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Sighel D, Destefanis E, Quattrone A. Therapeutic strategies to target the epitranscriptomic machinery. Curr Opin Genet Dev 2024; 87:102230. [PMID: 39024774 DOI: 10.1016/j.gde.2024.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Altered RNA modification patterns and dysregulated expression of epitranscriptomic machinery proteins (EMPs) have been causatively correlated with several diseases. Modulation of EMP gene expression has shown promise in reversing disease-associated phenotypes, making EMPs attractive therapeutic targets. Various therapeutic strategies, including small-molecule modulators, proteolysis-targeting chimeras, and molecular tools for site-specific engineering of RNA modifications, have been introduced to modulate EMPs and RNA modifications themselves and are currently being investigated to enrich the physician's armamentarium. At the forefront of research are small-molecule inhibitors of the key players involved in the N6-methyladenosine RNA modification, with an inhibitor of methyltransferase 3 in clinical trials. Preclinical studies have also demonstrated proof-of-concept for the other approaches, raising expectations for this exciting new frontier of therapy.
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Affiliation(s)
- Denise Sighel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy. https://twitter.com/@DSighel
| | - Eliana Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy. https://twitter.com/@Destefanis_E
| | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy.
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2
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Dalhat MH, Narayan S, Serio H, Arango D. Dissecting the oncogenic properties of essential RNA-modifying enzymes: a focus on NAT10. Oncogene 2024; 43:1077-1086. [PMID: 38409550 PMCID: PMC11092965 DOI: 10.1038/s41388-024-02975-9] [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: 12/26/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024]
Abstract
Chemical modifications of ribonucleotides significantly alter the physicochemical properties and functions of RNA. Initially perceived as static and essential marks in ribosomal RNA (rRNA) and transfer RNA (tRNA), recent discoveries unveiled a dynamic landscape of RNA modifications in messenger RNA (mRNA) and other regulatory RNAs. These findings spurred extensive efforts to map the distribution and function of RNA modifications, aiming to elucidate their distribution and functional significance in normal cellular homeostasis and pathological states. Significant dysregulation of RNA modifications is extensively documented in cancers, accentuating the potential of RNA-modifying enzymes as therapeutic targets. However, the essential role of several RNA-modifying enzymes in normal physiological functions raises concerns about potential side effects. A notable example is N-acetyltransferase 10 (NAT10), which is responsible for acetylating cytidines in RNA. While emerging evidence positions NAT10 as an oncogenic factor and a potential target in various cancer types, its essential role in normal cellular processes complicates the development of targeted therapies. This review aims to comprehensively analyze the essential and oncogenic properties of NAT10. We discuss its crucial role in normal cell biology and aging alongside its contribution to cancer development and progression. We advocate for agnostic approaches to disentangling the intertwined essential and oncogenic functions of RNA-modifying enzymes. Such approaches are crucial for understanding the full spectrum of RNA-modifying enzymes and imperative for designing effective and safe therapeutic strategies.
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Affiliation(s)
- Mahmood H Dalhat
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Sharath Narayan
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
- Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, IL, USA
| | - Hannah Serio
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Daniel Arango
- Department of Pharmacology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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3
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Errani F, Invernizzi A, Herok M, Bochenkova E, Stamm F, Corbeski I, Romanucci V, Di Fabio G, Zálešák F, Caflisch A. Proteolysis Targeting Chimera Degraders of the METTL3-14 m 6A-RNA Methyltransferase. JACS AU 2024; 4:713-729. [PMID: 38425900 PMCID: PMC10900215 DOI: 10.1021/jacsau.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
Methylation of adenine N6 (m6A) is the most frequent RNA modification. On mRNA, it is catalyzed by the METTL3-14 heterodimer complex, which plays a key role in acute myeloid leukemia (AML) and other types of blood cancers and solid tumors. Here, we disclose the first proteolysis targeting chimeras (PROTACs) for an epitranscriptomics protein. For designing the PROTACs, we made use of the crystal structure of the complex of METTL3-14 with a potent and selective small-molecule inhibitor (called UZH2). The optimization of the linker started from a desfluoro precursor of UZH2 whose synthesis is more efficient than that of UZH2. The first nine PROTAC molecules featured PEG- or alkyl-based linkers, but only the latter showed cell penetration. With this information in hand, we synthesized 26 PROTACs based on UZH2 and alkyl linkers of different lengths and rigidity. The formation of the ternary complex was validated by a FRET-based biochemical assay and an in vitro ubiquitination assay. The PROTACs 14, 20, 22, 24, and 30, featuring different linker types and lengths, showed 50% or higher degradation of METTL3 and/or METTL14 measured by Western blot in MOLM-13 cells. They also showed substantial degradation on three other AML cell lines and prostate cancer cell line PC3.
