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Munz N, Cascione L, Parmigiani L, Tarantelli C, Rinaldi A, Cmiljanovic N, Cmiljanovic V, Giugno R, Bertoni F, Napoli S. Exon-Intron Differential Analysis Reveals the Role of Competing Endogenous RNAs in Post-Transcriptional Regulation of Translation. Noncoding RNA 2021; 7:ncrna7020026. [PMID: 33923420 PMCID: PMC8167571 DOI: 10.3390/ncrna7020026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Nicolas Munz
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Luca Parmigiani
- Computer Science Department, University of Verona, 37129 Verona, Italy; (L.P.); (R.G.)
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
| | | | | | - Rosalba Giugno
- Computer Science Department, University of Verona, 37129 Verona, Italy; (L.P.); (R.G.)
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, Universita`Svizzera Italiana, 6500 Bellinzona, Switzerland; (N.M.); (L.C.); (C.T.); (A.R.); (F.B.)
- Correspondence:
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Hacbarth-Freire ET, Pileggi P, Quaresma M, Mizerkowski T, Parmigiani L, De Vitto R, Costa RC. ESPONDILOARTROPATIAS TRATADAS COM AGENTES BIOL??GICOS ??? ESTUDO OBSERVACIONAL. J Clin Rheumatol 2006. [DOI: 10.1097/01.rhu.0000226680.34936.7c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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