Long noncoding RNA EPCART regulates translation through PI3K/AKT/mTOR pathway and PDCD4 in prostate cancer

While hundreds of cancer-associate long noncoding RNAs (lncRNAs) have been discovered, their functional role in cancer cells is still a mystery for the majority of them. Increasing number of lncRNAs are recognized to function in the cytoplasm, including as modulators of translation. Here, we investigated the detailed molecular identity and functional role of EPCART, a lncRNA we previously discovered to be a potential oncogene in AR- and ERG-regulated prostate cancer (PCa) tumors. First, we confirmed EPCART to be a non-peptide-coding lncRNA with in silico methods and validated the transcript structure of EPCART in vitro. Pathway analysis of differentially expressed protein-coding genes in EPCART knockout cells implied EPCART to inhibit translational machinery of PCa cells. While drastic changes in the global translation were not detected in EPCART knockout cells by polysome profiling, EPCART located largely in the cytoplasm and at the sites of translation. With quantitative whole proteome studies on EPCART knockout cells we discovered PDCD4, an inhibitor of protein translation, to be increased by EPCART reduction. Further studies indicated that the inhibitory effect of EPCART on translation was mediated by reduced activation of AKT and inhibition of mTORC1 pathway. Together, our findings identify EPCART as a translation-associated lncRNA that functions via modulation of AKT/mTORC1/PDCD4 pathway in PCa cells. Furthermore, we provide evidence for prognostic potential of PDCD4 in PCa tumors in connection with EPCART. Read counts of RNA-seq data for two EPCART knockout cell clones (del-4 and del-56) and one wild-type clone (WT) created by CRISPR-Cas9 in LNCaP cells. Three biological replicates were sequenced on each clone.