1
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Štefan U, Brázda V, Plavec J, Marušič M. The influence of G-tract and loop length on the topological variability of putative five and six G-quartet DNA structures in the human genome. Int J Biol Macromol 2024; 280:136008. [PMID: 39326605 DOI: 10.1016/j.ijbiomac.2024.136008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 09/23/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Local variation of DNA structure and its dynamic nature play an essential role in the regulation of important biological processes. One of the most prominent noncanonical structures are G-quadruplexes, which form in vivo within guanine-rich regions and have been demonstrated to be involved in the regulation of transcription, translation and telomere maintenance. We provide an analysis of G-quadruplex formation in sequences with five and six guanine residues long G-tracts, which have emerged from the investigation of the gapless human genome and are associated with genes related to cancer and neurodegenerative diseases. We systematically explored the effect of G-tract and loop elongations by means of NMR and CD spectroscopy and polyacrylamide electrophoresis. Despite both types of elongation leading up to structural polymorphism, we successfully determined the topologies of four out of eight examined sequences, one of which contributes to a very scarce selection of currently known intramolecular four G-quartet structures in potassium solutions. We demonstrate that examined sequences are incompatible with five or six G-quartet structures with propeller loops, although the compatibility with other loop types cannot be factored out. Lastly, we propose a novel approach towards specific G-quadruplex targeting that could be implemented in structures with more than four G-quartets.
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Affiliation(s)
- Urša Štefan
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
| | - Janez Plavec
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia; Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; EN-FIST Center of Excellence, SI-1000 Ljubljana, Slovenia
| | - Maja Marušič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
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2
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Ciaco S, Aronne R, Fiabane M, Mori M. The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery. ACS OMEGA 2024; 9:24163-24180. [PMID: 38882119 PMCID: PMC11170735 DOI: 10.1021/acsomega.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Antimicrobial resistance (AMR) is a silent critical issue that poses several challenges to health systems. While the discovery of novel antibiotics is currently stalled and prevalently focused on chemical variations of the scaffolds of available drugs, novel targets and innovative strategies are urgently needed to face this global threat. In this context, bacterial G-quadruplexes (G4s) are emerging as timely and profitable targets for the design and development of antimicrobial agents. Indeed, they are expressed in regulatory regions of bacterial genomes, and their modulation has been observed to provide antimicrobial effects with translational perspectives in the context of AMR. In this work, we review the current knowledge of bacterial G4s as well as their modulation by small molecules, including tools and techniques suitable for these investigations. Finally, we critically analyze the needs and future directions in the field, with a focus on the development of small molecules as bacterial G4s modulators endowed with remarkable drug-likeness.
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Affiliation(s)
- Stefano Ciaco
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Martina Fiabane
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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3
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Brázda V, Šislerová L, Cucchiarini A, Mergny JL. G-quadruplex propensity in H. neanderthalensis, H. sapiens and Denisovans mitochondrial genomes. NAR Genom Bioinform 2024; 6:lqae060. [PMID: 38817800 PMCID: PMC11137754 DOI: 10.1093/nargab/lqae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/18/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Current methods of processing archaeological samples combined with advances in sequencing methods lead to disclosure of a large part of H. neanderthalensis and Denisovans genetic information. It is hardly surprising that the genome variability between modern humans, Denisovans and H. neanderthalensis is relatively limited. Genomic studies may provide insight on the metabolism of extinct human species or lineages. Detailed analysis of G-quadruplex sequences in H. neanderthalensis and Denisovans mitochondrial DNA showed us interesting features. Relatively similar patterns in mitochondrial DNA are found compared to modern humans, with one notable exception for H. neanderthalensis. An interesting difference between H. neanderthalensis and H. sapiens corresponds to a motif found in the D-loop region of mtDNA, which is responsible for mitochondrial DNA replication. This area is directly responsible for the number of mitochondria and consequently for the efficient energy metabolism of cell. H. neanderthalensis harbor a long uninterrupted run of guanines in this region, which may cause problems for replication, in contrast with H. sapiens, for which this run is generally shorter and interrupted. One may propose that the predominant H. sapiens motif provided a selective advantage for modern humans regarding mtDNA replication and function.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Lucie Šislerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Anne Cucchiarini
