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Small-molecule-based regulation of RNA-delivered circuits in mammalian cells

Nature Chemical Biology volume 14, pages 1043–1050 (2018)Cite this article

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Abstract

Synthetic mRNA is an attractive vehicle for gene therapies because of its transient nature and improved safety profile over DNA. However, unlike DNA, broadly applicable methods to control expression from mRNA are lacking. Here we describe a platform for small-molecule-based regulation of expression from modified RNA (modRNA) and self-replicating RNA (replicon) delivered to mammalian cells. Specifically, we engineer small-molecule-responsive RNA binding proteins to control expression of proteins from RNA-encoded genetic circuits. Coupled with specific modRNA dosages or engineered elements from a replicon, including a subgenomic promoter library, we demonstrate the capability to externally regulate the timing and level of protein expression. These control mechanisms facilitate the construction of ON, OFF, and two-output switches, with potential therapeutic applications such as inducible cancer immunotherapies. These circuits, along with other synthetic networks that can be developed using these tools, will expand the utility of synthetic mRNA as a therapeutic modality.

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Fig. 1: Small-molecule-based regulation of expression from modRNA.
Fig. 2: Small-molecule-based regulation of expression from replicons.
Fig. 3: Small-molecule-based ON switches driven from replicons.
Fig. 4: Small-molecule-based two-output switches driven from replicons.

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Data availability

The authors declare that data supporting the finding of this study are available within the article and its Supplementary Information. Sample analysis of cytometry data can be found in Supplementary Fig. 29. Replicon MoClo assembly plasmids have been submitted to Addgene with the accession numbers 115928, 115929, 115930, 115931, 115932, 115933, 115934, 115935, 115936, 115937, 115938, 115939, 115940, 115941, 115942, 115943, 115944, 115945, 115946, 115947, 115948, 115949, 115950, 115951, 115952, 115953, 115954, 115955, 115956, 115957, 115958, 115959, 115960, 115961, 115962, 115963, 115964, 115965, 115966, and 115967. A more detailed table can be found in Supplementary Fig. 30. Additional data are available from the corresponding authors upon reasonable request.

References

  1. Naldini, L. Gene therapy returns to centre stage. Nature 526, 351–360 (2015).

    Article  CAS  Google Scholar 

  2. Rangarajan, S. et al. AAV5-factor VIII gene transfer in severe hemophilia A. N. Engl. J. Med. 377, 2519–2530 (2017).

    Article  Google Scholar 

  3. George, L. A. et al. Hemophilia B gene therapy with a high-specific-activity factor IX variant. N. Engl. J. Med. 377, 2215–2227 (2017).

    Article  CAS  Google Scholar 

  4. Sahin, U., Karikó, K. & Türeci, Ö. mRNA-based therapeutics–developing a new class of drugs. Nat. Rev. Drug Discov. 13, 759–780 (2014).

    Article  CAS  Google Scholar 

  5. 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).

    Article  Google Scholar 

  6. Karikó, K. et al. Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability. Mol. Ther. 16, 1833–1840 (2008).

    Article  Google Scholar 

  7. Ljungberg, K. & Liljeström, P. Self-replicating alphavirus RNA vaccines. Expert Rev. Vaccines 14, 177–194 (2015).

    Article  CAS  Google Scholar 

  8. Strauss, J. H. & Strauss, E. G. The alphaviruses: gene expression, replication, and evolution. Microbiol. Rev. 58, 491–562 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Kitada, T., DiAndreth, B., Teague, B. & Weiss, R. Programming gene and engineered-cell therapies with synthetic biology. Science 359, eaad1067 (2018).

    Article  Google Scholar 

  10. Jenkins, P. V., Rawley, O., Smith, O. P. & O’Donnell, J. S. Elevated factor VIII levels and risk of venous thrombosis. Br. J. Haematol. 157, 653–663 (2012).

    Article  CAS  Google Scholar 

  11. Heikal, N. M. et al. Elevated factor IX activity is associated with an increased odds ratio for both arterial and venous thrombotic events. Am. J. Clin. Pathol. 140, 680–685 (2013).

    Article  Google Scholar 

  12. Leonard, J. P. et al. Effects of single-dose interleukin-12 exposure on interleukin-12-associated toxicity and interferon-gamma production. Blood 90, 2541–2548 (1997).

    CAS  PubMed  Google Scholar 

  13. Ryding, A. D., Sharp, M. G. & Mullins, J. J. Conditional transgenic technologies. J. Endocrinol. 171, 1–14 (2001).

    Article  CAS  Google Scholar 

  14. Townshend, B., Kennedy, A. B., Xiang, J. S. & Smolke, C. D. High-throughput cellular RNA device engineering. Nat. Methods 12, 989–994 (2015).

    Article  CAS  Google Scholar 

  15. Banaszynski, L. A., Chen, L. C., Maynard-Smith, L. A., Ooi, A. G. L. & Wandless, T. J. A. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules. Cell 126, 995–1004 (2006).

