Silencing of genes responsible for polyQ diseases using chemically modified single-stranded siRNAs
Polyglutamine (polyQ) diseases comprise a group of nine genetic disorders that are caused by the expansion of the CAG triplet repeat, which encodes glutamine, in unrelated single genes. The pathogenesis is caused by the disruption of cellular pathways by the expression products of the mutant gene, i.e., proteins containing polyQ tracts and mutant transcripts. In considering oligonucleotide (ON)-based therapeutic approaches for polyQ diseases, the very attractive CAG repeat-targeting strategy offers selective silencing of the mutant allele by directly targeting the mutation site. CAG repeat-targeting miRNA-like siRNAs have been shown to specifically inhibit mutant gene expression, and their characteristic feature is the formation of mismatches in their interactions with the target site.Here, we designed novel single-stranded siRNAs that contain base substitutions and chemical modifications and tested these oligonucleotides in cellular models of Huntington’s disease (HD), spinocerebellar ataxia type 3 (SCA3) and dentatorubral-pallidoluysian atrophy (DRPLA), including HD mouse striatal cells. Selected siRNAs caused the efficient and selective downregulation of the mutant protein levels.
Aiba, Yuichiro, Jiaxin Hu, Jing Liu, Qin Xiang, Carlos Martinez, and David R Corey. 2013. “Allele-Selective Inhibition of Huntingtin and Ataxin-3 Expression by RNA Duplexes Containing Unlocked Nucleic Acid (UNA) Substitutions.” Biochemistry 52 (November): 9329–9338. doi:10.1021/bi4014209.
Amarzguioui, Mohammed, Torgeir Holen, Eshrat Babaie, and Hans Prydz. 2003. “Tolerance for Mutations and Chemical Modifications in a siRNA.” Nucleic Acids Research 31 (2): 589–595. doi:10.1093/nar/gkg147.
Bennett, C Frank, and Eric E Swayze. 2010. “RNA Targeting Therapeutics: Molecular Mechanisms of Antisense Oligonucleotides as a Therapeutic Platform.” Annual Review of Pharmacology and Toxicology 50 (January): 259–293. doi:10.1146/annurev.pharmtox.010909.105654.
Bramsen, J B, M B Laursen, A F Nielsen, T B Hansen, C Bus, N Langkjaer, B R Babu, et al. 2009. “A Large-Scale Chemical Modification Screen Identifies Design Rules to Generate siRNAs with High Activity, High Stability and Low Toxicity.” Nucleic Acids Res 37 (9): 2867–2881.
Chorn, Guillaume, Molly Klein-McDowell, Lihong Zhao, Matthew a Saunders, W Michael Flanagan, Aarron T Willingham, and Lee P Lim. 2012. “Single-Stranded microRNA Mimics.” RNA (New York, N.Y.) 18 (10): 1796–1804. doi:10.1261/rna.031278.111.
DiFiglia, M, M Sena-Esteves, K Chase, E Sapp, E Pfister, M Sass, J Yoder, et al. 2007. “Therapeutic Silencing of Mutant Huntingtin with siRNA Attenuates Striatal and Cortical Neuropathology and Behavioral Deficits.” Proc Natl Acad Sci U S A 104 (43): 17204–17209.
Dua, P, J W Yoo, S Kim, and D K Lee. 2011. “Modified siRNA Structure with a Single Nucleotide Bulge Overcomes Conventional siRNA-Mediated off-Target Silencing.” Mol Ther 19 (9): 1676–1687.
Engels, Joachim W. 2013. “Gene Silencing by Chemically Modified siRNAs.” New Biotechnology 30 (3): 302–307. doi:10.1016/j.nbt.2012.07.002.
Evers, Melvin M, Lodewijk J A Toonen, and Willeke M C van Roon-Mom. 2013. “Ataxin-3 Protein and RNA Toxicity in Spinocerebellar Ataxia Type 3: Current Insights and Emerging Therapeutic Strategies.” Molecular Neurobiology, November. doi:10.1007/s12035-013-8596-2.
Fan, Hueng-Chuen, Li-Ing Ho, Ching-Shiang Chi, Shyi-Jou Chen, Giia-Sheun Peng, Tzu-Min Chan, Shinn-Zong Lin, and Horng-Jyh Harn. 2014. “Polyglutamine (PolyQ) Diseases: Genetics to Treatments.” Cell Transplantation 23 (4). Cognizant Communication Corporation: 441–458. doi:10.3727/096368914X678454.
Fiszer, Agnieszka, and Wlodzimierz J Krzyzosiak. 2013. “RNA Toxicity in Polyglutamine Disorders: Concepts, Models, and Progress of Research.” Journal of Molecular Medicine (Berlin, Germany) 91 (6): 683–691. doi:10.1007/s00109-013-1016-2.
