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Gambi G, Mengus G, Davidson G, Demesmaeker E, Cuomo A, Bonaldi T, Katopodi V, Malouf GG, Leucci E, Davidson I. The LncRNA LENOX Interacts with RAP2C to Regulate Metabolism and Promote Resistance to MAPK Inhibition in Melanoma. Cancer Res 2022; 82:4555-4570. [PMID: 36214632 PMCID: PMC9755964 DOI: 10.1158/0008-5472.can-22-0959] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 01/24/2023]
Abstract
Tumor heterogeneity is a key feature of melanomas that hinders development of effective treatments. Aiming to overcome this, we identified LINC00518 (LENOX; lincRNA-enhancer of oxidative phosphorylation) as a melanoma-specific lncRNA expressed in all known melanoma cell states and essential for melanoma survival in vitro and in vivo. Mechanistically, LENOX promoted association of the RAP2C GTPase with mitochondrial fission regulator DRP1, increasing DRP1 S637 phosphorylation, mitochondrial fusion, and oxidative phosphorylation. LENOX expression was upregulated following treatment with MAPK inhibitors, facilitating a metabolic switch from glycolysis to oxidative phosphorylation and conferring resistance to MAPK inhibition. Consequently, combined silencing of LENOX and RAP2C synergized with MAPK inhibitors to eradicate melanoma cells. Melanomas are thus addicted to the lncRNA LENOX, which acts to optimize mitochondrial function during melanoma development and progression. SIGNIFICANCE The lncRNA LENOX is a novel regulator of melanoma metabolism, which can be targeted in conjunction with MAPK inhibitors to eradicate melanoma cells.
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Affiliation(s)
- Giovanni Gambi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alessandro Cuomo
- Nuclear Proteomics Institute to Study Gene Expression, Milano, Italy
| | - Tiziana Bonaldi
- Nuclear Proteomics Institute to Study Gene Expression, Milano, Italy
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, KU Leuven, Leuven, Belgium
| | - Gabriel G. Malouf
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, KU Leuven, Leuven, Belgium.,Corresponding Authors: Irwin Davidson, Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch, 67404, France. E-mail: ; and Eleonora Leucci, Laboratory for RNA Cancer Biology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. E-mail:
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Equipe Labélisée Ligue contre le Cancer.,Corresponding Authors: Irwin Davidson, Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch, 67404, France. E-mail: ; and Eleonora Leucci, Laboratory for RNA Cancer Biology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. E-mail:
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Vendramin R, Katopodi V, Cinque S, Konnova A, Knezevic Z, Adnane S, Verheyden Y, Karras P, Demesmaeker E, Bosisio FM, Kucera L, Rozman J, Gladwyn-Ng I, Rizzotto L, Dassi E, Millevoi S, Bechter O, Marine JC, Leucci E. Activation of the integrated stress response confers vulnerability to mitoribosome-targeting antibiotics in melanoma. J Exp Med 2021; 218:e20210571. [PMID: 34287642 PMCID: PMC8424468 DOI: 10.1084/jem.20210571] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
The ability to adapt to environmental stress, including therapeutic insult, contributes to tumor evolution and drug resistance. In suboptimal conditions, the integrated stress response (ISR) promotes survival by dampening cytosolic translation. We show that ISR-dependent survival also relies on a concomitant up-regulation of mitochondrial protein synthesis, a vulnerability that can be exploited using mitoribosome-targeting antibiotics. Accordingly, such agents sensitized to MAPK inhibition, thus preventing the development of resistance in BRAFV600E melanoma models. Additionally, this treatment compromised the growth of melanomas that exhibited elevated ISR activity and resistance to both immunotherapy and targeted therapy. In keeping with this, pharmacological inactivation of ISR, or silencing of ATF4, rescued the antitumoral response to the tetracyclines. Moreover, a melanoma patient exposed to doxycycline experienced complete and long-lasting response of a treatment-resistant lesion. Our study indicates that the repurposing of mitoribosome-targeting antibiotics offers a rational salvage strategy for targeted therapy in BRAF mutant melanoma and a therapeutic option for NRAS-driven and immunotherapy-resistant tumors.
