Engineered VPg saRNA achieves cap-independent, low-immunogenic and precise encoding of therapeutic proteins in vivo

engineered-vpg-sarna-achieves-cap-independent,-low-immunogenic-and-precise-encoding-of-therapeutic-proteins-in-vivo
Engineered VPg saRNA achieves cap-independent, low-immunogenic and precise encoding of therapeutic proteins in vivo

Data availability

Source data for Figs. 1–7 and Supplementary Figs. 17 are provided as Source Data files. LC–MS/MS raw datasets and Sanger sequencing chromatograms generated in this study have been deposited in Figshare and are available at https://doi.org/10.6084/m9.figshare.3078216546 and https://doi.org/10.6084/m9.figshare.3069415146. Raw fluorescence microscopy, cryo-transmission electron microscopy (cryo-TEM), immunohistochemistry (IHC), and hematoxylin and eosin (H&E) staining images are not publicly available due to large file sizes, instrument-specific formats, and institutional data management restrictions; however, all processed and representative images supporting the findings of this study are included in the paper and its supplementary materials. All other data, including raw imaging data, are available from the corresponding author upon request. Source Data are provided with this paper.

References

  1. Skowronski, D. M. & De Serres, G. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N. Engl. J. Med. 384, 1576–1577 (2021).

    Google Scholar 

  2. Qiu, X. et al. Development of mRNA vaccines against respiratory syncytial virus (RSV). Cytokine Growth Factor Rev. 68, 37–53 (2022).

    Google Scholar 

  3. Liu, C. et al. mRNA-based cancer therapeutics. Nat. Rev. Cancer 23, 526–543 (2023).

    Google Scholar 

  4. Kim, Y. K. RNA therapy: rich history, various applications and unlimited future prospects. Exp. Mol. Med. 54, 455–465 (2022).

    Google Scholar 

  5. Pardi, N., Hogan, M. J., Porter, F. W. & Weissman, D. mRNA vaccines-a new era in vaccinology. Nat. Rev. Drug Discov. 17, 261–279 (2018).

    Google Scholar 

  6. Anderson, B. R. et al. Nucleoside modifications in RNA limit activation of 2’-5’-oligoadenylate synthetase and increase resistance to cleavage by RNase L. Nucleic Acids Res. 39, 9329–9338 (2011).

    Google Scholar 

  7. Blakney, A. K., Ip, S. & Geall, A. J. An update on self-amplifying mRNA vaccine development. Vaccines 9, 97 (2021).

    Google Scholar 

  8. Rohner, E., Yang, R., Foo, K. S., Goedel, A. & Chien, K. R. Unlocking the promise of mRNA therapeutics. Nat. Biotechnol. 40, 1586–1600 (2022).

    Google Scholar 

  9. Minnaert, A. K. et al. Strategies for controlling the innate immune activity of conventional and self-amplifying mRNA therapeutics: getting the message across. Adv. Drug Deliv. Rev. 176, 113900 (2021).

    Google Scholar 

  10. Chen, R. et al. Engineering circular RNA for enhanced protein production. Nat. Biotechnol. 41, 262–272 (2023).

    Google Scholar 

  11. Perkovic, M. et al. A trans-amplifying RNA simplified to essential elements is highly replicative and robustly immunogenic in mice. Mol. Ther. 32, 257–259 (2024).

    Google Scholar 

  12. Bloom, K., van den Berg, F. & Arbuthnot, P. Self-amplifying RNA vaccines for infectious diseases. Gene Ther. 28, 117–129 (2021).

    Google Scholar 

  13. Schmidt, C. & Schnierle, B. S. Self-amplifying RNA vaccine candidates: alternative platforms for mRNA vaccine development. Pathogens 12, 138 (2023).

    Google Scholar 

  14. Ventoso, I. et al. Translational resistance of late alphavirus mRNA to eIF2alpha phosphorylation: a strategy to overcome the antiviral effect of protein kinase PKR. Genes Dev. 20, 87–100 (2006).

    Google Scholar 

  15. García, M. A. et al. Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action. Microbiol. Mol. Biol. Rev. 70, 1032–1060 (2006).

    Google Scholar 

  16. Rudd, P. A. et al. Interferon response factors 3 and 7 protect against Chikungunya virus hemorrhagic fever and shock. J. Virol. 86, 9888–9898 (2012).

    Google Scholar 

  17. Wauquier, N. et al. The acute phase of Chikungunya virus infection in humans is associated with strong innate immunity and T CD8 cell activation. J. Infect. Dis. 204, 115–123 (2011).