Fiszer, Agnieszka, and Wlodzimierz J Krzyzosiak. 2014. “Oligonucleotide-Based Strategies to Combat Polyglutamine Diseases.” Nucleic Acids Research, May. doi:10.1093/nar/gku385.
Fiszer, Agnieszka, Agnieszka Mykowska, and Wlodzimierz J Krzyzosiak. 2011. “Inhibition of Mutant Huntingtin Expression by RNA Duplex Targeting Expanded CAG Repeats.” Nucleic Acids Research 39 (13): 5578–5585.
Fiszer, Agnieszka, Marta Olejniczak, Paulina Galka-Marciniak, Agnieszka Mykowska, and Wlodzimierz J Krzyzosiak. 2013. “Self-Duplexing CUG Repeats Selectively Inhibit Mutant Huntingtin Expression.” Nucleic Acids Research 41: 10426–10437. doi:10.1093/nar/gkt825.
Fiszer, Agnieszka, Marta Olejniczak, Pawel M Switonski, Joanna P Wroblewska, Joanna Wisniewska-Kruk, Agnieszka Mykowska, and Wlodzimierz J Krzyzosiak. 2012. “An Evaluation of Oligonucleotide-Based Therapeutic Strategies for polyQ Diseases.” BMC Molecular Biology 13 (1): 6. doi:10.1186/1471-2199-13-6.
Haringsma, Henry J, Jenny J Li, Ferdie Soriano, Denise M Kenski, W Michael Flanagan, and Aarron T Willingham. 2012. “mRNA Knockdown by Single Strand RNA Is Improved by Chemical Modifications.” Nucleic Acids Research 40 (9): 4125–4136. doi:10.1093/nar/gkr1301.
Holen, Torgeir, Mohammed Amarzguioui, Eshrat Babaie, and Hans Prydz. 2003. “Similar Behaviour of Single-Strand and Double-Strand siRNAs Suggests They Act through a Common RNAi Pathway.” Nucleic Acids Res 31 (9): 2401–2407. doi:10.1093/nar/gkg338.
Hossbach, M, J Gruber, M Osborn, K Weber, and T Tuschl. 2006. “Gene Silencing with siRNA Duplexes Composed of Target-mRNA-Complementary and Partially Palindromic or Partially Complementary Single-Stranded siRNAs.” RNA Biol 3 (2): 82–89.
Hu, J, K T Gagnon, J Liu, J K Watts, J Syeda-Nawaz, C F Bennett, E E Swayze, J Randolph, J Chattopadhyaya, and D R Corey. 2011. “Allele-Selective Inhibition of Ataxin-3 (ATX3) Expression by Antisense Oligomers and Duplex RNAs.” Biol Chem 392 (4): 315–325.
Hu, J, J Liu, and D R Corey. 2010. “Allele-Selective Inhibition of Huntingtin Expression by Switching to an miRNA-like RNAi Mechanism.” Chem Biol 17 (11): 1183–1188.
Hu, Jiaxin, Jing Liu, K Jayaprakash Narayanannair, Jeremy G Lackey, Satya Kuchimanchi, Kallanthottathil G Rajeev, Muthiah Manoharan, et al. 2014. “Allele-Selective Inhibition of Mutant Atrophin-1 Expression by Duplex and Single-Stranded RNAs.” Biochemistry 53 (28): 4510–4518. doi:10.1021/bi500610r.
Hu, Jiaxin, Jing Liu, Dongbo Yu, Yuichiro Aiba, Suheung Lee, Hannah Pendergraff, Jihane Boubaker, et al. 2014. “Exploring the Effect of Sequence Length and Composition on Allele-Selective Inhibition of Human Huntingtin Expression by Single-Stranded Silencing RNAs.” Nucleic Acid Therapeutics, April. doi:10.1089/nat.2013.0476.
Hu, Jiaxin, Masayuki Matsui, Keith T Gagnon, Jacob C Schwartz, Sylvie Gabillet, Khalil Arar, Jun Wu, Ilya Bezprozvanny, and David R Corey. 2009. “Allele-Specific Silencing of Mutant Huntingtin and Ataxin-3 Genes by Targeting Expanded CAG Repeats in mRNAs.” Nat Biotechnol 27 (5): 478–484. doi:10.1038/nbt.1539.
Kole, R, A R Krainer, and S Altman. 2012. “RNA Therapeutics: Beyond RNA Interference and Antisense Oligonucleotides.” Nat Rev Drug Discov 11 (2): 125–140.
Kordasiewicz, Holly B., Lisa M. Stanek, Edward V. Wancewicz, Curt Mazur, Melissa M. McAlonis, Kimberly A. Pytel, Jonathan W. Artates, et al. 2012. “Sustained Therapeutic Reversal of Huntington’s Disease by Transient Repression of Huntingtin Synthesis.” Neuron 74 (6). Elsevier Inc.: 1031–1044. doi:10.1016/j.neuron.2012.05.009.
