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Luo N, Huang Q, Zhang M, Yi C. Functions and therapeutic applications of pseudouridylation. Nat Rev Mol Cell Biol 2025:10.1038/s41580-025-00852-1. [PMID: 40394244 DOI: 10.1038/s41580-025-00852-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2025] [Indexed: 05/22/2025]
Abstract
The success of using pseudouridine (Ψ) and its methylation derivative in mRNA vaccines against SARS-CoV-2 has sparked a renewed interest in this RNA modification, known as the 'fifth nucleotide' of RNA. In this Review, we discuss the emerging functions of pseudouridylation in gene regulation, focusing on how pseudouridine in mRNA, tRNA and ribosomal RNA (rRNA) regulates translation. We also discuss the effects of pseudouridylation on RNA secondary structure, pre-mRNA splicing, and in vitro mRNA stability. In addition to nuclear-genome-encoded RNAs, pseudouridine is also present in mitochondria-encoded rRNA, mRNA and tRNA, where it has different distributions and functions compared with their nuclear counterparts. We then discuss the therapeutic potential of programmable pseudouridylation and mRNA vaccine optimization through pseudouridylation. Lastly, we briefly describe the latest quantitative pseudouridine detection methods. We posit that pseudouridine is a highly promising modification that merits further epitranscriptomics investigation and therapeutic application.
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Affiliation(s)
- Nan Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Qiang Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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Rubtsova M, Mokrushina Y, Andreev D, Poteshnova M, Shepelev N, Koryagina M, Moiseeva E, Malabuiok D, Prokopenko Y, Terekhov S, Chernov A, Vodovozova E, Smirnov I, Dontsova O, Gabibov A, Rubtsov Y. A Luciferase-Based Approach for Functional Screening of 5' and 3' Untranslated Regions of the mRNA Component for mRNA Vaccines. Vaccines (Basel) 2025; 13:530. [PMID: 40432139 PMCID: PMC12115628 DOI: 10.3390/vaccines13050530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2025] [Revised: 05/05/2025] [Accepted: 05/12/2025] [Indexed: 05/29/2025] Open
Abstract
Background/Objectives: The recent COVID-19 pandemic caused by SARS-CoV-2 infection has highlighted the need for protocols for rapid development of efficient screening methods to search for the optimal mRNA vaccine structures against mutable viral agents. The unmatched success of mRNA vaccines by Pfizer and Moderna encoding the spike protein of SARS-CoV-2 confirms the potential of lipid nanoparticles for mRNA delivery for an accelerated development of new vaccines. The efficacy of vaccination and the production cost of mRNA-based vaccines largely depend on the composition of mRNA components, since the synthesis of an immunogenic protein requires precise and efficient translation in vivo. The composition of 5' and 3' UTR combinations of mRNA has a strong impact on the translation efficiency. The major objective of this study was to increase the probability of producing the immunogenic protein encoded by vaccine mRNA. For this purpose, we proposed to find a new combination of natural UTRs and, in parallel with that, to design and test the system for in vivo selection of translationally active UTRs. Methods: By using Ribo-Seq analysis, sets of candidate short UTRs were generated. These UTRs were tested both in cell cultures and in mice for effective production of secreted nanoluciferase (NLuc) and the S protein of SARS-CoV-2. A combination of the most effective UTRs was used to generate a prototype of an mRNA vaccine capable of inducing neutralizing antibodies against coronavirus. Results: The usefulness of the selected UTRs for vaccine development was tested by implicating the full-length coding sequence of SARS-CoV-2 S protein to produce the main immunogen. As a result, the system for functional screening of UTRs was created by using the NLuc gene. Conclusions: The proposed approach allows non-invasive quantitative assessment of the translational activity of UTRs in the blood serum of mice. By using the full-length sequence of SARS-CoV-2 S protein as a prototype, we demonstrated that the combination of UTRs selected using our luciferase-based reporter assay induces IgG titers and neutralization rates comparable to those obtained by using UTRs from commercial S-protein-based mRNA vaccines.
