Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

RNA therapeutics: beyond RNA interference and antisense oligonucleotides

Nature Reviews Drug Discovery volume 11, pages 125–140 (2012)Cite this article

Subjects

Key Points

  • All RNA-targeted therapeutic technologies exploit oligonucleotides that bind to target RNA, but they differ in their mechanism of action and produce different effects.

  • Small interfering RNAs, antisense oligonucleotides and external guide sequences lead to enzyme-dependent degradation of targeted mRNA. Drugs involving these approaches are designed to reduce the level of harmful gene products such as viral or bacterial proteins or disease-promoting cellular proteins. They could be useful against cancer as well as viral and bacterial infections, or used to prevent the accumulation of high levels of cholesterol in the bloodstream.

  • Steric-blocking oligonucleotides block the access of cellular machinery to pre-mRNA and mRNA without degrading RNA. Splice-switching oligonucleotides are discussed in detail in this Review; these oligonucleotides redirect alternative splicing, repair defective RNA or restore the production of proteins that are missing because of genetic defects. Splice-switching oligonucleotide-based drugs should be useful for the treatment of genetic diseases such as Duchenne muscular dystrophy, spinal muscular atrophy and β-thalassaemia.

  • Compared to classical small-molecule drugs, it is much more difficult to achieve intracellular delivery with oligonucleotides; this is still a major issue for this class of drugs. The advantage of oligonucleotides is their high specificity, which results from sequence-specific base pairing to target RNA.

  • The oligonucleotide-based drug fomivirsen was approved by the US Food and Drug Administration in 1998 for the treatment of viral retinitis in patients with AIDS. Oligonucleotide-based drugs are now in advanced clinical trials for the treatment of cancer and Duchenne muscular dystrophy as well as for lowering high cholesterol levels.

Abstract

Here, we discuss three RNA-based therapeutic technologies exploiting various oligonucleotides that bind to RNA by base pairing in a sequence-specific manner yet have different mechanisms of action and effects. RNA interference and antisense oligonucleotides downregulate gene expression by inducing enzyme-dependent degradation of targeted mRNA. Steric-blocking oligonucleotides block the access of cellular machinery to pre-mRNA and mRNA without degrading the RNA. Through this mechanism, steric-blocking oligonucleotides can redirect alternative splicing, repair defective RNA, restore protein production or downregulate gene expression. Moreover, they can be extensively chemically modified to acquire more drug-like properties. The ability of RNA-blocking oligonucleotides to restore gene function makes them best suited for the treatment of genetic disorders. Positive results from clinical trials for the treatment of Duchenne muscular dystrophy show that this technology is close to achieving its clinical potential.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mechanisms of oligonucleotide-induced downregulation of gene expression.
Figure 2: Oligonucleotide chemistries.
Figure 3: Mechanisms of oligonucleotide-induced modulation of gene expression.

References

  1. Davidson, B. L. & McCray, P. B. Jr. Current prospects for RNA interference-based therapies. Nature Rev. Genet. 12, 329–340 (2011).

    CAS  PubMed  Google Scholar 

  2. Goodchild, J. Therapeutic oligonucleotides. Methods Mol. Biol. 764, 1–15 (2011).

    CAS  PubMed  Google Scholar 

  3. Crooke, S. T. Vitravene — another piece in the mosaic. Antisense Nucleic Acid Drug Dev. 8, vii–viii (1998). This is a paper on the first — and so far the only — antisense oligonucleotide drug approved for use as a treatment for cytomegalovirus-induced retinitis in patients with advanced AIDS.

    CAS  PubMed  Google Scholar 

  4. Moshfeghi, A. A. & Puliafito, C. A. Pegaptanib sodium for the treatment of neovascular age-related macular degeneration. Expert Opin. Investig. Drugs 14, 671–682 (2005).

    CAS  PubMed  Google Scholar 

  5. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).

    CAS  PubMed  Google Scholar 

  6. de Fougerolles, A., Vornlocher, H. P., Maraganore, J. & Lieberman, J. Interfering with disease: a progress report on siRNA-based therapeutics. Nature Rev. Drug Discov. 6, 443–453 (2007).