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Affiliation(s)
- Francesco Errani
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Annalisa Invernizzi
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Marcin Herok
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Elena Bochenkova
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Fiona Stamm
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Ivan Corbeski
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Valeria Romanucci
- Università
degli Studi di Napoli Federico II, Via Cintia 4, Napoli I-80126, Italia
| | - Giovanni Di Fabio
- Università
degli Studi di Napoli Federico II, Via Cintia 4, Napoli I-80126, Italia
| | - František Zálešák
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
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Cesaro B, Iaiza A, Piscopo F, Tarullo M, Cesari E, Rotili D, Mai A, Diana A, Londero M, Del Giacco L, Masetti R, Di Leone A, Naro C, Masciarelli S, Fontemaggi G, Sette C, Fazi F, Fatica A. Enhancing sensitivity of triple-negative breast cancer to DNA-damaging therapy through chemical inhibition of the m6A methyltransferase METTL3. Cancer Commun (Lond) 2024; 44:282-286. [PMID: 38102821 PMCID: PMC10876187 DOI: 10.1002/cac2.12509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023] Open
Affiliation(s)
- Bianca Cesaro
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical EmbryologySapienza University of RomeRomeItaly
| | - Alessia Iaiza
- Department of Biology and Biotechnologies “Charles Darwin”Sapienza University of RomeRomeItaly
| | - Fabio Piscopo
- Department of Biology and Biotechnologies “Charles Darwin”Sapienza University of RomeRomeItaly
| | - Marco Tarullo
- Department of Biology and Biotechnologies “Charles Darwin”Sapienza University of RomeRomeItaly
| | - Eleonora Cesari
- GSTeP Organoids Research Core FacilityFondazione Policlinico A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)RomeItaly
| | - Dante Rotili
- Department of Drug Chemistry and TechnologiesSapienza University of RomeRomeItaly
| | - Antonello Mai
- Department of Drug Chemistry and TechnologiesSapienza University of RomeRomeItaly
- Pasteur Institute, Cenci‐Bolognetti Foundation, Sapienza University of RomeRomeItaly
| | - Alberto Diana
- Department of BioSciencesUniversity of MilanMilanItaly
| | | | | | - Riccardo Masetti
- GSTeP Organoids Research Core FacilityFondazione Policlinico A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)RomeItaly
- Multidisciplinary Breast Center, Dipartimento Scienze della Salute della Donna e del Bambino e di Sanità Pubblica, Catholic University of the Sacred HeartRomeItaly
| | - Alba Di Leone
- GSTeP Organoids Research Core FacilityFondazione Policlinico A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)RomeItaly
- Multidisciplinary Breast Center, Dipartimento Scienze della Salute della Donna e del Bambino e di Sanità Pubblica, Catholic University of the Sacred HeartRomeItaly
| | - Chiara Naro
- GSTeP Organoids Research Core FacilityFondazione Policlinico A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)RomeItaly
- Department of Neuroscience, Section of Human AnatomyCatholic University of the Sacred HeartRomeItaly
| | - Silvia Masciarelli
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical EmbryologySapienza University of RomeRomeItaly
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Claudio Sette
- GSTeP Organoids Research Core FacilityFondazione Policlinico A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)RomeItaly
- Department of Neuroscience, Section of Human AnatomyCatholic University of the Sacred HeartRomeItaly
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical EmbryologySapienza University of RomeRomeItaly
- Pasteur Institute, Cenci‐Bolognetti Foundation, Sapienza University of RomeRomeItaly
| | - Alessandro Fatica
- Department of Biology and Biotechnologies “Charles Darwin”Sapienza University of RomeRomeItaly
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