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Affiliation(s)
- Maria Rubtsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Yuliana Mokrushina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Dmitry Andreev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Maria Poteshnova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Nikita Shepelev
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Mariya Koryagina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
| | - Ekaterina Moiseeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Diana Malabuiok
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Yury Prokopenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Stanislav Terekhov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Aleksander Chernov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Elena Vodovozova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Ivan Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
- Endocrinology Research Center of the Ministry of Health of the Russian Federation, 117292 Moscow, Russia
| | - Olga Dontsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.P.); (N.S.); (M.K.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143025 Moscow, Russia
| | - Alexander Gabibov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
| | - Yury Rubtsov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia; (M.R.); (Y.M.); (D.A.); (E.M.); (D.M.); (Y.P.); (S.T.); (A.C.); (E.V.); (I.S.); (O.D.)
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Heiser BJ, Veyssi A, Ghosh D. Recent strategies for enhanced delivery of mRNA to the lungs. Nanomedicine (Lond) 2025; 20:1043-1069. [PMID: 40190037 PMCID: PMC12051540 DOI: 10.1080/17435889.2025.2485669] [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: 12/20/2024] [Accepted: 03/25/2025] [Indexed: 05/02/2025] Open
Abstract
mRNA-based therapies have emerged as a transformative tool in modern medicine, gaining significant attention following their successful use in COVID-19 vaccines. Delivery to the lungs offers several compelling advantages for mRNA delivery. The lungs are one of the most vascularized organs in the body, which provides an extensive surface area that can facilitate efficient drug transport. Local delivery to the lungs bypasses gastrointestinal degradation, potentially enhancing therapeutic efficacy. In addition, the extensive capillary network of the lungs provides an ideal target for systemic delivery. However, developing effective mRNA therapies for the lungs presents significant challenges. The complex anatomy of the lungs and the body's immune response to foreign particles create barriers to delivery. This review discusses key approaches for overcoming these challenges and improving mRNA delivery to the lungs. It examines both local and systemic delivery strategies aimed at improving lung delivery while mitigating off-target effects. Although substantial progress has been made in lung-targeted mRNA therapies, challenges remain in optimizing cellular uptake and achieving therapeutic efficacy within pulmonary tissues. The continued refinement of delivery strategies that enhance lung-specific targeting while minimizing degradation is critical for the clinical success of mRNA-based pulmonary therapies.
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Affiliation(s)
- Brittany J. Heiser
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Arian Veyssi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Debadyuti Ghosh
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
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Leong KY, Tham SK, Poh CL. Revolutionizing immunization: a comprehensive review of mRNA vaccine technology and applications. Virol J 2025; 22:71. [PMID: 40075519 PMCID: PMC11900334 DOI: 10.1186/s12985-025-02645-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Accepted: 01/30/2025] [Indexed: 03/14/2025] Open
Abstract
Messenger RNA (mRNA) vaccines have emerged as a transformative platform in modern vaccinology. mRNA vaccine is a powerful alternative to traditional vaccines due to their high potency, safety, and efficacy, coupled with the ability for rapid clinical development, scalability and cost-effectiveness in manufacturing. Initially conceptualized in the 1970s, the first study about the effectiveness of a mRNA vaccine against influenza was conducted in 1993. Since then, the development of mRNA vaccines has rapidly gained significance, especially in combating the COVID-19 pandemic. Their unprecedented success during the COVID-19 pandemic, as demonstrated by the Pfizer-BioNTech and Moderna vaccines, highlighted their transformative potential. This review provides a comprehensive analysis of the mRNA vaccine technology, detailing the structure of the mRNA vaccine and its mechanism of action in inducing immunity. Advancements in nanotechnology, particularly lipid nanoparticles (LNPs) as delivery vehicles, have revolutionized the field. The manufacturing processes, including upstream production, downstream purification, and formulation are also reviewed. The clinical progress of mRNA vaccines targeting viruses causing infectious diseases is discussed, emphasizing their versatility and therapeutic potential. Despite their success, the mRNA vaccine platform faces several challenges, including improved stability to reduce dependence on cold chain logistics in transport, enhanced delivery mechanisms to target specific tissues or cells, and addressing the risk of rare adverse events. High costs associated with encapsulation in LNPs and the potential for unequal global access further complicate their widespread adoption. As the world continues to confront emerging viral threats, overcoming these challenges will be essential to fully harness the potential of mRNA vaccines. It is anticipated that mRNA vaccines will play a major role in defining and shaping the future of global health.