    CAS  Google Scholar 

  7. Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001). This was the first demonstration that short double-stranded RNAs, now known as siRNAs can induce mRNA degradation via the RNAi pathway in human cells.

    CAS  PubMed  Google Scholar 

  8. Song, E. et al. RNA interference targeting Fas protects mice from fulminant hepatitis. Nature Med. 9, 347–351 (2003).

    CAS  PubMed  Google Scholar 

  9. Watts, J. K., Deleavey, G. F. & Damha, M. J. Chemically modified siRNA: tools and applications. Drug Discov. Today 13, 842–855 (2008).

    CAS  PubMed  Google Scholar 

  10. DeVincenzo, J. et al. Evaluation of the safety, tolerability and pharmacokinetics of ALN-RSV01, a novel RNAi antiviral therapeutic directed against respiratory syncytial virus (RSV). Antiviral Res. 77, 225–231 (2008).

    CAS  PubMed  Google Scholar 

  11. Semple, S. C. et al. Rational design of cationic lipids for siRNA delivery. Nature Biotech. 28, 172–176 (2010).

    CAS  Google Scholar 

  12. Jackson, A. L. & Linsley, P. S. Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nature Rev. Drug Discov. 9, 57–67 (2010).

    CAS  Google Scholar 

  13. Bonetta, L. RNA-based therapeutics: ready for delivery? Cell 136, 581–584 (2009).

    CAS  PubMed  Google Scholar 

  14. Couzin-Frankel, J. Drug research. Roche exits RNAi field, cuts 4800 jobs. Science 330, 1163 (2010).

    CAS  PubMed  Google Scholar 

  15. Krieg, A. M. Is RNAi dead? Mol. Ther. 19, 1001–1002 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Stein, C. A. Does antisense exist? Nature Med. 1, 1119–1121 (1995).

    CAS  PubMed  Google Scholar 

  17. Zamecnik, P. C. & Stephenson, M. L. Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc. Natl Acad. Sci. USA 75, 280–284 (1978).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Lima, W., Wu, H. & Crooke, S. T. in Antisense Drug Technology: Principles, Strategies, and Applications 2nd edn (ed. Crooke, S. T.) 47–74 (CRC Press, Boca Raton, Florida, 2007).

    Google Scholar 

  19. Raal, F. J. et al. Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolemia: a randomized, double-blind, placebo-controlled trial. Lancet 375, 998–1006 (2010).

    CAS  PubMed  Google Scholar 

  20. Chi, K. N. et al. Randomized Phase II study of docetaxel and prednisone with or without OGX-011 in patients with metastatic castration-resistant prostate cancer. J. Clin. Oncol. 28, 4247–4254 (2010).

    CAS  PubMed  Google Scholar 

  21. Chia, S. et al. Phase II trial of OGX-011 in combination with docetaxel in metastatic breast cancer. Clin. Cancer Res. 15, 708–713 (2009).

    CAS  PubMed  Google Scholar 

  22. Smith, C. C., Aurelian, L., Reddy, M. P., Miller, P. S. & Ts'o, P. O. Antiviral effect of an oligo(nucleoside methylphosphonate) complementary to the splice junction of herpes simplex virus type 1 immediate early pre-mRNAs 4 and 5. Proc. Natl Acad. Sci. USA 83, 2787–2791 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Stirchak, E. P., Summerton, J. E. & Weller, D. D. Uncharged stereoregular nucleic acid analogs: 2. Morpholino nucleoside oligomers with carbamate internucleoside linkages. Nucleic Acids Res. 17, 6129–6141 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Ozsolak, F. & Milos, P. M. RNA sequencing: advances, challenges and opportunities. Nature Rev. Genet. 12, 87–98 (2011).

    CAS  PubMed  Google Scholar 

  25. Sazani, P., Graziewicz, M. & Kole, R. in Antisense Drug Technology: Principles, Strategies, and Applications 2nd edn (ed. Crooke, S. T.) 89–114 (CRC Press, Boca Raton, 2007).