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
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4
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Miranda A, Cucchiarini A, Esnault C, Andrau JC, Oliveira PA, Mergny JL, Cruz C. G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene. Int J Biol Macromol 2024; 270:132244. [PMID: 38729459 DOI: 10.1016/j.ijbiomac.2024.132244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/10/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
To combat cancer, a comprehensive understanding of the molecular mechanisms and behaviors involved in carcinogenesis is crucial, as tumorigenesis is a complex process influenced by various genetic events and disease hallmarks. The B-MYB gene encodes a transcription factor involved in cell cycle regulation, survival, and differentiation in normal cells. B-MYB can be transformed into an oncogene through mutations, and abnormal expression of B-MYB has been identified in various cancers, including lung cancer, and is associated with poor prognosis. Targeting this oncogene is a promising approach for anti-cancer drug design. B-MYB has been deemed undruggable in previous reports, necessitating the search for novel therapeutic options. In this study, we found that the B-MYB gene promoter contains several G/C rich motifs compatible with G-quadruplex (G4) formation. We investigated and validated the existence of G4 structures in the promoter region of B-MYB, first in vitro using a combination of bioinformatics, biophysical, and biochemical methods, then in cell with the recently developed G4access method.
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Affiliation(s)
- André Miranda
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Cyril Esnault
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR, 5535 Montpellier, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR, 5535 Montpellier, France
| | - Paula A Oliveira
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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5
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Bartas M, Brázda V, Pečinka P. Special Issue "Bioinformatics of Unusual DNA and RNA Structures". Int J Mol Sci 2024; 25:5226. [PMID: 38791265 PMCID: PMC11121459 DOI: 10.3390/ijms25105226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...].
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Václav Brázda
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic;
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
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6
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Katrivas L, Makarovsky A, Kempinski B, Randazzo A, Improta R, Rotem D, Porath D, Kotlyar AB. Ag +-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:663. [PMID: 38668157 PMCID: PMC11055002 DOI: 10.3390/nano14080663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a "hairpin" fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA-silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Anna Makarovsky
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Napoli, Italy;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy;
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Alexander B. Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
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7
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Luo Y, Živković ML, Wang J, Ryneš J, Foldynová-Trantírková S, Trantírek L, Verga D, Mergny JL. A sodium/potassium switch for G4-prone G/C-rich sequences. Nucleic Acids Res 2024; 52:448-461. [PMID: 37986223 PMCID: PMC10783510 DOI: 10.1093/nar/gkad1073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Metal ions are essential components for the survival of living organisms. For most species, intracellular and extracellular ionic conditions differ significantly. As G-quadruplexes (G4s) are ion-dependent structures, changes in the [Na+]/[K+] ratio may affect the folding of genomic G4s. More than 11000 putative G4 sequences in the human genome (hg19) contain at least two runs of three continuous cytosines, and these mixed G/C-rich sequences may form a quadruplex or a competing hairpin structure based on G-C base pairing. In this study, we examine how the [Na+]/[K+] ratio influences the structures of G/C-rich sequences. The natural G4 structure with a 9-nt long central loop, CEBwt, was chosen as a model sequence, and the loop bases were gradually replaced by cytosines. The series of CEB mutations revealed that the presence of cytosines in G4 loops does not prevent G4 folding or decrease G4 stability but increases the probability of forming a competing structure, either a hairpin or an intermolecular duplex. Slow conversion to the quadruplex in vitro (in a potassium-rich buffer) and cells was demonstrated by NMR. 'Shape-shifting' sequences may respond to [Na+]/[K+] changes with delayed kinetics.
