In recent years we have witnessed a paradigm shift concerning the long-lasting controversy over “junk DNA” in the human genome. It is now well established that, besides the roughly 25 000 protein-coding genes, the genome contains tens of thousands of functional elements. In addition, the completion of the ENCODE project—the functional annotation of all regulatory regions of the human genome—has confirmed that 80% of genome is transcribed into RNA, whereas <than 2% is translated into proteins. Thus, an as yet unknown number of transcripts lacking significant coding potential, including long noncoding RNAs (lncRNAs), exceed the number of protein-coding genes . However, the expression, regulation, sequence, function, and mechanism of action of the vast majority of lncRNAs are currently largely unknown.
For the few lncRNAs that are characterized at the functional level, evidence is accumulating that they play important roles in malignant diseases: All hallmarks of cancer that define the malignant phenotype of tumor cells are controlled by one or another lncRNA : LncRNAs contribute toward sustaining proliferative signaling, evading growth suppression, resisting apoptosis, enabling replicative immortality, activating invasion and metastasis, and inducing angiogenesis in a large variety of tumor entities. The lncRNA HOX transcript antisense RNA (HOTAIR), for example, promotes breast cancer metastasis by binding to polycomb repressive complex 2 (PRC2), thereby inhibiting gene expression . The lncRNA X inactive specific transcript (XIST) is a central player in X chromosome inactivation during embryonal development but also acts as a tumor suppressor in myeloproliferative neoplasms . The lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is a key factor in metastasis formation in lung cancer and is a potential therapeutic target .
XIST, HOTAIR and MALAT1, and potentially many other lncRNAs, share similar mechanisms in the epigenetic control of transcription in cis or in trans. They can bind directly to RNA or DNA, provide scaffolds for multimodular complexes controlling gene transcription, or exert guide functions to target proteins to specific genomic locations . LncRNAs have been also implicated in post-transcriptional gene regulation. They can act as so-called microRNA (miRNA) sponges or competing endogenous RNAs (ceRNAs) and bind to and sequester miRNAs and thereby indirectly induce miRNA target genes. Phosphatase and tensin homolog (PTEN) pseudogene 1, for example, can serve as a decoy for regulatory miRNAs targeting the tumor suppressor gene PTEN . However, the elucidation of miRNA decoy mechanisms critically depends on the quantitative characterization of miRNA and target site copy numbers in a given cell to ensure that the miRNA sponge or ceRNA can quantitatively affect the miRNA activity rather than act via independent mechanisms.
Beyond these two better characterized mechanisms of action—epigenetic gene regulation and miRNA decoy functions—many more mechanisms of nuclear and cytoplasmic lncRNAs and ribonucleoprotein complexes remain enigmatic and still await their discovery.
In this issue of European Urology, Martens-Uzunova and colleagues provide a comprehensive overview of the regulation and function of lncRNAs in urologic tumors. A well-known example of a lncRNA in prostate cancer is prostate cancer antigen 3 (PCA3; also known as DD3), which is overexpressed and is already available as a diagnostic test in urine. However, numerous additional lncRNAs highlighted in this review suggest that the impact of lncRNAs in tumors of the prostate, kidney, and bladder is beginning to be unveiled.
Novel technologies drive new discoveries, and next-generation sequencing has greatly accelerated the pace at which genetic elements are being discovered at the genomic level. Consequently, a comprehensive catalog of >120 novel potential lncRNAs in prostate cancer has been published and given rise to the detailed characterization of the prostate cancer associated transcript 1 (PCAT1) tumor suppressor lncRNA, which is transcriptionally repressed through the PRC2 complex. In addition, the SWI/SNF complex antagonist associated with prostate cancer 1 (SCHLAP1) transcript influences the regulatory function of the SWI/SNF chromatin-modifying complex, which is another example of a lncRNA involved in epigenetic processes. More important, both PCAT1 and SCHLAP1 are associated with prostate cancer progression: Given the notorious lack of prognostic molecular markers in prostate cancer, the analysis of the marker potential of the plethora of uncharacterized lncRNAs is urgently needed. In this respect, the present review is an important compendium and summary of the current knowledge and a timely plea for further efforts in this relatively new area of cancer research.
Another important aspect concerns the translational potential of noncoding RNAs (ncRNAs): Some of these molecules, especially the short ncRNAs, are likely protected from degradation in the extracellular space. PCA3 and miRNAs, for example, are stably detectable in body fluids of prostate cancer patients. Hence, the search should be intensified to find as yet uncharacterized stable lncRNAs in blood or urine, which potentially could be molecular biomarkers for early detection, diagnosis, or prognosis of urologic tumors. These clinical samples can be obtained with minimally invasive procedures, and the quantification of nucleic acids from such liquid biopsies is easily feasible with polymerase chain reaction or sequencing technologies. However, prior to a routine application of such markers, it will be essential to investigate their roles in tumor development and progression, to clarify the mechanisms of their release (freely, bound to proteins, or contained in microvesicles), and to understand their dynamic changes over time.
In summary, the discovery of the ncRNA world has initiated an ongoing revolution of our view of the molecular mechanisms underlying urologic carcinogenesis, and now those mechanisms need to be translated as biomarkers or therapeutic targets into a clinical benefit for the patient.
- Sültmann H, Diederichs S. (2014) Long Noncoding RNA: “LNCs” to Cancer. Eur Urol [Epub ahead of print]. [abstract]