In principle, almost any RNA molecule that possesses at least one MRE accessible to microRNA binding could act as a ceRNA. Therefore, to characterize the ceRNA networks requires the accurate identification of MREs within RNA molecules. Indeed, we speculate that this type of analysis could uncover molecular interactions and gene regulatory networks that have been missed by proteomic and conventional genomic methods. In this framework, aberrant expression of coding and non-coding genes should be systematically studied in the context of human disease.
Pseudogenes are a compelling example of ceRNA because they likely posses many (if not all) of the same MREs that are harbored on their ancestral genes and thus can act as “perfect sponges.” However, the ability of pseudogenes to regulate the biology of a cell may go beyond the modulation of the levels of their ancestral genes. For instance, PTENP1
is biologically active even in a PTEN
null context, as it alters the microRNA network normally regulating PTEN (Poliseno et al., 2010
). Moreover, genes such as OCT4, NPM1
, and many ribosomal protein pseudogenes often have numerous differentially regulated pseudogenes (Balasubramanian et al., 2009
), indicating that, gene-pseudogene networks can become extensive and intricately dynamic.
In the context of cancer, a straightforward implication of our hypothesis is that pseudogenes and lncRNAs should now be systematically studied as potential tumor suppressors and oncogenes through their ceRNA function. Accordingly, the notion of endogenous lncRNA sponges was recently linked to the progression of liver cancer. It was reported that the lncRNA HULC is one of the most upregulated of all genes in hepatocellular carcinoma (Panzitt et al., 2007
). Wang and colleagues identified that CREB (cAMP response element binding protein) is involved in the upregulation of HULC (Wang et al., 2010
). They also demonstrated that HULC RNA inhibits miR-372 activity through a ceRNA function. This in turn leads to derepression of one of its target genes, PRKACB, which can then induce the phosphorylation and activation of CREB. Overall, HULC lncRNA is part of a self-amplifying autoregulatory loop in which it sponges miR-372 to activate CREB, and in turn upregulates its own levels.
Gross genomic losses and amplifications commonly observed in cancer could have potentially dramatic consequences for the ceRNAs contained in those regions. Moreover, under the ceRNA hypothesis, gene loss events should be clearly distinguished from point mutations that abolish protein function but retain full ceRNA function.
If the ceRNA hypothesis proves correct, then one would need to consider the repercussions of knocking out and overexpressing ceRNAs when modeling diseases in mice. For instance, when generating knockout mice, one must consider whether only the transcript or also the protein expression is disrupted. Many experimental techniques normally neglect UTRs and limit functional studies to gene coding regions. For example, when generating transgenic mice, it has been standard to only overexpress coding sequences, but not UTRs. However, binding sites for microRNAs could occur in 3’UTRs, 5’UTRs, and coding regions (Tay et al., 2008
), suggesting that the entire transcript may possess an inherent trans
regulatory function. Thus, by limiting their focus or scope to coding region, many conventional tools and techniques may have been neglecting the full function of the gene.
Chromosomal translocation events and recurrent “readthrough” transcripts are common in cancers. For example, the t(15;17) translocation which generates PML-RARα
fusion transcripts, is often seen in Acute Promyelocytic Leukemia, whereas the or “readthrough” transcript CDK2-RAB5B
is common in melanoma (Berger et al., 2010
; Scaglioni and Pandolfi, 2007
). Such events could be considered “UTR-swaps,” leading to perturbed MRE levels due to misplacement and consequent altered expression of UTRs (). ceRNA
perturbation could also possibly occur as a consequence of somatic genomic rearrangements affecting non-coding regions, which are emerging as hitherto unappreciated events in many cancers (Stephens et al., 2009
Potential pathological alterations of cellular ceRNA
Aberrant alternative splicing events could also introduce new RNA sequences and potentially new MREs into the cell. Because splicing can be perturbed in disease and cancer (Venables et al., 2009
), the associated perturbation of the ceRNA
network may also contribute to pathologies. Similarly the shortening of 3’UTRs as observed in human cancer cells (Mayr and Bartel, 2009
) would not only impact microRNA-dependent mRNA regulation, but on the flipside, could also alter the capacity of a given mRNA transcript to “sponge” or titrate away microRNAs.
All these described events have a single commonality; they represent perturbations in the expression levels of a given transcript (and consequentially MREs), irrespective of whether or not the transcript is translated into a protein. Thus, it will be interesting to determine if elevated or depressed levels of a given transcript could exert oncogenic activities by altering competition for miRNAs.