    Google Scholar 

  26. Lu, Q. L. et al. Systemic delivery of antisense oligoribonucleotide restores dystrophin expression in body-wide skeletal muscles. Proc. Natl Acad. Sci. USA 102, 198–203 (2005).

    CAS  PubMed  Google Scholar 

  27. Sazani, P. et al. Systemically delivered antisense oligomers upregulate gene expression in mouse tissues. Nature Biotech. 20, 1228–1233 (2002).

    CAS  Google Scholar 

  28. Dillman, J. et al. Efficient and persistent splice switching by systemically delivered LNA oligonucleotides in mice. Mol. Ther. 14, 471–475 (2006).

    Google Scholar 

  29. van Deutekom, J. C. et al. Local dystrophin restoration with antisense oligonucleotide PRO051. N. Engl. J. Med. 357, 2677–2686 (2007).

    CAS  PubMed  Google Scholar 

  30. Kinali, M. et al. Local restoration of dystrophin expression with the morpholino oligomer AVI-4658 in Duchenne muscular dystrophy: a single-blind, placebo-controlled, dose-escalation, proof-of-concept study. Lancet Neurol. 8, 918–928 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Goemans, N. M. et al. Systemic administration of PRO051 in Duchenne's muscular dystrophy. N. Engl. J. Med. 364, 1513–1522 (2011).

    CAS  PubMed  Google Scholar 

  32. Cirak, S. et al. Exon skipping and dystrophin restoration in patients with Duchenne muscular dystrophy after systemic phosphorodiamidate morpholino oligomer treatment: an open-label, Phase 2, dose-escalation study. Lancet 378, 595–605 (2011). These two studies showed encouraging results in clinical trials applying two SSO variants, 2′-OMe phosphorothioate (reference 31) and PMO (reference 32), for the systemic treatment of Duchenne muscular dystrophy.

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Van Ommen, G. J., van Deutekom, J. & Aaartsma-Rus, A. The therapeutic potential of antisense-mediated exon skipping. Curr. Opin. Mol. Ther. 10, 140–149 (2008).

    CAS  PubMed  Google Scholar 

  34. Muntoni, F., Torelli, S. & Ferlini, A. Dystrophin and mutations: one gene, several proteins, multiple phenotypes. Lancet Neurol. 2, 731–740 (2003).

    CAS  PubMed  Google Scholar 

  35. Matsuo, M. et al. Exon skipping during splicing of dystrophin mRNA precursor due to an intraexon deletion in the dystrophin gene of Duchenne muscular dystrophy kobe. J. Clin. Invest. 87, 2127–2131 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Aartsma-Rus, A. et al. Theoretic applicability of antisense-mediated exon skipping for Duchenne muscular dystrophy mutations. Hum. Mutat. 30, 293–299 (2009).

    PubMed  Google Scholar 

  37. Wilton, S. D. et al. Specific removal of the nonsense mutation from the mdx dystrophin mRNA using antisense oligonucleotides. Neuromuscul. Disord. 9, 330–338 (1999).

    CAS  PubMed  Google Scholar 

  38. Bulfield, G., Siller, W., Wight, P. & Moore, K. X chromosome-linked muscular dystrophy (mdx) in the mouse. Proc. Natl Acad. Sci. USA 81, 1189–1192 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Lu, Q. L. et al. Functional amounts of dystrophin produced by skipping the mutated exon in the mdx dystrophic mouse. Nature Med. 9, 1009–1014 (2003).

    CAS  PubMed  Google Scholar 

  40. Takeshima, Y. et al. Oligonucleotides against a splicing enhancer sequence led to dystrophin production in muscle cells from a Duchenne muscular dystrophy patient. Brain Dev. 23, 788–790 (2001).

    CAS  PubMed  Google Scholar 

  41. van Deutekom, J. C. et al. Antisense-induced exon skipping restores dystrophin expression in DMD patient derived muscle cells. Hum. Mol. Genet. 10, 1547–1554 (2001).

    CAS  PubMed  Google Scholar 

  42. Heemskerk, H. A. et al. In vivo comparison of 2′-O-methyl phosphorothioate and morpholino antisense oligonucleotides for Duchenne muscular dystrophy exon skipping. J. Gene Med. 11, 257–266 (2009).

