, and to introduce therapeutic concepts that could be used to ‘correct’ Molecular therapy in the microRNA era T Wurdinger and FF Costa 298 abnormalities in miRNA/mRNA expression associated with disease. We have named this new therapeutic opportunity a new modality of ‘epigenetic therapy’ and it might be applicable to multigenic diseases caused by deregulated expression of miRNAs. miRNAs in normal and pathological states It is already clear that miRNAs can negatively regulate their mRNA targets in two different ways depending on the degree of base pair complementarity. In the first case, miRNAs that bind with perfect – or nearly perfect – complementarity to protein-coding mRNA sequences are able to induce the RNA-mediated interference (RNAi) pathway. mRNA transcripts are then cleaved by endoribonucleases in the RNA Induced-Silencing Complex (RISC), which results in the irreversible degradation of target mRNAs. This mechanism of miRNA-mediated gene silencing is generally found in plants.17 On the other hand, animal miRNAs can use a second mechanism of gene regulation termed translational repression that does not result in the degradation of their mRNA targets.18–20 These miRNAs act by binding imperfectly within the 30 untranslated regions (UTRs) of their mRNA targets with concomitant repression of their translation.18–20 miRNAs that use this mechanism are able to reduce the protein levels of their target genes, but the mRNA levels of these genes are not affected per se.18–20 The degradation pathway and the translational repression pathway both result in Post-Transcriptional Gene Silencing or PTGS. Bioinformatic analysis can be effective in the identification of miRNA/mRNA interactions. Although not always accurate, putative miRNA ‘seeds’ of no more that 7 nt which are conserved between animal miRNAs and the 30 UTRs of their mRNA targets frequently predict miRNA/ mRNA interactions.21,22 Even though a number of questions remain to be answered regarding miRNA biogenesis and function, the decrease in target protein translation is a well established feature of miRNA function. Several reports have implicated miRNAs in important aspects of differentiation and development in a cell type and tissue-specific manner. For example, miRNAs have been recently implicated in orchestrating epithelium differentiation in the formation of layers of skin.23 Additionally, Schratt et al.24 showed that a miRNA named miR-134 is a brain-specific ncRNA that regulates CNS development in mice, contributing to synaptic plasticity, development and maturation. These short RNA molecules are also expressed in specific stages of mammalian embryonic development, being able to control expression of genes implicated in tissue differentiation. For example, two miRNAs have been associated with skeletal muscle gene expression in a small circuitry. Interestingly, miR-1 was found to be able to promote myogenesis by targeting the transcript for histone deacetylase 4 (HDAC4), which represses transcription of muscle genes, and miR-133 was able to enhance myoblast proliferation (...truncated)