Rational design of rigid mRNA folding architecture to enhance intracellular processing and protein production
Source abstract
Abstract
The application of messenger RNA (mRNA) beyond infectious diseases is challenged by inefficient protein production. Whereas the engineering of secondary mRNA structures has been shown to increase mRNA half-life, it remains unclear whether tertiary mRNA structures influence therapeutic efficacy. Here we develop a metal-ion-assisted RNA folding (MARF) strategy and show that, when delivered with lipid nanoparticles (LNPs), specific metals promote mRNA folding architectures that result in the amplification of protein expression by up to 7.3-fold compared with control mRNA. This effect is due to altered mechanical interactions between the mRNA LNPs and the surrounding biosystem, resulting in enhanced intracellular processing and prolonged retention of delivered mRNA in targeted cells. Administered intravenously, MARF LNPs achieved effective and durable genome editing of the clinically relevant Pcsk9 gene through treatment with a single dose. Overall, this work provides a new MARF technology for more effective mRNA therapy and highlights the potential of mechanical cues in designing nanoparticles for improved mRNA delivery.
Source: europepmc · Quality: candidate unverified · Source record ↗
Research context
OpenAlex topics: RNA Interference and Gene Delivery · RNA and protein synthesis mechanisms · Lipid Membrane Structure and Behavior
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (43)
Show source-provided references
1. Kulkarni, J. A. et al. The current landscape of nucleic acid therapeutics. Nat. Nanotechnol. 16, 630–643 (2021).10.1038/s41565-021-00898-0 ↗
2. Mendes, B. B. et al. Nanodelivery of nucleic acids. Nat. Rev. Methods Primers 2, 24 (2022).10.1038/s43586-022-00104-y ↗
3. Hogan, M. J. & Pardi, N. mRNA vaccines in the COVID-19 pandemic and beyond. Annu. Rev. Med. 73, 17–39 (2022).10.1146/annurev-med-042420-112725 ↗
4. Liu, C. et al. mRNA-based cancer therapeutics. Nat. Rev. Cancer 23, 526–543 (2023).10.1038/s41568-023-00586-2 ↗
5. Kowalski, P. S., Rudra, A., Miao, L. & Anderson, D. G. Delivering the messenger: advances in technologies for therapeutic mRNA delivery. Mol. Ther. 27, 710–728 (2019).10.1016/j.ymthe.2019.02.012 ↗
6. 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 23, 165–175 (2005).10.1016/j.immuni.2005.06.008 ↗
7. Rohner, E., Yang, R., Foo, K. S., Goedel, A. & Chien, K. R. Unlocking the promise of mRNA therapeutics. Nat. Biotechnol. 40, 1586–1600 (2022).10.1038/s41587-022-01491-z ↗
8. Rappaport, A. R. et al. Low-dose self-amplifying mRNA COVID-19 vaccine drives strong protective immunity in non-human primates against SARS-CoV-2 infection. Nat. Commun. 13, 3289 (2022).10.1038/s41467-022-31005-z ↗
9. Qu, L. et al. Circular RNA vaccines against SARS-CoV-2 and emerging variants. Cell 185, 1728–1744 (2022).10.1016/j.cell.2022.03.044 ↗
10. Leppek, K. et al. Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. Nat. Commun. 13, 1536 (2022).10.1038/s41467-022-28776-w ↗
11. Zhang, H. et al. Algorithm for optimized mRNA design improves stability and immunogenicity. Nature 621, 396–403 (2023).10.1038/s41586-023-06127-z ↗
12. Wojtczak, B. A. et al. 5′-Phosphorothiolate dinucleotide cap analogues: reagents for messenger RNA modification and potent small-molecular inhibitors of decapping enzymes. J. Am. Chem. Soc. 140, 5987–5999 (2018).10.1021/jacs.8b02597 ↗
13. Holtkamp, S. et al. Modification of antigen-encoding RNA increases stability, translational efficacy, and T-cell stimulatory capacity of dendritic cells. Blood 108, 4009–4017 (2006).10.1182/blood-2006-04-015024 ↗
14. Chen, H. et al. Chemical and topological design of multicapped mRNA and capped circular RNA to augment translation. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02393-y (2024).10.1038/s41587-024-02393-y ↗
15. Chen, H. et al. Branched chemically modified poly(A) tails enhance the translation capacity of mRNA. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02174-7 (2024).10.1038/s41587-024-02174-7 ↗
16. Liu, B. & Pan, T. Building better mRNA for therapeutics. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02424-8 (2024).10.1038/s41587-024-02424-8 ↗
17. Pyle, A. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7, 679–690 (2002).10.1007/s00775-002-0387-6 ↗