    CAS  PubMed  Google Scholar 

  43. Alter, J. et al. Systemic delivery of morpholino oligonucleotide restores dystrophin expression bodywide and improves dystrophic pathology. Nature Med. 12, 175–177 (2006).

    CAS  PubMed  Google Scholar 

  44. Yokota, T. Efficacy of systemic morpholino exon-skipping in Duchenne dystrophy dogs. Ann. Neurol. 65, 667–676 (2009).

    PubMed  PubMed Central  Google Scholar 

  45. Muntoni, F. & Wood, M. J. Targeting RNA to treat neuromuscular disease. Nature Rev. Drug Discov. 10, 621–637 (2011).

    CAS  Google Scholar 

  46. Sazani, P., Weller, D. L. & Shrewsbury, S. B. Safety pharmacology and genotoxicity evaluation of AVI-4658. Int. J. Toxicol. 29, 143–156 (2010).

    CAS  PubMed  Google Scholar 

  47. Wu, B. et al. Dose-dependent restoration of dystrophin expression in cardiac muscle of dystrophic mice by systemically delivered morpholino. Gene Ther. 17, 132–140 (2010).

    CAS  PubMed  Google Scholar 

  48. Heemskerk, H. et al. Preclinical PK and PD studies on 2′-O-methyl-phosphorothioate RNA antisense oligonucleotides in the mdx mouse model. Mol. Ther. 18, 1210–1217 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Jearawiriyapaisarn, N. et al. Sustained dystrophin expression induced by peptide-conjugated morpholino oligomers in the muscles of mdx mice. Mol. Ther. 16, 1624–1629 (2008).

    CAS  PubMed  Google Scholar 

  50. Jearawiriyapaisarn, N., Moulton, H. M., Sazani, P., Kole, R. & Willis, M. S. Long-term improvement in mdx cardiomyopathy after therapy with peptide-conjugated morpholino oligomers. Cardiovasc. Res. 85, 444–453 (2010).

    CAS  PubMed  Google Scholar 

  51. Wu, B. et al. Effective rescue of dystrophin improves cardiac function in dystrophin-deficient mice by a modified morpholino oligomer. Proc. Natl Acad. Sci. USA 105, 14814–14819 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Goyenvalle, A. et al. Prevention of dystrophic pathology in severely affected dystrophin/utrophin-deficient mice by morpholino-oligomer-mediated exon-skipping. Mol. Ther. 18, 198–205 (2010).

    CAS  PubMed  Google Scholar 

  53. Yin, H. et al. Pip5 transduction peptides direct high efficiency oligonucleotide-mediated dystrophin exon skipping in heart and phenotypic correction in mdx mice. Mol. Ther. 19, 1295–1303 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Youngblood, D. S., Hatlevig, S. A., Hassinger, J. N., Iversen, P. L. & Moulton, H. M. Stability of cell-penetrating peptide–morpholino oligomer conjugates in human serum and in cells. Bioconjug. Chem. 18, 50–60 (2007).

    CAS  PubMed  Google Scholar 

  55. Lefebvre, S. et al. Identification and characterization of a spinal muscular atrophy-determining gene. Cell 80, 155–165 (1995).

    Article  CAS  PubMed  Google Scholar 

  56. Lorson, C. L., Hahnen, E., Androphy, E. J. & Wirth, B. A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. Proc. Natl Acad. Sci. USA 96, 6307–6311 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Hua, Y., Vickers, T. A., Baker, B. F., Bennett, C. F. & Krainer, A. R. Enhancement of SMN2 exon 7 inclusion by antisense oligonucleotides targeting the exon. PLoS Biol. 5, e73 (2007).

