Exon-Intron Differential Analysis Reveals the Role of Competing Endogenous RNAs in Post-Transcriptional Regulation of Translation.

Nicolas Munz,Chiara Tarantelli,Natasa Cmiljanovic,Luca Parmigiani,Sara Napoli,Andrea Rinaldi,Vladimir Cmiljanovic,Luciano Cascione,Rosalba Giugno,Francesco Bertoni

doi:10.3390/ncrna7020026

Abstract

Stressful conditions induce the cell to save energy and activate a rescue program modulated by mammalian target of rapamycin (mTOR). Along with transcriptional and translational regulation, the cell relies also on post-transcriptional modulation to quickly adapt the translation of essential proteins. MicroRNAs play an important role in the regulation of protein translation, and their availability is tightly regulated by RNA competing mechanisms often mediated by long noncoding RNAs (lncRNAs). In our paper, we simulated the response to growth adverse condition by bimiralisib, a dual PI3K/mTOR inhibitor, in diffuse large B cell lymphoma cell lines, and we studied post-transcriptional regulation by the differential analysis of exonic and intronic RNA expression. In particular, we observed the upregulation of a lncRNA, lncTNK2-2:1, which correlated with the stabilization of transcripts involved in the regulation of translation and DNA damage after bimiralisib treatment. We identified miR-21-3p as miRNA likely sponged by lncTNK2-2:1, with consequent stabilization of the mRNA of p53, which is a master regulator of cell growth in response to DNA damage.

Highlights

The transcriptome is tightly regulated at different levels: along with the regulation of new transcription, RNA molecules can be modulated at the post-transcriptional level, and noncoding RNAs play a relevant role in this process [1,2]
We have previously reported that dual PIK3/mammalian target of rapamycin (mTOR) pharmacological inhibition using bimiralisib has in vitro and in vivo anti-tumor activity and that it induces transcriptional changes in diffuse large B cell lymphoma (DLBCL) cell lines [8]
As a central controller of cell growth, mTOR regulates ribosome biogenesis. The latter is the most energy-demanding cellular process, and mTOR controls it by promoting the translation of riboproteins and by affecting ribosomal RNA synthesis

Summary

Introduction

The transcriptome is tightly regulated at different levels: along with the regulation of new transcription, RNA molecules can be modulated at the post-transcriptional level, and noncoding RNAs play a relevant role in this process [1,2]. We can discriminate whether RNA levels are modulated at the transcriptional and post-transcriptional level applying an exon–intron split analysis (EISA), which compares intronic and exonic changes across different experimental conditions [7]. We applied this approach to determine whether post-transcriptional regulation mediated by lncRNAs might be an additional layer to quickly control protein expression in diffuse large B cell lymphoma (DLBCL) cells exposed to bimiralisib, a dual PI3K/mTOR inhibitor with proven preclinical and early clinical anti-lymphoma activity [8,9]. In addition to various anabolic processes as protein, lipid and nucleotide synthesis, mTOR promotes cell growth by suppressing protein catabolism. mTOR is a downstream mediator of several growth factor and mitogen-dependent signaling pathways and reacts to intracellular stresses that are incompatible with growth such as low ATP levels, hypoxia, or DNA damage

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Conclusion