    Article  CAS  Google Scholar 

  16. Bonger, K. M., Chen, L. C., Liu, C. W. & Wandless, T. J. Small-molecule displacement of a cryptic degron causes conditional protein degradation. Nat. Chem. Biol. 7, 531–537 (2011).

    Article  CAS  Google Scholar 

  17. Chung, H. K. et al. Tunable and reversible drug control of protein production via a self-excising degron. Nat. Chem. Biol. 11, 713–720 (2015).

    Article  CAS  Google Scholar 

  18. An, W. et al. Engineering FKBP-based destabilizing domains to build sophisticated protein regulation systems. PLoS One 10, e0145783 (2015).

    Article  Google Scholar 

  19. Wroblewska, L. et al. Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery. Nat. Biotechnol. 33, 839–841 (2015).

    Article  CAS  Google Scholar 

  20. Kaczmarek, J. C., Kowalski, P. S. & Anderson, D. G. Advances in the delivery of RNA therapeutics: from concept to clinical reality. Genome Med. 9, 60 (2017).

    Article  Google Scholar 

  21. Garber, K. Alnylam terminates revusiran program, stock plunges. Nat. Biotechnol. 34, 1213–1214 (2016).

    Article  CAS  Google Scholar 

  22. Andries, O. et al. N1-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice. J. Control. Release 217, 337–344 (2015).

    Article  CAS  Google Scholar 

  23. Iwamoto, M., Björklund, T., Lundberg, C., Kirik, D. & Wandless, T. J. A general chemical method to regulate protein stability in the mammalian central nervous system. Chem. Biol. 17, 981–988 (2010).

    Article  CAS  Google Scholar 

  24. Sellmyer, M. A., Chen, L. C., Egeler, E. L., Rakhit, R. & Wandless, T. J. Intracellular context affects levels of a chemically dependent destabilizing domain. PLoS One 7, e43297 (2012).

    Article  CAS  Google Scholar 

  25. Saito, H. et al. Synthetic translational regulation by an L7Ae-kink-turn RNP switch. Nat. Chem. Biol. 6, 71–78 (2010).

    Article  CAS  Google Scholar 

  26. Gossen, M. & Bujard, H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. USA 89, 5547–5551 (1992).

    Article  CAS  Google Scholar 

  27. Belmont, B. J. & Niles, J. C. Engineering a direct and inducible protein-RNA interaction to regulate RNA biology. ACS Chem. Biol. 5, 851–861 (2010).

    Article  CAS  Google Scholar 

  28. Ganesan, S. M., Falla, A., Goldfless, S. J., Nasamu, A. S. & Niles, J. C. Synthetic RNA-protein modules integrated with native translation mechanisms to control gene expression in malaria parasites. Nat. Commun. 7, 10727 (2016).

    Article  CAS  Google Scholar 

  29. Yoshioka, N. et al. Efficient generation of human iPSCs by a synthetic self-replicative RNA. Cell Stem Cell 13, 246–254 (2013).

    Article  CAS  Google Scholar 

  30. Lundstrom, K. Alphavirus-based vaccines. Viruses 6, 2392–2415 (2014).

    Article  CAS  Google Scholar 

  31. Beal, J. et al. Model-driven engineering of gene expression from RNA replicons. ACS Synth. Biol. 4, 48–56 (2015).

    Article  CAS  Google Scholar 

  32. Frolov, I. et al. Alphavirus-based expression vectors: strategies and applications. Proc. Natl. Acad. Sci. USA 93, 11371–11377 (1996).

    Article  CAS  Google Scholar 

  33. Levis, R., Schlesinger, S. & Huang, H. V. Promoter for Sindbis virus RNA-dependent subgenomic RNA transcription. J. Virol. 64, 1726–1733 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Weber, E., Emgler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A modular cloning system for standardized assembly of multigene constructs. PLoS One 6, e16765–1733 (2018).

    Article  CAS  Google Scholar 

  35. Culver, J. N., Lehto, K., Close, S. M., Hilf, M. E. & Dawson, W. O. Genomic position affects the expression of tobacco mosaic virus movement and coat protein genes. Proc. Natl. Acad. Sci. USA 90, 2055–2059 (1993).

    Article  CAS  Google Scholar 

  36. Andries, O., Kitada, T., Bodner, K., Sanders, N. N. & Weiss, R. Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review. Expert Rev. Vaccines 14, 313–331 (2015).

    Article  CAS  Google Scholar 

  37. Hoarau, J. J. et al. Identical strength of the T cell responses against E2, nsP1 and capsid CHIKV proteins in recovered and chronic patients after the epidemics of 2005-2006 in La Reunion Island. PLoS One 8, e84695 (2013).

    Article  Google Scholar 

  38. Nathwani, A. C. et al. Long-term safety and efficacy of factor IX gene therapy in hemophilia B. N. Engl. J. Med. 371, 1994–2004 (2014).

    Article  Google Scholar 

  39. Maldonado, R. A. et al. Polymeric synthetic nanoparticles for the induction of antigen-specific immunological tolerance. Proc. Natl. Acad. Sci. USA 112, E156–E165 (2015).