    Google Scholar 

  18. McNab, F., Mayer-Barber, K., Sher, A., Wack, A. & O’Garra, A. Type I interferons in infectious disease. Nat. Rev. Immunol. 15, 87–103 (2015).

    Google Scholar 

  19. Pindel, A. & Sadler, A. The role of protein kinase R in the interferon response. J. Interferon Cytokine Res. 31, 59–70 (2011).

    Google Scholar 

  20. Castro, C., Arnold, J. J. & Cameron, C. E. Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Res. 107, 141–149 (2005).

    Google Scholar 

  21. Patterson, E. I. et al. Measuring alphavirus fidelity using non-infectious virus particles. Viruses 12, 546 (2020).

    Google Scholar 

  22. Thorne, L. G. & Goodfellow, I. G. Norovirus gene expression and replication. J. Gen. Virol. 95, 278–291 (2014).

    Google Scholar 

  23. Doerflinger, S. Y. et al. Membrane alterations induced by nonstructural proteins of human norovirus. PLoS Pathog. 13, e1006705 (2017).

    Google Scholar 

  24. Wolff, G., Melia, C. E., Snijder, E. J. & Bárcena, M. Double-membrane vesicles as platforms for viral replication. Trends Microbiol. 28, 1022–1033 (2020).

    Google Scholar 

  25. Alexopoulou, L., Holt, A. C., Medzhitov, R. & Flavell, R. A. Recognition of double-stranded RNA and activation of NF-kappaB by toll-like receptor 3. Nature 413, 732–738 (2001).

    Google Scholar 

  26. Leen, E. N. et al. A conserved interaction between a C-terminal motif in norovirus VPg and the HEAT-1 domain of eIF4G is essential for translation initiation. PLoS Pathog. 12, e1005379 (2016).

    Google Scholar 

  27. Belliot, G., Sosnovtsev, S. V., Chang, K. O., McPhie, P. & Green, K. Y. Nucleotidylylation of the VPg protein of a human norovirus by its proteinase-polymerase precursor protein. Virology 374, 33–49 (2008).

    Google Scholar 

  28. Goodfellow, I. The genome-linked protein VPg of vertebrate viruses-a multifaceted protein. Curr. Opin. Virol. 1, 355–362 (2011).

    Google Scholar 

  29. Högbom, M., Jäger, K., Robel, I., Unge, T. & Rohayem, J. The active form of the norovirus RNA-dependent RNA polymerase is a homodimer with cooperative activity. J. Gen. Virol. 90, 281–291 (2009).

    Google Scholar 

  30. Yang, X. et al. Motif D of viral RNA-dependent RNA polymerases determines efficiency and fidelity of nucleotide addition. Structure 20, 1519–1527 (2012).

    Google Scholar 

  31. Gong, P. & Peersen, O. B. Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase. Proc. Natl. Acad. Sci. USA 107, 22505–22510 (2010).

    Google Scholar 

  32. Liu, W., Shi, X. & Gong, P. A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase. Nucleic Acids Res. 46, 10840–10854 (2018).

    Google Scholar 

  33. Rohayem, J., Robel, I., Jäger, K., Scheffler, U. & Rudolph, W. Protein-primed and de novo initiation of RNA synthesis by norovirus 3Dpol. J. Virol. 80, 7060–7069 (2006).

    Google Scholar 

  34. Subba-Reddy, C. V., Goodfellow, I. & Kao, C. C. VPg-primed RNA synthesis of norovirus RNA-dependent RNA polymerases by using a novel cell-based assay. J. Virol. 85, 13027–13037 (2011).

    Google Scholar 

  35. Paul, A. V. & Wimmer, E. Initiation of protein-primed picornavirus RNA synthesis. Virus Res. 206, 12–26 (2015).

    Google Scholar 

  36. te Velthuis, A. J. Common and unique features of viral RNA-dependent polymerases. Cell. Mol. Life Sci. 71, 4403–4420 (2014).

    Google Scholar 

  37. Chung, L. et al. Norovirus translation requires an interaction between the C terminus of the genome-linked viral protein VPg and eukaryotic translation initiation factor 4G. J. Biol. Chem. 289, 21738–21750 (2014).

    Google Scholar 

  38. Qin, X., Jiang, B. & Zhang, Y. 4E-BP1, a multifactor regulated multifunctional protein. Cell Cycle 15, 781–786 (2016).