    PubMed  PubMed Central  Google Scholar 

  58. Singh, N. K., Singh, N. N., Androphy, E. J. & Singh, R. N. Splicing of a critical exon of human survival motor neuron is regulated by a unique silencer element located in the last intron. Mol. Cell Biol. 26, 1333–1346 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Hua, Y., Vickers, T. A., Okunola, H. L., Bennett, C. F. & Krainer, A. R. Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am. J. Hum. Genet. 82, 834–848 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Williams, J. H. et al. Oligonucleotide-mediated survival of motor neuron protein expression in CNS improves phenotype in a mouse model of spinal muscular atrophy. J. Neurosci. 29, 7633–7638 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Hua, Y. et al. Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes Dev. 24, 1634–1644 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Passini, M. A. et al. Antisense oligonucleotides delivered to the mouse CNS ameliorate symptoms of severe spinal muscular atrophy. Sci. Transl. Med. 3, 72ra18 (2011).

    PubMed  PubMed Central  Google Scholar 

  63. Hua, Y. et al. Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model. Nature 478, 123–126 (2011). This paper reported the unexpected discovery that in a mouse model of spinal muscular atrophy the phenotype can be reversed not only by intrathecal but also by systemic peripheral delivery of an SSO that promotes the correct expression of the SMN2 gene.

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Gibbons, R., Higgs, D. R., Olivieri, N. F. & Wood, W. G. in The Thalassaemia Syndromes 4th edn Ch. 7 (eds Weatherall, D. J. & Clegg, J. B.) 287–356 (Blackwell Science, Oxford, 2001).

    Google Scholar 

  65. Dominski, Z. & Kole, R. Restoration of correct splicing in thalassemic pre-mRNA by antisense oligonucleotides. Proc. Natl Acad. Sci. USA 90, 8673–8677 (1993). This was the first report of oligonucleotide-mediated RNA repair of thalassaemic pre-mRNA by SSOs.

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Lewis, J. et al. A common human β globin splicing mutation modeled in mice. Blood 91, 2152–2156 (1998).

    CAS  PubMed  Google Scholar 

  67. Svasti, S. et al. RNA repair restores hemoglobin expression in IVS2-654 thalassemic mice. Proc. Natl Acad. Sci. USA 106, 1205–1210 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Xie, S. Y. et al. Correction of β654-thalassaemia mice using direct intravenous injection of siRNA and antisense RNA vectors. Int. J. Hematol. 93, 301–310 (2011).

    CAS  PubMed  Google Scholar 

  69. Cao, A. & Galanello, R. β-thalassemia. Genet. Med. 12, 61–76 (2010).

    CAS  PubMed  Google Scholar 

  70. Taylor, J. K., Zhang, Q. Q., Wyatt, J. R. & Dean, N. M. Induction of endogenous Bcl-xS through the control of Bcl-x pre-mRNA splicing by antisense oligonucleotides. Nature Biotech. 17, 1097–1100 (1999).

    CAS  Google Scholar 

  71. Mercatante, D. R., Bortner, C. D., Cidlowski, J. A. & Kole, R. Modification of alternative splicing of Bcl-x pre-mRNA in prostate and breast cancer cells. analysis of apoptosis and cell death. J. Biol. Chem. 276, 16411–16417 (2001).

    CAS  PubMed  Google Scholar 

  72. Graziewicz, M. A. et al. An endogenous TNF-α antagonist induced by splice-switching oligonucleotides reduces inflammation in hepatitis and arthritis mouse models. Mol. Ther. 16, 1316–1322 (2008).

    CAS  PubMed  Google Scholar 

  73. Paquet, J. et al. Alternative for anti-TNF antibodies for arthritis treatment. Mol. Ther. 19, 1887–1895 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Miller, J. W. et al. Recruitment of human muscleblind proteins to (CUG)n expansions associated with myotonic dystrophy. EMBO J. 19, 4439–4448 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Lee, J. E. & Cooper, T. A. Pathogenic mechanisms of myotonic dystrophy. Biochem. Soc. Trans. 37, 1281–1286 (2009).

    CAS  PubMed  Google Scholar 

  76. Wheeler, T. M. et al. Reversal of RNA dominance by displacement of protein sequestered on triplet repeat RNA. Science 325, 336–339 (2009). This paper describes the in vivo application of SSO-displacing splicing factors bound to an expanded triplet repeat as a potential treatment for myotonic dystrophy.