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Affiliation(s)
- Yu Luo
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Martina Lenarčič Živković
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Jan Ryneš
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | | | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
| | - Jean-Louis Mergny
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France
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8
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Figueiredo J, Djavaheri-Mergny M, Ferret L, Mergny JL, Cruz C. Harnessing G-quadruplex ligands for lung cancer treatment: A comprehensive overview. Drug Discov Today 2023; 28:103808. [PMID: 38414431 DOI: 10.1016/j.drudis.2023.103808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 02/29/2024]
Abstract
Lung cancer (LC) remains a leading cause of mortality worldwide, and new therapeutic strategies are urgently needed. One such approach revolves around the utilization of four-stranded nucleic acid secondary structures, known as G-quadruplexes (G4), which are formed by G-rich sequences. Ligands that bind selectively to G4 structures present a promising strategy for regulating crucial cellular processes involved in the progression of LC, rendering them potent agents for lung cancer treatment. In this review, we offer a summary of recent advancements in the development of G4 ligands capable of targeting specific genes associated with the development and progression of lung cancer.
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Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Mojgan Djavaheri-Mergny
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe Labellisée par la Ligue contre le Cancer, Institut Universitaire de France, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
| | - Lucille Ferret
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe Labellisée par la Ligue contre le Cancer, Institut Universitaire de France, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France; Faculté de Médecine, Université de Paris Saclay, Paris, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Institut Polytechnique de Paris, CNRS, INSERM, Université Paris-Saclay, 91120 Palaiseau, France.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; Departamento de Química, Faculdade de Ciências da Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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9
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Le NBT, Tu ATT, Zhao D, Yoshikawa C, Kawakami K, Kaizuka Y, Yamazaki T. Influence of the Charge Ratio of Guanine-Quadruplex Structure-Based CpG Oligodeoxynucleotides and Cationic DOTAP Liposomes on Cytokine Induction Profiles. Biomolecules 2023; 13:1639. [PMID: 38002321 PMCID: PMC10669863 DOI: 10.3390/biom13111639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Cationic liposomes, specifically 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) liposomes, serve as successful carriers for guanine-quadruplex (G4) structure-based cytosine-guanine oligodeoxynucleotides (CpG ODNs). The combined benefits of CpG ODNs forming a G4 structure and a non-viral vector carrier endow the ensuing complex with promising adjuvant properties. Although G4-CpG ODN-DOTAP complexes show a higher immunostimulatory effect than naked G4-CpG ODNs, the effects of the complex composition, especially charge ratios, on the production of the pro-inflammatory cytokines interleukin (IL)-6 and interferon (IFN)-α remain unclear. Here, we examined whether charge ratios drive the bifurcation of cytokine inductions in human peripheral blood mononuclear cells. Linear CpG ODN-DOTAP liposome complexes formed micrometer-sized positively charged agglomerates; G4-CpG ODN-DOTAP liposome complexes with low charge ratios (0.5 and 1.5) formed ~250 nm-sized negatively charged complexes. Notably, low-charge-ratio (0.5 and 1.5) complexes induced significantly higher IL-6 and IFN-α levels simultaneously than high-charge-ratio (2 and 2.5) complexes. Moreover, confocal microscopy indicated a positive correlation between the cellular uptake of the complex and amount of cytokine induced. The observed effects of charge ratios on complex size, surface charge, and affinity for factors that modify cellular-uptake, intracellular-activity, and cytokine-production efficiency highlight the importance of a rational complex design for delivering and controlling G4-CpG ODN activity.
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Affiliation(s)
- Nguyen Bui Thao Le
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan; (N.B.T.L.); (A.T.T.T.); (D.Z.); (C.Y.); (K.K.); (Y.K.)
- Division of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
| | - Anh Thi Tram Tu
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan; (N.B.T.L.); (A.T.T.T.); (D.Z.); (C.Y.); (K.K.); (Y.K.)
- Department of Magnetic and Biomedical Materials, Faculty of Materials Science and Technology, VNUHCM-University of Science, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh City 70000, Vietnam
- Ho Chi Minh City Campus, Vietnam National University, Linh Trung, Thu Duc, Ho Chi Minh City 70000, Vietnam
| | - Dandan Zhao
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan; (N.B.T.L.); (A.T.T.T.); (D.Z.); (C.Y.); (K.K.); (Y.K.)
| | - Chiaki Yoshikawa
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan; (N.B.T.L.); (A.T.T.T.); (D.Z.); (C.Y.); (K.K.); (Y.K.)