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Affiliation(s)
- Kai Yuan Leong
- MyGenome, ALPS Global Holding Berhad, Kuala Lumpur, Malaysia
| | - Seng Kong Tham
- MyGenome, ALPS Global Holding Berhad, Kuala Lumpur, Malaysia
| | - Chit Laa Poh
- MyGenome, ALPS Global Holding Berhad, Kuala Lumpur, Malaysia.
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Danchin A. Use and dual use of synthetic biology. C R Biol 2025; 348:71-88. [PMID: 40052950 DOI: 10.5802/crbiol.173] [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: 10/08/2024] [Revised: 11/29/2024] [Accepted: 12/20/2024] [Indexed: 03/26/2025]
Abstract
A brief history of the field shows that the impression of novelty we have today when we talk about synthetic biology is merely the sign of a rapid loss of memory of the events surrounding its creation. The dangers of misuse were identified even before the first experiments, but this has not led to a shared awareness. Building a cell ab initio involves combining a machine (called a chassis by specialists in the field) and a program in the form of synthetic DNA. Only the latter—the program—is the subject of the vast majority of work in the field, and it is there that the risks of misuse appear. Combined with knowledge of the genomic sequence of pathogens, DNA synthesis makes it possible to reconstitute dangerous organisms or even to develop new ways of propagating malicious software. Finally, the lack of thought given to the risk of accidents when laboratories develop gain-of-function experiments that increase the virulence of a pathogen makes a world where this type of experiments is developed particularly dangerous.
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Kompatscher M, Gonnella I, Erlacher M. Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities. J Mol Biol 2025:168934. [PMID: 39756793 DOI: 10.1016/j.jmb.2024.168934] [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: 11/13/2024] [Revised: 12/19/2024] [Accepted: 12/31/2024] [Indexed: 01/07/2025]
Abstract
tRNAs are essential molecules in protein synthesis, responsible for translating the four-nucleotide genetic code into the corresponding amino acid sequence. RNA modifications play a crucial role in influencing tRNA folding, structure, and function. These modifications, ranging from simple methylations to complex hypermodified species, are distributed throughout the tRNA molecule. Depending on their type and position, they contribute to the accuracy and efficiency of decoding by participating in a complex network of interactions. The enzymatic processes introducing these modifications are equally intricate and diverse, adding further complexity. As a result, studying tRNA modifications faces limitations at multiple levels. This review addresses the challenges involved in manipulating and studying the function of tRNA modifications and discusses experimental strategies and possibilities to overcome these obstacles.
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Affiliation(s)
- Maria Kompatscher
- Institute of Genomics and RNomics, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Isabell Gonnella
- Institute of Genomics and RNomics, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Matthias Erlacher
- Institute of Genomics and RNomics, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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Wen J, Zhu Q, Liu Y, Gou LT. RNA modifications: emerging players in the regulation of reproduction and development. Acta Biochim Biophys Sin (Shanghai) 2024; 57:33-58. [PMID: 39574165 PMCID: PMC11802351 DOI: 10.3724/abbs.2024201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 11/05/2024] [Indexed: 01/25/2025] Open
Abstract
The intricate world of RNA modifications, collectively termed the epitranscriptome, covers over 170 identified modifications and impacts RNA metabolism and, consequently, almost all biological processes. In this review, we focus on the regulatory roles and biological functions of a panel of dominant RNA modifications (including m 6A, m 5C, Ψ, ac 4C, m 1A, and m 7G) on three RNA types-mRNA, tRNA, and rRNA-in mammalian development, particularly in the context of reproduction as well as embryonic development. We discuss in detail how those modifications, along with their regulatory proteins, affect RNA processing, structure, localization, stability, and translation efficiency. We also highlight the associations among dysfunctions in RNA modification-related proteins, abnormal modification deposition and various diseases, emphasizing the roles of RNA modifications in critical developmental processes such as stem cell self-renewal and cell fate transition. Elucidating the molecular mechanisms by which RNA modifications influence diverse developmental processes holds promise for developing innovative strategies to manage developmental disorders. Finally, we outline several unexplored areas in the field of RNA modification that warrant further investigation.
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Affiliation(s)
- Junfei Wen
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyCAS Center for Excellence in Molecular. Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Qifan Zhu
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyCAS Center for Excellence in Molecular. Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yong Liu
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyCAS Center for Excellence in Molecular. Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
| | - Lan-Tao Gou
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyCAS Center for Excellence in Molecular. Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
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