    Google Scholar 

  39. Geremia, A. et al. Activation of Akt-mTORC1 signalling reverts cancer-dependent muscle wasting. J. Cachexia Sarcopenia Muscle 13, 648–661 (2022).

    Google Scholar 

  40. Baracos, V. E., Martin, L., Korc, M., Guttridge, D. C. & Fearon, K. C. H. Cancer-associated cachexia. Nat. Rev. Dis. Primers 4, 17105 (2018).

    Google Scholar 

  41. Currow, D. C. & Abernethy, A. P. Anamorelin hydrochloride in the treatment of cancer anorexia-cachexia syndrome. Future Oncol. 10, 789–802 (2014).

    Google Scholar 

  42. Dalton, J. T., Taylor, R. P., Mohler, M. L. & Steiner, M. S. Selective androgen receptor modulators for the prevention and treatment of muscle wasting associated with cancer. Curr. Opin. Support. Palliat. Care 7, 345–351 (2013).

    Google Scholar 

  43. Renz, B. W. et al. β2 adrenergic-neurotrophin feedforward loop promotes pancreatic cancer. Cancer Cell 33, 75–90(2018).

    Google Scholar 

  44. Kojima, M. et al. Ghrelin is a growth-hormone-releasing acylated peptide from stomach. Nature 402, 656–660 (1999).

    Google Scholar 

  45. Feng, Z. et al. An in vitro-transcribed circular RNA targets the mitochondrial inner membrane cardiolipin to ablate EIF4G2+/PTBP1+ pan-adenocarcinoma. Nat. Cancer 5, 30–46 (2024).

    Google Scholar 

  46. Feng, Z. Engineered VPg saRNA achieves cap-independent, low-immunogenic and precise encoding of therapeutic proteins in vivo. figshare https://doi.org/10.6084/m9.figshare.30694151.v1 (2025).

  47. Yan, L. et al. Targeting glucose metabolism sensitizes pancreatic cancer to MEK inhibition. Cancer Res. 81, 4054–4065 (2021).

    Google Scholar 

  48. Griffin, J. H., Zlokovic, B. V. & Mosnier, L. O. Activated protein C: biased for translation. Blood 125, 2898–2907 (2015).

    Google Scholar 

  49. Ranjan, S. et al. Activated protein C protects from GvHD via PAR2/PAR3 signalling in regulatory T-cells. Nat. Commun. 8, 311 (2017).

    Google Scholar 

  50. Sinha, R. K. et al. Activated protein C ameliorates chronic graft-versus-host disease by PAR1-dependent biased cell signaling on T cells. Blood 134, 776–781 (2019).

    Google Scholar 

  51. Sanjuán, R., Nebot, M. R., Chirico, N., Mansky, L. M. & Belshaw, R. Viral mutation rates. J Virol 84, 9733–9748 (2010).

    Google Scholar 

  52. Poirier, E. Z. et al. Low-fidelity polymerases of alphaviruses recombine at higher rates to overproduce defective interfering particles. J. Virol. 90, 2446–2454 (2015).

    Google Scholar 

  53. Langsjoen, R. M., Muruato, A. E., Kunkel, S. R., Jaworski, E. & Routh, A. Differential alphavirus defective RNA diversity between intracellular and extracellular compartments is driven by subgenomic recombination events. mBio 11, e00731–20 (2020).

    Google Scholar 

  54. Anderson, B. R. et al. Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation. Nucleic Acids Res. 38, 5884–5892 (2010).

    Google Scholar 

  55. Kormann, M. S. et al. Expression of therapeutic proteins after delivery of chemically modified mRNA in mice. Nat. Biotechnol. 29, 154–157 (2011).

    Google Scholar 

  56. McGee, J. E. et al. Complete substitution with modified nucleotides in self-amplifying RNA suppresses the interferon response and increases potency. Nat. Biotechnol. 43, 720–726 (2025).

  57. Lei, J. & Hilgenfeld, R. RNA-virus proteases counteracting host innate immunity. FEBS Lett. 591, 3190–3210 (2017).

    Google Scholar 

  58. Koudelka, T. et al. N-terminomics for the identification of in vitro substrates and cleavage site specificity of the SARS-CoV-2 main protease. Proteomics 21, e2000246 (2021).

    Google Scholar 

  59. Chhabra, P. et al. Updated classification of norovirus genogroups and genotypes. J. Gen. Virol. 100, 1393–1406 (2019).