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Mulders, S. A. et al. Triplet-repeat oligonucleotide mediated reversal of RNA toxicity in myotonic dystrophy. Proc. Natl Acad. Sci. USA 106, 13915–13920 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Nakamori, M., Gourdon, G. & Thornton, C. A. Stabilization of expanded (CTG)•(CAG) repeats by antisense oligonucleotides. Mol. Ther. 19, 2222–2227 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Geller, B. L., Deere, J., Tilley, L. & Iversen, P. L. Antisense phosphorodiamidate morpholino oligomer inhibits viability of Escherichia coli in pure culture and in mouse peritonitis. J. Antimicrob. Chemother. 55, 983–988 (2005).

    CAS  PubMed  Google Scholar 

  80. Mellbye, B. L., Puckett, S. E., Tilley, L. D., Iversen, P. L. & Geller, B. L. Variations in amino acid composition of antisense peptide-phosphorodiamidate morpholino oligomer affect potency against Escherichia coli in vitro and in vivo. Antimicrob. Agents Chemother. 53, 525–530 (2009).

    CAS  PubMed  Google Scholar 

  81. Mellbye, B. L. et al. Cationic phosphorodiamidate morpholino oligomers efficiently prevent growth of Escherichia coli in vitro and in vivo. J. Antimicrob. Chemother. 65, 98–106 (2010).

    CAS  PubMed  Google Scholar 

  82. Shen, N. et al. Inactivation of expression of several genes in a variety of bacterial species by EGS technology. Proc. Natl Acad. Sci. USA 106, 8163–8168 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Lundblad, E. W. & Altman, S. Inhibition of gene expression by RNase P. Nature Biotech. 27, 212–221 (2010).

    CAS  Google Scholar 

  84. Wesolowski, D. et al. Basicpeptide–morpholino oligomer conjugate that is very effective in killing bacteria by gene-specific and nonspecific modes. Proc. Natl Acad. Sci. USA 108, 16582–16587 (2011). This paper describes the application of EGS technology using PPMOs as a potential treatment for drug-resistant bacterial infections.

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Jiang, X. et al. Engineered external guide sequences effectively block viral gene expression and replication in cultured cells. J. Biol. Chem. 286, 322–330 (2011).

    CAS  PubMed  Google Scholar 

  86. Warren, T. K. et al. Advanced antisense therapies for postexposure protection against lethal filovirus infections. Nature Med. 16, 991–994 (2010). This study showed that PMO-based translation-suppressing oligomers protect monkeys from lethal haemorrhagic infection by Ebola and Marburg viruses.

    CAS  PubMed  Google Scholar 

  87. Lai, S. H. et al. Inhibition of respiratory syncytial virus infections with morpholino oligomers in cell cultures and in mice. Mol. Ther. 16, 1120–1128 (2008).

    CAS  PubMed  Google Scholar 

  88. Eide, K. et al. Reduction of herpes simplex virus type-2 replication in cell cultures and in rodent models with peptide-conjugated morpholino oligomers. Antivir. Ther. 15, 1141–1149 (2010).

    CAS  PubMed  Google Scholar 

  89. Stone, J. K. et al. A morpholino oligomer targeting highly conserved internal ribosome entry site sequence is able to inhibit multiple species of picornavirus. Antimicrob. Agents Chemother. 52, 1970–1981 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Gabriel, G., Nordmann, A., Stein, D. A., Iversen, P. L. & Klenk, H. D. Morpholino oligomers targeting the PB1 and NP genes enhance the survival of mice infected with highly pathogenic influenza A H7N7 virus. J. Gen. Virol. 89, 939–948 (2008).

    CAS  PubMed  Google Scholar 

  91. Lupfer, C. et al. Inhibition of influenza A H3N8 virus infections in mice by morpholino oligomers. Arch. Virol. 153, 929–937 (2008).

    CAS  PubMed  Google Scholar 

  92. Paessler, S. et al. Inhibition of alphavirus infection in cell culture and in mice with antisense morpholino oligomers. Virology 376, 357–370 (2008).

    CAS  PubMed  Google Scholar 

  93. Lipinski, C. A. Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods 44, 235–249 (2000). This paper describes desirable properties for an effective drug, and leads the reader to the conclusion that oligonucleotides lack such criteria.

