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Malard F, Wolter AC, Marquevielle J, Morvan E, Ecoutin A, Rüdisser S, Allain FT, Campagne S. The diversity of splicing modifiers acting on A-1 bulged 5'-splice sites reveals rules for rational drug design. Nucleic Acids Res 2024; 52:4124-4136. [PMID: 38554107 PMCID: PMC11077090 DOI: 10.1093/nar/gkae201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/07/2023] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
Pharmacological modulation of RNA splicing by small molecules is an emerging facet of drug discovery. In this context, the SMN2 splicing modifier SMN-C5 was used as a prototype to understand the mode of action of small molecule splicing modifiers and propose the concept of 5'-splice site bulge repair. In this study, we combined in vitro binding assays and structure determination by NMR spectroscopy to identify the binding modes of four other small molecule splicing modifiers that switch the splicing of either the SMN2 or the HTT gene. Here, we determined the solution structures of risdiplam, branaplam, SMN-CX and SMN-CY bound to the intermolecular RNA helix epitope containing an unpaired adenine within the G-2A-1G+1U+2 motif of the 5'-splice site. Despite notable differences in their scaffolds, risdiplam, SMN-CX, SMN-CY and branaplam contact the RNA epitope similarly to SMN-C5, suggesting that the 5'-splice site bulge repair mechanism can be generalised. These findings not only deepen our understanding of the chemical diversity of splicing modifiers that target A-1 bulged 5'-splice sites, but also identify common pharmacophores required for modulating 5'-splice site selection with small molecules.
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Affiliation(s)
- Florian Malard
- Université de Bordeaux, Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
- Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Antje C Wolter
- ETH Zürich, Department of Biology, Institute of Biochemistry, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Julien Marquevielle
- Université de Bordeaux, Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
- Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie, UAR3033 CNRS, Université de Bordeaux, INSERM US01, Pessac 33600, France
| | - Agathe Ecoutin
- Université de Bordeaux, Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
- Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Simon H Rüdisser
- ETH Zürich, Department of Biology, BioNMR platform, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Frédéric H T Allain
- ETH Zürich, Department of Biology, Institute of Biochemistry, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Sebastien Campagne
- Université de Bordeaux, Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
- Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
- ETH Zürich, Department of Biology, Institute of Biochemistry, Hönggerbergring 64, 8093 Zürich, Switzerland
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Bracher L, Ferro I, Pulido-Quetglas C, Ruepp MD, Johnson R, Polacek N. Human vtRNA1-1 Levels Modulate Signaling Pathways and Regulate Apoptosis in Human Cancer Cells. Biomolecules 2020; 10:biom10040614. [PMID: 32316166 PMCID: PMC7226377 DOI: 10.3390/biom10040614] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2022] Open
Abstract
Regulatory non-protein coding RNAs perform a remarkable variety of complex biological functions. Previously, we demonstrated a role of the human non-coding vault RNA1-1 (vtRNA1-1) in inhibiting intrinsic and extrinsic apoptosis in several cancer cell lines. Yet on the molecular level, the function of the vtRNA1-1 is still not fully clear. Here, we created HeLa knock-out cell lines revealing that prolonged starvation triggers elevated levels of apoptosis in the absence of vtRNA1-1 but not in vtRNA1-3 knock-out cells. Next-generation deep sequencing of the mRNome identified the PI3K/Akt pathway and the ERK1/2 MAPK cascade, two prominent signaling axes, to be misregulated in the absence of vtRNA1-1 during starvation-mediated cell death conditions. Expression of vtRNA1-1 mutants identified a short stretch of 24 nucleotides of the vtRNA1-1 central domain as being essential for successful maintenance of apoptosis resistance. This study describes a cell signaling-dependent contribution of the human vtRNA1-1 to starvation-induced programmed cell death.
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Affiliation(s)
- Lisamaria Bracher
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland;
| | - Iolanda Ferro
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
| | - Carlos Pulido-Quetglas
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland;
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland;
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
- United Kingdom Dementia Research Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London SE5 9NU, UK
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland;
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
- Correspondence:
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