    Article  CAS  Google Scholar 

  40. Kishimoto, T. K. et al. Improving the efficacy and safety of biologic drugs with tolerogenic nanoparticles. Nat. Nanotechnol. 11, 890–899 (2016).

    Article  CAS  Google Scholar 

  41. Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. A. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355–1358 (2010).

    Article  CAS  Google Scholar 

  42. Engler, C., Gruetzner, R., Kandzia, R. & Marillonnet, S. Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One 4, e5553 (2009).

    Article  Google Scholar 

  43. Wielgosz, M. M., Raju, R. & Huang, H. V. Sequence requirements for Sindbis virus subgenomic mRNA promoter function in cultured cells. J. Virol. 75, 3509–3519 (2001).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank J. Niles, B.J. Belmont, and S. Maddur Ganesan (MIT) for discussions regarding the TetR–aptamer system, A. Ghodasara (MIT) for discussions and technical assistance related to aptamers/aptazymes, and R. Petersen (Designs By Robin) for consultations with figure design and layout. This work was supported by research grants from the Defense Advanced Research Projects Agency (W911NF-11-2-0054: awarded to J.B., D.D., and R.W., supported T.W., J.B.R., X.Z., E.P., J.B., D.D., T.K., and R.W. and W32P4Q-13-1-0011: awarded to R.W., supported X.Z., T.K., and R.W.), the National Science Foundation (NSF#1522074, NSF#1521759: awarded to D.D., supported T.W. and D.D., CCF-1521925: awarded to D.D. and R.W., supported T.W, J.R.B., D.D., and R.W., CNS-1446607: awarded to R.W., supported J.R.B., B.T., and R.W., and MCB-1745645: awarded to R.W., supported J.R.B. and R.W.), the National Institutes of Health (5-R01-CA206218: awarded to R.W., supported J.B.R., E.P., and R.W.), the Ragon Institute of MGH, MIT and Harvard (awarded to R.W., supported A.W. and R.W.), the Special Research Fund from Ghent University (awarded to N.N.S.), and The Research Foundation - Flanders (FWO; G.0235.11N and G.0621.10N: awarded to N.N.S.). This work was also supported by a sponsored research agreement with Crucell Holland B.V. (awarded to R.W., supported: B.D., E.P., and R.W.). We further acknowledge the following support: MIT-Amgen UROP Scholars Program (K.B.), Gabilan Stanford Graduate Fellowship (K.B.), Fannie and John Hertz Foundation Fellowship - Hertz-Draper Fellow (K.B.), Stanford EDGE-STEM Doctoral Fellowship (K.B.), PhD fellowship and international mobility grant from FWO (O.A.), and the Emmanuel van der Schueren fellowship from “Kom op tegen Kanker” (O.A.).

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Author notes

  1. Katie Bodner

    Present address: Department of Bioengineering, Stanford University, Stanford, CA, USA

  2. Oliwia Andries

    Present address: Perrigo Company PLC, Nazareth, Belgium

  3. Tasuku Kitada

    Present address: Candriam Investors Group, Brussels, Belgium

  4. These authors contributed equally: Tyler E. Wagner, Jacob R. Becraft.

  5. These authors jointly directed this work: Tasuku Kitada, Ron Weiss.

Authors and Affiliations

  1. Department of Biomedical Engineering, Boston University, Boston, MA, USA

    Tyler E. Wagner & Douglas Densmore

  2. Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA

    Tyler E. Wagner, Jacob R. Becraft, Katie Bodner, Brian Teague, Xin Zhang, Amanda Woo, Ely Porter, Brian Dobosh, Tasuku Kitada & Ron Weiss

  3. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Jacob R. Becraft, Katie Bodner, Bremy Alburquerque & Ron Weiss

  4. Faculty of Veterinary Medicine, Department of Nutrition, Genetics and Ethology, Laboratory for Gene Therapy, Ghent University, Gent, Belgium

    Oliwia Andries & Niek N. Sanders

  5. Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium

    Niek N. Sanders

  6. Raytheon BBN Technologies, Cambridge, MA, USA

    Jacob Beal

  7. Biological Design Center, Boston University, Boston, MA, USA

    Douglas Densmore

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Contributions

J.R.B., T.W., K.B., and T.K. designed and performed experiments and analyzed data. X.Z., A.W., E.P., and B.D. performed experiments and interpreted data. O.A., N.N.S., and D.D. designed experiments. B.A. performed experiments. J.B. analyzed data. T.K. and R.W. supervised the study. T.W., J.R.B., B.T., T.K., and R.W. wrote the manuscript with the support of all other authors.

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Correspondence to Tasuku Kitada or Ron Weiss.

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Competing interests

MIT has filed a patent application (No. 15/509,258) pertaining to the technology described in this paper. T.W., J.R.B., K.B., T.K., and R.W. are co-inventors on this patent application. J.R.B. and T.K. are shareholders of a company founded based on the technology described in this article.

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Wagner, T.E., Becraft, J.R., Bodner, K. et al. Small-molecule-based regulation of RNA-delivered circuits in mammalian cells. Nat Chem Biol 14, 1043–1050 (2018). https://doi.org/10.1038/s41589-018-0146-9

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