- Division of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
| | - Kohsaku Kawakami
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan; (N.B.T.L.); (A.T.T.T.); (D.Z.); (C.Y.); (K.K.); (Y.K.)
| | - Yoshihisa Kaizuka
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan; (N.B.T.L.); (A.T.T.T.); (D.Z.); (C.Y.); (K.K.); (Y.K.)
| | - Tomohiko Yamazaki
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba 305-0047, Japan; (N.B.T.L.); (A.T.T.T.); (D.Z.); (C.Y.); (K.K.); (Y.K.)
- Division of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
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10
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Le Sénéchal R, Keruzoré M, Quillévéré A, Loaëc N, Dinh VT, Reznichenko O, Guixens-Gallardo P, Corcos L, Teulade-Fichou MP, Granzhan A, Blondel M. Alternative splicing of BCL-x is controlled by RBM25 binding to a G-quadruplex in BCL-x pre-mRNA. Nucleic Acids Res 2023; 51:11239-11257. [PMID: 37811881 PMCID: PMC10639069 DOI: 10.1093/nar/gkad772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/05/2023] [Accepted: 09/09/2023] [Indexed: 10/10/2023] Open
Abstract
BCL-x is a master regulator of apoptosis whose pre-mRNA is alternatively spliced into either a long (canonical) anti-apoptotic Bcl-xL isoform, or a short (alternative) pro-apoptotic Bcl-xS isoform. The balance between these two antagonistic isoforms is tightly regulated and overexpression of Bcl-xL has been linked to resistance to chemotherapy in several cancers, whereas overexpression of Bcl-xS is associated to some forms of diabetes and cardiac disorders. The splicing factor RBM25 controls alternative splicing of BCL-x: its overexpression favours the production of Bcl-xS, whereas its downregulation has the opposite effect. Here we show that RBM25 directly and specifically binds to GQ-2, an RNA G-quadruplex (rG4) of BCL-x pre-mRNA that forms at the vicinity of the alternative 5' splice site leading to the alternative Bcl-xS isoform. This RBM25/rG4 interaction is crucial for the production of Bcl-xS and depends on the RE (arginine-glutamate-rich) motif of RBM25, thus defining a new type of rG4-interacting domain. PhenDC3, a benchmark G4 ligand, enhances the binding of RBM25 to the GQ-2 rG4 of BCL-x pre-mRNA, thereby promoting the alternative pro-apoptotic Bcl-xS isoform and triggering apoptosis. Furthermore, the screening of a combinatorial library of 90 putative G4 ligands led to the identification of two original compounds, PhenDH8 and PhenDH9, superior to PhenDC3 in promoting the Bcl-xS isoform and apoptosis. Thus, favouring the interaction between RBM25 and the GQ-2 rG4 of BCL-x pre-mRNA represents a relevant intervention point to re-sensitize cancer cells to chemotherapy.
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Affiliation(s)
- Ronan Le Sénéchal
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Marc Keruzoré
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Alicia Quillévéré
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Nadège Loaëc
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Van-Trang Dinh
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Oksana Reznichenko
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Pedro Guixens-Gallardo
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Laurent Corcos
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Marie-Paule Teulade-Fichou
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Marc Blondel
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
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Mergny JL, Trantírek L, Capranico G. Last year at Marienbad: Unusual nucleic acid structures. Biochimie 2023; 214:1-4. [PMID: 37748749 DOI: 10.1016/j.biochi.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Affiliation(s)
- Jean-Louis Mergny
- Laboratoire d'Optique & Biosciences, Institut Polytechnique de Paris, Inserm, CNRS, Ecole Polytechnique, Palaiseau, 91120, France; Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Giovanni Capranico
- Department of Pharmacy & Biotechnology, University of Bologna, 40126, Bologna, Italy
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