Epigenetics and genetics. MicroRNAs en route to the clinic: progress in validating and targeting microRNAs for cancer therapy

Abstract

In normal cells multiple microRNAs (miRNAs) converge to maintain a proper balance of various processes, including proliferation, differentiation and cell death. miRNA dysregulation can have profound cellular consequences, especially because individual miRNAs can bind to and regulate multiple mRNAs. In cancer, the loss of tumour-suppressive miRNAs enhances the expression of target oncogenes, whereas increased expression of oncogenic miRNAs (known as oncomirs) can repress target tumour suppressor genes. This realization has resulted in a quest to understand the pathways that are regulated by these miRNAs using in vivo model systems, and to comprehend the feasibility of targeting oncogenic miRNAs and restoring tumour-suppressive miRNAs for cancer therapy. Here we discuss progress in using mouse models to understand the roles of miRNAs in cancer and the potential for manipulating miRNAs for cancer therapy as these molecules make their way towards clinical trials.

Figure 1. Opposing roles of miRNAs in cancer

a | Oncogenic (shown in green) versus tumour-suppressive (shown in red) functions of miR-146 can be explained based on upstream nuclear factor κB (NF-κB) signals. In cells that are dependent on interleukin 1 receptor-associated kinase 1 (IRAK1) and TNF receptor-associated factor 6 (TRAF6) for NF-κB signalling, miR-146 expression prevents NF-κB activation, resulting in a tumour-suppressive phenotype. However, if an alternative mechanism for NF-κB activation is present (other than through IRAK1 and TRAF6), activated NF-κB would transactivate miR-146. In addition to targeting IRAK1 and TRAF6, miR-146 also targets BRCA1, thus preventing the pro-apoptotic effects of BRCA1 and resulting in a pro-survival response. b | Tumour-suppressive miR-29a targets multiple oncogenes, such as cyclin-dependent kinase 6 (CDK6), DNA (cytosine-5)-methyltransferase 3A (DNMT3A), DNMT3B, myeloid cell leukaemia sequence 1 (MCL1) and T-cell leukaemia/lymphoma 1A (TCL1A). Targeting inhibits growth and proliferation and, in the case of B cell chronic lymphocytic leukaemia (B-CLL), aggressive disease. Oncogenic miR-29a prevents cell adhesion through repressing peroxidasin homologue (PXDN). 7mG, 7-methylguanine; miRNA, microRNA.

Figure 2. RNAs are subject to genomic, transcriptional and post-transcriptional modes of regulation

a | Allelic amplification (which is typical of oncogenic microRNAs (miRNAs)) results in decreased expression of target genes, including those targets with less miRNA affinity that may not normally be repressed. b | Genomic deletion (which is typical of tumour-suppressive miRNAs) enhances target gene expression. c | Single nucleotide polymorphisms (SNPs) in the miRNA can either create or destroy miRNA binding sites (BOX 1). This alteration in the miRNA changes the ability of the miRNA to bind to and repress target genes. In cancer, SNPs can alter the miRNA such that it now targets tumour-suppressive genes while losing its ability to target oncogenes. d | At the transcriptional level, cis-acting changes to the promoter, including epigenetic regulation (such as promoter methylation, which is depicted by the blue circles) or genomic mutation (which is depicted as ‘×’) and the availability of trans-acting factors change the expression profile of miRNAs in a cell. Finally, miRNA processing defects can change the population of mature miRNAs in a cell. These processing steps include: primary miRNA (pri-miRNA) to precursor miRNA (pre-miRNA) cleavage by the DROSHA–DGCR8 complex; nuclear export by the RAN GTPase and exportin 5; a final cleavage event by DICER; and loading of the mature miRNA into the RNA-induced silencing complex (RISC). 7mG, 7-methylguanine; ORF, open reading frame.

Figure 3. RNA expression patterns dictate miRNA repressibility in cells

a | Alternative polyadenylation signals give an mRNA transcript the ability to evade regulation by microRNAs (miRNAs). Longer 3′ untranslated regions (UTRs) usually contain more miRNA binding sites and are therefore more sensitive to repression by miRNAs. b | An increased abundance of additional target genes can ’soak-up’ the miRNA pools, leading to target gene derepression. c | Mutations in the target gene can create or destroy miRNA binding sites. 7mG, 7-methylguanine; ORF, open reading frame.

Figure 4. miRNAs that contribute to metastasis

Metastasis occurs through a series of stages: local invasion, intravasation, extravasation and colonization (as indicated by the blue boxes). Protein-coding genes and microRNAs (miRNAs) that promote (shown in green) or prevent (shown in red) metastasis are involved at each step (the figure covers only those pathways that are discussed in the main text). miR-200 directly represses the expression of the mesenchymal markers zinc finger E-box-binding homeobox 1 (ZEB1) and ZEB2 in quiescent cells. As such, during the epithelial to mesenchymal transition (EMT) when miR-200 levels are reduced, the expression of ZEB1 and ZEB2 becomes elevated. ZEB1 and ZEB2 transcriptionally repress E-cadherin, a cell adhesion molecule that is lost in aggressive and metastatic tumours; thus, cells missing miR-200 are more able to disseminate and invade surrounding tissue. Furthermore, the inhibition between miR-200, and ZEB1 and ZEB2 is mutual, leading to a potentially bistable system: either high miR-200 and low ZEB1 and ZEB2 levels, or high ZEB1 and ZEB2 and low miR-200 levels. This latter state would seem to be particularly dangerous and could lead to aggressive tumours. Based on its miRNA-processing ability, DICER is positioned upstream of miR-200. DICER1 itself is positively regulated at the transcriptional level by the full-length isoform of p63 (TAp63), and is negatively regulated by miR-103, miR-107 and let-7. In addition to suppressing DICER expression, let-7 also inhibits the oncogenic RAS–RAF–MEK pathway and HMGA2, an upstream activator of SNAIL. SNAIL inhibits E-cadherin, leading to local invasion and intravasation. Antimetastatic miRNAs that are involved outside of the E-cadherin pathway include miR-10b, which suppresses the expression of HOXD10; miR-335, which impairs SOX4 and tenascin C (TNC) signalling; and miR-31, which prevents all steps of metastasis through inhibiting the expression of integrin-α5, radixin (RDX) and RHOA. RKIP, RAF kinase inhibitory protein.