Layer by layer

By Nicola McCarthy

The view that cancer is purely a genetic disease has taken a battering over recent years, perhaps most extensively from the recent discovery that between transcription and translation sits a whole host of regulatory RNAs, chiefly in the guise of microRNAs (miRNAs). Now, we can add yet another layer of regulation: the evidence from three papers that protein-coding and non-coding RNAs influence the interaction of miRNAs with their target RNAs.

Pier Paolo Pandolfi and colleagues had previously suggested that the miRNA response element (MRE) in the 3′ untranslated region (UTR) of RNAs could be used to decipher a network of RNAs that are bound by a common set of miRNAs. RNAs within this network would function as competing endogenous RNAs (ceRNAs) that can regulate one another by competing for specific miRNAs. Using an integrated computer analysis and an experimental validation process that they termed mutually targeted MRE enrichment (MuTaME), Tay et al., identified a set of PTEN ceRNAs in prostate cancer and glioblastoma samples. As predicted, some of these ceRNAs are regulated by the same set of miRNAs that regulate PTEN and have similar expression profiles to PTEN. For example, knockdown of the ceRNAs VAPA or CNOT6L using small interfering RNAs (siRNAs) resulted in reduced expression levels of PTEN and conversely, expression of the ceRNA 3′ UTRs to which the miRNAs bind resulted in an increase in expression of PTEN 3′ UTR–luciferase constructs. Importantly, the link between PTEN, VAPA and
CNOT6 was lost in cells that had defective miRNA processing, indicating that miRNAs are crucial for these effects.

Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Andrea Califano and colleagues investigated the mRNA and miRNA network in glioblastoma cells. They found a surprisingly large post-translational regulatory network, involving some 7,000 RNAs that can function as miRNA sponges and 148 genes that affect miRNA–RNA interactions through non-sponge effects. In tumours that have an intact or heterozygously deleted PTEN locus, expression levels of the protein vary substantially, indicating that other modulators of expression are at work. Analysis of 13 genes that are frequently deleted in patients with glioma and that encode miRNA sponges that compete with PTEN in the RNA network showed that a change in their mRNA expression had a significant effect on the level of PTEN mRNA. Specifically, siRNA-mediated silencing of ten of the 13 genes reduced PTEN levels and substantially increased proliferation of glioblastoma cells. Conversely, expression of the PTEN 3′ UTR increased the expression of these 13 miRNA sponges.

These results indicate that reduced expression of a specific set of mRNAs can affect the expression of other RNAs that form part of an miRNA–mRNA network. Moreover, they hint at the subtlety of changes that could be occurring during tumorigenesis, in which a small reduction in the expression level of a few mRNAs could have wide-ranging effects.