    Google Scholar 

  60. Warzak, D. A., Pike, W. A. & Luttgeharm, K. D. Capillary electrophoresis methods for determining the IVT mRNA critical quality attributes of size and purity. SLAS Technol. 28, 369–374 (2023).

    Google Scholar 

  61. Cooke, K. R. et al. An experimental model of idiopathic pneumonia syndrome after bone marrow transplantation: I. The roles of minor H antigens and endotoxin. Blood 88, 3230–3239 (1996).

    Google Scholar 

Download references

Acknowledgements

This research was supported by the National Natural Science Foundation of China (32471002, 82401829, 82472617, and 82404553; F.Z.Y.), the National University of Singapore (NUHSRO/2020/133/Startup/08, NUHSRO/2023/008/NUSMed/TCE/LOA, NUHSRO/2021/034/TRP/09/Nanomedicine, NUHSRO/2021/044/Kickstart/09/LOA, 23-0173-A0001; C.X.Y.), the National Medical Research Council (MOH-001388-00, CG21APR1005, MOH-001500-00, MOH-001609-00; C.X.Y.), the Singapore Ministry of Education (MOE-000387-00; C.X.Y.), the National Research Foundation (NRF-000352-00; C.X.Y.), the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang (2023R01002; Z.G.W.), the Distinguished Young Scientists Fund of Zhejiang (LR25H250001; Z.G.W.), and the National Science and Technology Major Project of China (No. 2025ZD1802201; Z.G.W.).

Author information

Authors and Affiliations

  1. State Key Laboratory of Macromolecular Drugs and Large-scale Preparation, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China

    Zunyong Feng, Liuxi Chu, Jing Zhou, Ping Wu & Xiaokun Li

  2. The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China

    Liuxi Chu, Xiaokun Li & Zhouguang Wang

  3. Human Anatomy Experimental Training Center, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui, China

    Qiang Li, Zhiliang Xu, Liang Yan & Yanjiao Huang

  4. Respiratory Medicine and Acute Care Center, First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China

    Qiang Li & Qun Chen

  5. Department of Diagnostic Radiology, Yong Loo Lin School of Medicine; Department of Chemical and Biomolecular Engineering, College of Design and Engineering; Department of Biomedical Engineering, College of Design and Engineering; Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science; Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine; Nanomedicine Translational Research Program, Yong Loo Lin School of Medicine; Theranostics Center of Excellence (TCE), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Xuanbo Zhang, Yuanbo Pan, Jianhua Zou & Xiaoyuan Chen

  6. Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China

    Yuanbo Pan

  7. Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, China

    Zhouguang Wang

  8. Shandong Provincial Key Laboratory of Precision Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China

    Xiaoyuan Chen

  9. Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore

    Xiaoyuan Chen

Authors

  1. Zunyong Feng
  2. Liuxi Chu
  3. Qiang Li
  4. Jing Zhou
  5. Ping Wu
  6. Xuanbo Zhang
  7. Yuanbo Pan
  8. Jianhua Zou
  9. Qun Chen
  10. Zhiliang Xu
  11. Liang Yan
  12. Yanjiao Huang
  13. Xiaokun Li
  14. Zhouguang Wang
  15. Xiaoyuan Chen

Contributions

Z.Y.F. conceived and designed the overall study, supervised key experiments, and led data analysis and interpretation. Z.Y.F. and L.X.C. performed most molecular and cellular experiments. J.Z. and P.W. assisted with cell culture and animal studies. Q.L., Z.L.X., L.Y., and Y.J.H. contributed to data processing, statistical analysis, and figure preparation. X.B.Z., J.H.Z., and Q.C. provided essential reagents, technical guidance, and methodological support. Y.B.P. performed imaging and histopathological examinations. X.K.L., Z.G.W., and X.Y.C. jointly supervised the project, contributed to conceptual refinement, and provided funding and resources. Z.Y.F. wrote the manuscript with input from all authors. All authors discussed the results, revised the manuscript, and approved the final version.

Corresponding authors

Correspondence to Xiaokun Li, Zhouguang Wang or Xiaoyuan Chen.

Ethics declarations

Competing interests

Xiaoyuan Chen is a co-founder of and holds shares in Yantai Lannacheng Biotechnology Co., Ltd. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Communications thanks the anonymous reviewers for their contribution to the peer review of this work. A peer review file is available.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Source data

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Feng, Z., Chu, L., Li, Q. et al. Engineered VPg saRNA achieves cap-independent, low-immunogenic and precise encoding of therapeutic proteins in vivo. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68364-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/s41467-026-68364-w