18. Tinoco, I. Jr & Bustamante, C. How RNA folds. J. Mol. Biol. 293, 271–281 (1999).10.1006/jmbi.1999.3001 ↗
19. Draper, D. E., Grilley, D. & Soto, A. M. Ions and RNA folding. Annu. Rev. Biophys. Biomol. Struct. 34, 221–243 (2005).10.1146/annurev.biophys.34.040204.144511 ↗
20. Palermo, G. et al. Catalytic metal ions and enzymatic processing of DNA and RNA. Acc. Chem. Res. 48, 220–228 (2015).10.1021/ar500314j ↗
21. Zoroddu, M. A. et al. The essential metals for humans: a brief overview. J. Inorg. Biochem. 195, 120–129 (2019).10.1016/j.jinorgbio.2019.03.013 ↗
22. Guth-Metzler, R. et al. Goldilocks and RNA: where Mg2+ concentration is just right. Nucleic Acids Res. 51, 3529–3539 (2023).10.1093/nar/gkad124 ↗
23. Bepperling, A. & Richter, G. Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation. Eur. Biophys. J. 52, 393–400 (2023).10.1007/s00249-023-01663-y ↗
24. Smith, S. B., Cui, Y. & Bustamante, C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795–799 (1996).10.1126/science.271.5250.795 ↗
25. Baumann, C. G., Smith, S. B., Bloomfield, V. A. & Bustamante, C. Ionic effects on the elasticity of single DNA molecules. Proc. Natl Acad. Sci. USA 94, 6185–6190 (1997).10.1073/pnas.94.12.6185 ↗
26. Li, Z. et al. Mechano-boosting nanomedicine antitumour efficacy by blocking the reticuloendothelial system with stiff nanogels. Nat. Commun. 14, 1437 (2023).10.1038/s41467-023-37150-3 ↗
27. Hui, Y. et al. Nanoparticle elasticity regulates phagocytosis and cancer cell uptake. Sci. Adv. 6, eaaz4316 (2020).10.1126/sciadv.aaz4316 ↗
28. Zhu, Y.-L. et al. GALAMOST: GPU-accelerated large-scale molecular simulation toolkit. J. Comput. Chem. 34, 2197–2211 (2013).10.1002/jcc.23365 ↗
29. Uroda, T. et al. Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques. Nat. Protoc. 15, 2107–2139 (2020).10.1038/s41596-020-0323-7 ↗
30. Miao, L. et al. Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver. Nat. Commun. 11, 2424 (2020).10.1038/s41467-020-16248-y ↗
31. Sun, J. et al. Tunable rigidity of (polymeric core)–(lipid shell) nanoparticles for regulated cellular uptake. Adv. Mater. 27, 1402–1407 (2015).10.1002/adma.201404788 ↗
32. Shen, Z., Ye, H., Yi, X. & Li, Y. Membrane wrapping efficiency of elastic nanoparticles during endocytosis: size and shape matter. ACS Nano 13, 215–228 (2019).10.1021/acsnano.8b05340 ↗
33. Yi, X., Shi, X. & Gao, H. Cellular uptake of elastic nanoparticles. Phys. Rev. Lett. 107, 098101 (2011).10.1103/PhysRevLett.107.098101 ↗
34. Wang, Y. et al. Age-associated disparity in phagocytic clearance affects the efficacy of cancer nanotherapeutics. Nat. Nanotechnol. 19, 255–263 (2024).10.1038/s41565-023-01502-3 ↗
35. Wang, L. et al. Primary human breast cancer-associated endothelial cells favor interactions with nanomedicines. Adv. Mater. https://doi.org/10.1002/adma.202403986 (2024).10.1002/adma.202403986 ↗
36. Pattipeiluhu, R. et al. Anionic lipid nanoparticles preferentially deliver mRNA to the hepatic reticuloendothelial system. Adv. Mater. 34, 2201095 (2022).10.1002/adma.202201095 ↗
37. Nakamura, T., Yamada, K., Sato, Y. & Harashima, H. Lipid nanoparticles fuse with cell membranes of immune cells at low temperatures leading to the loss of transfection activity. Int. J. Pharm. 587, 119652 (2020).10.1016/j.ijpharm.2020.119652 ↗
38. Chatterjee, S., Kon, E., Sharma, P. & Peer, D. Endosomal escape: a bottleneck for LNP-mediated therapeutics. Proc. Natl Acad. Sci. USA 121, e2307800120 (2024).10.1073/pnas.2307800120 ↗
39. Akinc, A. et al. Targeted delivery of RNAi therapeutics with endogenous and exogenous ligand-based mechanisms. Mol. Ther. 18, 1357–1364 (2010).10.1038/mt.2010.85 ↗
40. Ezratty, E. J., Bertaux, C., Marcantonio, E. E. & Gundersen, G. G. Clathrin mediates integrin endocytosis for focal adhesion disassembly in migrating cells. J. Cell Biol. 187, 733–747 (2009).10.1083/jcb.200904054 ↗
41. Yin, B. et al. Sub-10 nm substrate roughness promotes the cellular uptake of nanoparticles by upregulating endocytosis-related genes. Nano Lett. 21, 1839–1847 (2021).10.1021/acs.nanolett.0c04932 ↗
42. Wang, X. et al. Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery. Nat. Protoc. 18, 265–291 (2023).10.1038/s41596-022-00755-x ↗
43. Cheng, Q. et al. Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR–Cas gene editing. Nat. Nanotechnol. 15, 313–320 (2020).10.1038/s41565-020-0669-6 ↗