    CAS  PubMed  Google Scholar 

  94. Köhler, G. & Milstein, C. Continuous cultures of fused cells secreting antibody of predefined specificity. Nature 256, 495–497 (1975).

    PubMed  Google Scholar 

  95. Waldmann, T. A. Immunotherapy: past, present and future. Nature Med. 9, 269–277 (2003).

    CAS  PubMed  Google Scholar 

  96. Stephenson, M. L. & Zamecnik, P. C. Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc. Natl Acad. Sci. USA 75, 285–288 (1978). This paper describes the discovery of an oligonucleotide that acts as an antisense compound that is capable of preventing viral replication.

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Matsukura, M. et al. Phosphorothioate analogs of oligodeoxynucleotides: inhibitors of replication and cytopathic effects of human immunodeficiency virus. Proc. Natl Acad. Sci. USA 84, 7706–7710 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Agrawal, S., Mayrand, S. H., Zamecnik, P. C. & Pederson, T. Site-specific excision from RNA by RNase H and mixed-phosphate-backbone oligodeoxynucleotides. Proc. Natl Acad. Sci. USA 87, 1401–1405 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Geary, R. S., Yu, R. Z. & Levin, A. A. in Antisense Drug Technologies: Principles, Strategies, and Applications 2nd edn (ed. Crooke, S. T.) 183–217 (CRC Press, Boca Raton, Florida, 2007).

    Google Scholar 

  100. Krieg, A. M. Therapeutic potential of Toll-like receptor 9 activation. Nature Rev. Drug Discov. 5, 471–484 (2006).

    CAS  Google Scholar 

  101. Agarwala, S. S. et al. LDH correlation with survival in advanced melanoma from two large, randomised trials (Oblimersen GM301 and EORTC 18951). Eur. J. Cancer 45, 1807–1814 (2009).

    PubMed  Google Scholar 

  102. Chanan-Khan, A. A. et al. Phase III randomised study of dexamethasone with or without oblimersen sodium for patients with advanced multiple myeloma. Leuk. Lymphoma 50, 559–565 (2009).

    CAS  PubMed  Google Scholar 

  103. Morrison, T. Genta plunges on failed Phase III survival analysis for Genasense. BioWorld website [online], (2011).

    Google Scholar 

  104. Berget, S. M., Moore, C. & Sharp, P. A. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc. Natl Acad. Sci. USA 74, 3171–3175 (1977).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Chow, L. T., Gelinas, R. E., Broker, T. R. & Roberts, R. J. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12, 1–8 (1977).

    CAS  PubMed  Google Scholar 

  106. Spritz, R. A. et al. Base substitution in an intervening sequence of a beta+-thalassemic human globin gene. Proc. Natl Acad. Sci. USA 78, 2455–2459 (1981).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Busslinger, M., Moschonas, N. & Flavell, R. A. β+ thalassemia: aberrant splicing results from a single point mutation in an intron. Cell 27, 289–298 (1981).

    CAS  PubMed  Google Scholar 

  108. Tazi, J., Bakkour, N. & Stamm, S. Alternative splicing and disease. Biochim. Biophys. Acta 1792, 14–26 (2009).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

R.K. would like to thank his past and present colleagues at AVI BioPharma for helpful comments on this article. A.R.K. thanks his collaborators at Cold Spring Harbor Laboratory and Isis Pharmaceuticals for helpful discussions.

Author information

Authors and Affiliations

  1. AVI BioPharma, 3450 Monte Villa Parkway, Bothell, 98021, Washington, USA

    Ryszard Kole

  2. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724, New York, USA

    Adrian R. Krainer

  3. Department of Molecular, Cellular and Developmental Biology, 219 Prospect Street, Yale University, New Haven, 06520, Connecticut, USA

    Sidney Altman

Authors
  1. Ryszard Kole
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adrian R. Krainer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sidney Altman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ryszard Kole.

Ethics declarations

Competing interests

Ryszard Kole is an employee and shareholder of AVI BioPharma.