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Affiliation(s)
- Roberto Vendramin
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sonia Cinque
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Angelina Konnova
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Zorica Knezevic
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sara Adnane
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Yvessa Verheyden
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, Katholieke Universiteit Leuven, Belgium
| | - Ewout Demesmaeker
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Lukas Kucera
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | | | - Lara Rizzotto
- Trace, Leuven Cancer Institute, Katholieke Universiteit Leuven, Belgium
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, Institut national de la santé et de la recherche médicale Joint Research Unit 1037, Toulouse, France
- Université Toulouse III Paul Sabatier, Toulouse, France
- Laboratoire d’Excellence “TOUCAN,” Toulouse, France
| | - Oliver Bechter
- Department of General Medical Oncology, Leuven Cancer Institute, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Oncology, Laboratory for Molecular Cancer Biology, Katholieke Universiteit Leuven, Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
- Trace, Leuven Cancer Institute, Katholieke Universiteit Leuven, Belgium
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Kyriakopoulos G, Katopodi V, Skeparnias I, Kaliatsi EG, Grafanaki K, Stathopoulos C. KRAS G12C Can Either Promote or Impair Cap-Dependent Translation in Two Different Lung Adenocarcinoma Cell Lines. Int J Mol Sci 2021; 22:ijms22042222. [PMID: 33672357 PMCID: PMC7926983 DOI: 10.3390/ijms22042222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
KRASG12C is among the most common oncogenic mutations in lung adenocarcinoma and a promising target for treatment by small-molecule inhibitors. KRAS oncogenic signaling is responsible for modulation of tumor microenvironment, with translation factors being among the most prominent deregulated targets. In the present study, we used TALENs to edit EGFRWT CL1-5 and A549 cells for integration of a Tet-inducible KRASG12C expression system. Subsequent analysis of both cell lines showed that cap-dependent translation was impaired in CL1-5 cells via involvement of mTORC2 and NF-κB. In contrast, in A549 cells, which additionally harbor the KRASG12S mutation, cap-dependent translation was favored via recruitment of mTORC1, c-MYC and the positive regulation of eIF4F complex. Downregulation of eIF1, eIF5 and eIF5B in the same cell line suggested a stringency loss of start codon selection during scanning of mRNAs. Puromycin staining and polysome profile analysis validated the enhanced translation rates in A549 cells and the impaired cap-dependent translation in CL1-5 cells. Interestingly, elevated translation rates were restored in CL1-5 cells after prolonged induction of KRASG12C through an mTORC1/p70S6K-independent way. Collectively, our results suggest that KRASG12C signaling differentially affects the regulation of the translational machinery. These differences could provide additional insights and facilitate current efforts to effectively target KRAS.
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Affiliation(s)
- George Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Vicky Katopodi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, 3001 Leuven, Belgium
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
| | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (G.K.)
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
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Aprile M, Katopodi V, Leucci E, Costa V. LncRNAs in Cancer: From garbage to Junk. Cancers (Basel) 2020; 12:cancers12113220. [PMID: 33142861 PMCID: PMC7692075 DOI: 10.3390/cancers12113220] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 10/10/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing-based transcriptomics has significantly redefined the concept of genome complexity, leading to the identification of thousands of lncRNA genes identification of thousands of lncRNA genes whose products possess transcriptional and/or post-transcriptional regulatory functions that help to shape cell functionality and fate. Indeed, it is well-established now that lncRNAs play a key role in the regulation of gene expression through epigenetic and posttranscriptional mechanims. The rapid increase of studies reporting lncRNAs alteration in cancers has also highlighted their relevance for tumorigenesis. Herein we describe the most prominent examples of well-established lncRNAs having oncogenic and/or tumor suppressive activity. We also discuss how technical advances have provided new therapeutic strategies based on their targeting, and also report the challenges towards their use in the clinical settings.
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Affiliation(s)
- Marianna Aprile
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, LKI, Herestraat 49, 3000 Leuven, Belgium; (V.K.); (E.L.)
| | - Valerio Costa
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy;
- Correspondence:
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