Kumar, Ashok, Sandeep Kumar Singh, Vijay Kumar, Dinesh Kumar, Sarita Agarwal, and Manoj Kumar Rana. 2015. “Huntington’s Disease: An Update of Therapeutic Strategies.” Gene 556 (2): 91–97. doi:10.1016/j.gene.2014.11.022.
Labbadia, John, and Richard I Morimoto. 2013. “Huntington’s Disease: Underlying Molecular Mechanisms and Emerging Concepts.” Trends in Biochemical Sciences 38 (8): 378–385. doi:10.1016/j.tibs.2013.05.003.
Lima, Walt F. F, Thazha P. P Prakash, Heather M. M Murray, Garth A. A Kinberger, Wenyu Li, Alfred E. E Chappell, Cheryl S. S Li, et al. 2012. “Single-Stranded siRNAs Activate RNAi in Animals.” Cell 150 (5): 883–894. doi:10.1016/j.cell.2012.08.014.
Liu, Jing, Hannah Pendergraff, K Jayaprakash Narayanannair, Jeremy G Lackey, Satya Kuchimanchi, Kallanthottathil G Rajeev, Muthiah Manoharan, Jiaxin Hu, and David R Corey. 2013. “RNA Duplexes with Abasic Substitutions Are Potent and Allele-Selective Inhibitors of Huntingtin and Ataxin-3 Expression.” Nucleic Acids Research 41 (18): 8788–8801. doi:10.1093/nar/gkt594.
Liu, Jing, Dongbo Yu, Yuichiro Aiba, Hannah Pendergraff, Eric E Swayze, Walt F Lima, Jiaxin Hu, Thazha P Prakash, and David R Corey. 2013. “Ss-siRNAs Allele Selectively Inhibit Ataxin-3 Expression: Multiple Mechanisms for an Alternative Gene Silencing Strategy.” Nucleic Acids Res 41 (20): 9570–9583. doi:10.1093/nar/gkt693.
Martinez, J, A Patkaniowska, H Urlaub, R Luhrmann, and T Tuschl. 2002. “Single-Stranded Antisense siRNAs Guide Target RNA Cleavage in RNAi.” Cell 110 (5): 563–574.
Ostergaard, M E, A L Southwell, H Kordasiewicz, A T Watt, N H Skotte, C N Doty, K Vaid, et al. 2013. “Rational Design of Antisense Oligonucleotides Targeting Single Nucleotide Polymorphisms for Potent and Allele Selective Suppression of Mutant Huntingtin in the CNS.” Nucleic Acids Res 41: 9634–9650.
Sibley, C R, Y Seow, and M J Wood. 2010. “Novel RNA-Based Strategies for Therapeutic Gene Silencing.” Mol Ther 18 (3): 466–476.
Sipa, Katarzyna, Elzbieta Sochacka, Julia Kazmierczak-Baranska, Maria Maszewska, Magdalena Janicka, Genowefa Nowak, and Barbara Nawrot. 2007. “Effect of Base Modifications on Structure, Thermodynamic Stability, and Gene Silencing Activity of Short Interfering RNA.” RNA (New York, N.Y.) 13 (8): 1301–1316. doi:10.1261/rna.538907.
Stiles, D, Z Zhang, P Ge, B Nelson, R Grondin, Y Ai, P Hardy, et al. 2011. “Widespread Suppression of Huntingtin with Convection-Enhanced Delivery of siRNA.” Exp Neurol 233: 463–471.
Trettel, F, D Rigamonti, P Hilditch-Maguire, V C Wheeler, A H Sharp, F Persichetti, E Cattaneo, and M E MacDonald. 2000. “Dominant Phenotypes Produced by the HD Mutation in STHdh(Q111) Striatal Cells.” Human Molecular Genetics 9 (19): 2799–2809.
Wang, Y L, W Liu, E Wada, M Murata, K Wada, and I Kanazawa. 2005. “Clinico-Pathological Rescue of a Model Mouse of Huntington’s Disease by siRNA.” Neurosci Res 53 (3): 241–249.
Xu, Y, A Linde, O Larsson, D Thormeyer, J Elmen, C Wahlestedt, and Z Liang. 2004. “Functional Comparison of Single- and Double-Stranded siRNAs in Mammalian Cells.” Biochem Biophys Res Commun 316 (3): 680–687.
Yu, Dongbo, Hannah Pendergraff, Jing Liu, Holly B. Kordasiewicz, Don W. W Cleveland, Eric E. E Swayze, Walt F. F Lima, Stanley T. T Crooke, Thazha P. P Prakash, and David R. R Corey. 2012. “Single-Stranded RNAs Use RNAi to Potently and Allele-Selectively Inhibit Mutant Huntingtin Expression.” Cell 150 (5): 895–908. doi:10.1016/j.cell.2012.08.002.
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