Adrian R. Krainer is a consultant for, and has ongoing collaborations with, Isis Pharmaceuticals.

Sidney Altman declares no competing financial interests.

Related links

Related links

FURTHER INFORMATION

Alnylam Pharmaceuticals website — 4 June 2011 press release

AVI BioPharma website — 25 March 2010 press release

AVI BioPharma website — Hemorrhagic Viruses

ClinicalTrials.gov website

Forbes website — 'Genta's Tangled Path' (29 April 2002)

GenomeWeb website — 'Pfizer to Shut Down Oligo Therapeutics Unit as Part of Restructuring' (3 February 2011)

OncoGenex website — 30 September 2010 press release

Proactive investors website — 'Will RNAi Therapeutics Ever Succeed? Roche, Pfizer, Abbott, Merck, Novartis trim commitments' (15 October 2011)

Glossary

RNA interference

(RNAi). A form of post-transcriptional gene silencing in which the expression or transfection of double-stranded RNA induces degradation by nucleases of the homologous endogenous transcripts, resulting in the reduction or loss of gene activity.

Antisense oligonucleotides

Oligonucleotides that bind to complementary mRNA by base pairing and induce cleavage of targeted mRNA by ribonuclease H, an enzyme that degrades RNA in RNA–DNA duplexes.

Small interfering RNAs

(siRNAs). Synthetic, short, 21–22-nucleotide-long double-stranded RNAs with chemical modifications designed to increase their stability and cellular uptake. One strand of siRNA hybridizes to targeted mRNA and allows mRNA degradation.

RNA-induced silencing complex

(RISC). A multiprotein complex that, when combined with small interfering RNA (siRNA), affects mRNA degradation. A key component of RISC is an endonuclease, argonaute 2, which cleaves the targeted mRNA within the siRNA–mRNA duplex.

Translation-suppressing oligonucleotides

(TSOs). Modified oligonucleotides that block mRNA sequences near the initiation of the translation codon (AUG), interfere with the binding of ribosomes to mRNA and inhibit the translation of undesirable proteins. TSO–mRNA duplexes are not recognized by ribonuclease H or RNA-induced silencing complex, and the mRNA is therefore not cleaved.

External guide sequence

(EGS). A short RNA sequence designed to bind to targeted mRNA and form a structure that is recognized by a tRNA-processing ribozyme, ribonuclease P. Ribonuclease P cleaves mRNA and thereby downregulates the function of a targeted gene.

Splice-switching oligonucleotides

(SSOs). Chemically modified oligonucleotides that block sequences in pre-mRNA that are involved in pre-mRNA splicing, and redirect mRNA splicing pathways. SSO–pre-mRNA duplexes are not recognized by ribonuclease H or the RNA-induced silencing complex, and the pre-mRNA is thus not cleaved.

Alternative splicing

Splicing of pre-mRNA to yield more than one kind of mRNA — that is, different splice variants — by frequently including or excluding an exon.

Translational reading frame

Arrangement of mRNA nucleotides into triplets (codons) that, when read by the ribosome, are translated into one amino acid per codon. The reading frame usually starts with a translation initiation codon, AUG — for example, AUG UUU ACA GCA. Deletion of a nucleotide, such as the third uridylic in the second codon, changes the reading frame to AUG 'UUA CAG CA', thus preventing the translation of the desired protein.

Exonic splicing silencers

Sequences present in exons in pre-mRNA that contribute to the modulation of splicing. They can inhibit the inclusion of a given exon into mature mRNA during splicing. Exonic splicing enhancers also exist.

Intronic splicing silencers

Sequences present in introns in pre-mRNA that contribute to the modulation of splicing. They can inhibit the inclusion of a given intron into mature mRNA during splicing. Intronic splicing enhancers also exist.

Cryptic splice site

A splice site that is not functional under normal conditions but becomes activated if a mutation modifies its sequence to resemble a functional splice site or if an adjacent normal splice site is inactivated by a mutation.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kole, R., Krainer, A. & Altman, S. RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov 11, 125–140 (2012). https://doi.org/10.1038/nrd3625

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrd3625

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research