PSEUDOURIDINE AND N1-METHYLPSEUDOURIDINE IN mRNA VACCINES MODULATE RETINOIC ACID INDUCIBLE GENE I (RIG-I) AND TOLL-LIKE RECEPTORS (TLR) ACTIVATION

Authors

  • Ni Wayan Erly Sintya Dewi Faculty of Medicine and Health Sciences, Warmadewa University, Indonesia https://orcid.org/0000-0002-4081-547X
  • Fatiha Khairunnisa School of Chemical, Materials, and Biological Engineering, University of Sheffield, United Kingdom, United Kingdom
  • Nita Cahyawati Faculty of medicine and Health Sciences, Warmadewa University, Indonesia, Indonesia
  • Muhammad Miftahussurur DataHelix, Jogyakarta, Indonesia, Indonesia
  • Punta Indratomo DataHelix, Jogyakarta, Indonesia, Indonesia

DOI:

https://doi.org/10.33992/meditory.v13i2.4781

Abstract

Background: The advent of mRNA vaccines has underscored the significance of nucleoside modifications in regulating innate immune recognition. Pseudouridine (Ψ) and its derivative, N1-methylpseudouridine (m1Ψ), are widely used to enhance the efficacy and safety of mRNA vaccines.

Objective: This review examines how Ψ and m1Ψ alter the activation of key innate immune sensors, including RIG-I, MDA5, and endosomal Toll-like receptors (TLR3, TLR7, TLR8).

Methods: A narrative review was conducted using PubMed, Scopus, and Web of Science databases, focusing on studies evaluating the molecular and immunological effects of Ψ and m¹Ψ on innate immune sensors.

Discussion: Incorporation of Ψ or m1Ψ in mRNA markedly suppresses activation of TLR3, TLR7, and TLR8. Ψ-containing RNA avoids detection by TLR7/8 via two mechanisms: it resists endosomal nuclease digestion into immunostimulatory fragments and is poorly recognized by the TLR7/8 ligand-binding sites. m1Ψ similarly evades nuclease processing yet, unlike Ψ, can directly activate TLR8. In the cytosol, Ψ/m1Ψ modifications strongly reduce RIG-I signaling without impeding MDA5.

Conclusions: By limiting innate PRR activation, these modifications increase the translation and stability of mRNA vaccines while reducing inflammatory interferon responses. This immune evasion is crucial for the high efficacy and tolerability of current mRNA vaccines; however, a trade-off exists between minimizing reactogenicity and the adjuvant benefits of innate stimulation.

References

Kuzmin I V, Soto Acosta R, Pruitt L, Wasdin PT, Kedarinath K, Hernandez KR, et al. Comparison of uridine and N1-methylpseudouridine mRNA platforms in development of an Andes virus vaccine. Nat Commun [Internet]. 2024;15(1):6421. Available from: https://doi.org/10.1038/s41467-024-50774-3

Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m6A RNA modifications. Front Immunol [Internet]. 2023; Volume 14-2023. Available from: https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1286820

Ceballos MA, Acevedo ML. The Role of Chemical Modifications in the Genome of Negative-Sense RNA Viruses on the Innate Immune Response. Viruses [Internet]. 2025;17(6). Available from: https://www.mdpi.com/1999-4915/17/6/795

Muslimov A, Tereshchenko V, Shevyrev D, Rogova A, Lepik K, Reshetnikov V, et al. The Dual Role of the Innate Immune System in the Effectiveness of mRNA Therapeutics. Int J Mol Sci. 2023;24(14820):1–34.

Morais P, Yu YT. Modified or Unmodified mRNA Vaccines? – The Biochemistry of Pseudouridine and mRNA Pseudouridylation. In: Trends in mRNA Vaccine Research [Internet]. John Wiley & Sons, Ltd; 2025. p. 69–107. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527838394.ch3

Shen S. The regulation of antiviral innate immunity through non-m 6 A RNA modi fi cations. Front Immunol. 2023;(October):1–17.

Niedz P. Factors affecting RIG-I-Like receptors activation - New research direction for viral hemorrhagic fevers. Front Immunol. 2022;(September):1–13.

Svitkin Y V, Gingras AC, Sonenberg N. Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs. Nucleic Acids Res [Internet]. 2021;50(13):7202–15. Available from: https://doi.org/10.1093/nar/gkab1241

Sioud M, Juzeniene A, Sæbøe-Larssen S. Exploring the Impact of mRNA Modifications on Translation Efficiency and Immune Tolerance to Self-Antigens. Vaccines [Internet]. 2024;12(6). Available from: https://www.mdpi.com/2076-393X/12/6/624

Volkhin IA, Paremskaia AI, Dashian MA, Smeshnova DS, Pavlov RE, Mityaeva ON, et al. Selection of UTRs in mRNA-Based Gene Therapy and Vaccines. Biochem [Internet]. 2025;90(6):725–53. Available from: https://doi.org/10.1134/S0006297924604659

Jeeva S, Kim KH, Shin CH, Wang BZ, Kang SM. An Update on mRNA-Based Viral Vaccines. Vaccines [Internet]. 2021;9(9). Available from: https://www.mdpi.com/2076-393X/9/9/965

Ashiqul AKM, Petra H, Sumit W, Rupert B, Mezger M, Kormann MSD, et al. RNA ImmunoGenic Assay : Simple method for detecting immunogenicity of in vitro transcribed mRNA. Adv Cell Gene Ther. 2020;(December 2019):1–10.

Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol. 2022;12(January):1–32.

Kobiyama K, Ishii KJ. Making innate sense of mRNA vaccine adjuvanticity. Nat Immunol. 2022;23(AprIl):474–6.

Liu X, Hu C, He Q, Bai Y, Zhang X, Fu Z. Expert Review of Vaccines Research progress on immune mechanism and control strategy of dsRNA impurities in mRNA vaccine. Expert Rev Vaccines [Internet]. 2025;24(1):457–69. Available from: https://doi.org/10.1080/14760584.2025.2510335

Martínez-Campos C, Lanz-Mendoza H, Cime-Castillo JA, Peralta-Zaragoza Ó, Madrid-Marina V. RNA Through Time: From the Origin of Life to Therapeutic Frontiers in Transcriptomics and Epitranscriptional Medicine. Int J Mol Sci [Internet]. 2025;26(11). Available from: https://www.mdpi.com/1422-0067/26/11/4964

Sociary NC. How the initial discovery of modified RNA enabled evasion of innate immune responses and facilitated the development of RNA therapeutics. Scan J Immunol. 2023;(April):1–12.

Bérouti M, Wagner M, Greulich W, Piseddu I, Gärtig J, Hansbauer L, et al. Pseudouridine RNA avoids immune detection through impaired endolysosomal processing and TLR engagement. Cell [Internet]. 2025;188(18):4880-4895.e15. Available from: https://www.sciencedirect.com/science/article/pii/S0092867425006191

Jia S, Yu X, Deng N, Zheng C, Ju M, Wang F, et al. Deciphering the pseudouridine nucleobase modification in human diseases: From molecular mechanisms to clinical perspectives. Clin Transl Med [Internet]. 2025;15(1):e70190. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1002/ctm2.70190

Karikó K, Buckstein M, Ni H, Weissman D. Suppression of RNA Recognition by Toll-like Receptors: The Impact of Nucleoside Modification and the Evolutionary Origin of RNA. Immunity [Internet]. 2005;23(2):165–75. Available from: https://www.sciencedirect.com/science/article/pii/S1074761305002116

Nance KD, Meier JL. Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines. ACS Cent Sci [Internet]. 2021 May 26;7(5):748–56. Available from: https://doi.org/10.1021/acscentsci.1c00197

Ghoshal B, Chakraborty D, Nag M, Varadarajan R, Jhunjhunwala S. Ex Vivo Delivery of mRNA to Immune Cells via a Nonendosomal Route Obviates the Need for Nucleoside Modification. ACS Bio Med Chem Au [Internet]. 2024 Dec 18;4(6):291–9. Available from: https://doi.org/10.1021/acsbiomedchemau.4c00057

Haar T Von Der, Mulroney TE, Hedayioglu F, Kurusamy S, Rust M, Lilley KS, et al. Translation of in vitro -transcribed RNA therapeutics. Front Mol Biosci. 2023;(February):1–10.

Tai J, Chen YG. Differences in the immunogenicity of engineered circular RNAs. J Mol Cell Biol. 2023;15:1–6.

Chen Y. The Emerging Role of RNA Modifications in the Regulation of Antiviral Innate Immunity. Front Microbiol. 2022;13(February):1–13.

Han D, Xu MM. RNA Modification in the Immune System. Annu Rev ofImmunology. 2023;41:73–98.

Bernard MC, Bazin E, Petiot N, Lemdani K, Commandeur S, Verdelet C, et al. The impact of nucleoside base modification in mRNA vaccines is influenced by the chemistry of their lipid nanoparticle delivery systems. Mol Ther Nucleic Acids [Internet]. 2023 Jun 13;32:794–806. Available from: https://doi.org/10.1016/j.omtn.2023.05.004

Mu X, Hur S. Immunogenicity of In Vitro-Transcribed RNA. Acc Chem Res [Internet]. 2021 Nov 2;54(21):4012–23. Available from: https://doi.org/10.1021/acs.accounts.1c00521

Liu A, Wang X. The Pivotal Role of Chemical Modifications in mRNA Therapeutics. Front Cell Dev Biol [Internet]. 2022;Volume 10-2022. Available from: https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2022.901510

Mu X, Hur S. Immunogenicity of In Vitro-Transcribed RNA. Acc Chem Res. 2022;54(21):797–810.

Verbeke R, Hogan MJ, Loré K, Pardi N. Innate immune mechanisms of mRNA vaccines. Immunity [Internet]. 2022 Nov 8;55(11):1993–2005. Available from: https://doi.org/10.1016/j.immuni.2022.10.014

Liu W wei, Zheng S qing, Li T, Fei Y fei, Wang C, Zhang S, et al. RNA modi fi cations in cellular metabolism : implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther. 2024;9(70):1–30.

Downloads

Published

2025-12-29

Citation Check