Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision

Molecular Therapy Nucleic Acids

Volumn 3, Issue , 2014, Pages

  Denise, Hubert ^a   Moschos, Sterghios A ^b   Sidders, Benjamin ^c   Burden, Frances ^c   Perkins, Hannah ^c   Carter, Nikki ^c   Stroud, Tim ^c   Kennedy, Michael ^c   Fancy, Sally Ann ^c   Lapthorn, Cris ^c   Lavender, Helen ^c   Kinloch, Ross ^c   Suhy, David ^d   Corbau, Romu ^c  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b UNIVERSITY OF WESTMINSTER   (United Kingdom)

^c PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

^d Tacere Therapeutics Inc   (United States)

Author keywords

gene therapy; hcv; mechanism of action; race seq; shrna; sirna

Indexed keywords

COMPLEMENTARY DNA; RNA; RNA LIGASE; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; TT 034; UNCLASSIFIED DRUG; ADENOVIRUS VECTOR;

ADENO ASSOCIATED VIRUS; ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; HEPATITIS C VIRUS; NONHUMAN; PRIORITY JOURNAL; RNA CLEAVAGE; RNA INTERFERENCE; RNA PROCESSING; SEROTYPE; CYTOTOXICITY; GENOME; HUMAN; HUMAN CELL; NEXT GENERATION SEQUENCING; REPLICON;

EID: 84893825866     PISSN: None     EISSN: 21622531     Source Type: Journal    
DOI: 10.1038/mtna.2013.73     Document Type: Article

References (49)

1. Fassio, E (2010). Hepatitis C and hepatocellular carcinoma. Ann Hepatol 9 Suppl: 119-122.
2. Di Bisceglie, AM, Goodman, ZD, Ishak, KG, Hoofnagle, JH, Melpolder, JJ and Alter, HJ (1991). Long-Term clinical and histopathological follow-up of chronic posttransfusion hepatitis. Hepatology 14: 969-974.
3. Hannon, GJ and Rossi, JJ (2004). Unlocking the potential of the human genome with RNA interference. Nature 431: 371-378. (Pubitemid 39265678)
4. Hanecak, R, Brown-Driver, V, Fox, MC, Azad, RF, Furusako, S, Nozaki, C et al. (1996). Antisense oligonucleotide inhibition of hepatitis C virus gene expression in transformed hepatocytes. J Virol 70: 5203-5212. (Pubitemid 26240692)
5. Jarczak, D, Korf, M, Beger, C, Manns, MP and Krger, M (2005). Hairpin ribozymes in combination with siRNAs against highly conserved hepatitis C virus sequence inhibit RNA replication and protein translation from hepatitis C virus subgenomic replicons. FEBS J 272: 5910-5922. (Pubitemid 41689362)
6. Seo, MY, Abrignani, S, Houghton, M and Han, JH (2003). Small interfering RNA-mediated inhibition of hepatitis C virus replication in the human hepatoma cell line Huh-7. J Virol 77: 810-812. (Pubitemid 36005024)
7. Sagan, SM, Nasheri, N, Luebbert, C and Pezacki, JP (2010). The efficacy of siRNAs against hepatitis C virus is strongly influenced by structure and target site accessibility. Chem Biol 17: 515-527.
8. Kim, SI, Shin, D, Lee, H, Ahn, BY, Yoon, Y and Kim, M (2009). Targeted delivery of siRNA against hepatitis C virus by apolipoprotein A-I-bound cationic liposomes. J Hepatol 50: 479-488.
9. Yokota, T, Sakamoto, N, Enomoto, N, Tanabe, Y, Miyagishi, M, Maekawa, S et al. (2003). Inhibition of intracellular hepatitis C virus replication by synthetic and vector-derived small interfering RNAs. EMBO Rep 4: 602-608. (Pubitemid 36939952)
10. Brummelkamp, TR, Bernards, R and Agami, R (2002). A system for stable expression of short interfering RNAs in mammalian cells. Science 296: 550-553. (Pubitemid 34408678)
11. Suhy, DA, Kao, SC, Mao, T, Whiteley, L, Denise, H, Souberbielle, B et al. (2012). Safe, long-Term hepatic expression of anti-HCV shRNA in a nonhuman primate model. Mol Ther 20: 1737-1749.
12. Lavender, H, Brady, K, Burden, F, Delpuech-Adams, O, Denise, H, Palmer, A et al. (2012). In vitro characterization of the activity of PF-05095808, a novel biological agent for hepatitis C virus therapy. Antimicrob Agents Chemother 56: 1364-1375.
13. Moschos, SA. (2013) In: Jones, L and McKnight, AJ (eds). Biotherapeutics: Recent Developments Using Chemical and Molecular Biology. Royal Society of Chemistry Publishing: London, UK. pp. 176-223.
14. Rao, DD, Vorhies, JS, Senzer, N and Nemunaitis, J (2009). siRNA vs. shRNA: similarities and differences. Adv Drug Deliv Rev 61: 746-759.
15. Meister, G and Tuschl, T (2004). Mechanisms of gene silencing by double-stranded RNA. Nature 431: 343-349. (Pubitemid 39265674)
16. Fuchs, U, Damm-Welk, C and Borkhardt, A (2004). Silencing of disease-related genes by small interfering RNAs. Curr Mol Med 4: 507-517. (Pubitemid 38961194)
17. Zhang, H, Kolb, FA, Brondani, V, Billy, E and Filipowicz, W (2002). Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 21: 5875-5885. (Pubitemid 35315285)
18. Park, JE, Heo, I, Tian, Y, Simanshu, DK, Chang, H, Jee, D et al. (2011). Dicer recognizes the 5 end of RNA for efficient and accurate processing. Nature 475: 201-205.
19. Khvorova, A, Reynolds, A and Jayasena, SD (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216. (Pubitemid 37329584)
20. Schwarz, DS, Hutvgner, G, Du, T, Xu, Z, Aronin, N and Zamore, PD (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208. (Pubitemid 37329583)
21. Paddison, PJ, Caudy, AA, Bernstein, E, Hannon, GJ and Conklin, DS (2002). Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16: 948-958. (Pubitemid 34408544)
22. Kozomara, A and Griffiths-Jones, S (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39(Database issue): D152-D157.
23. Lee, LW, Zhang, S, Etheridge, A, Ma, L, Martin, D, Galas, D et al. (2010). Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 16: 2170-2180.
24. Bartel, DP (2009). MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
25. Hoerter, JA, Krishnan, V, Lionberger, TA and Walter, NG (2011). siRNA-like doublestranded RNAs are specifically protected against degradation in human cell extract. PLoS ONE 6: e20359.
26. Houseley, J and Tollervey, D (2009). The many pathways of RNA degradation. Cell 136: 763-776.
27. Cifuentes, D, Xue, H, Taylor, DW, Patnode, H, Mishima, Y, Cheloufi, S et al. (2010). A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 328: 1694-1698.
28. Yang, JS and Lai, EC (2010). Dicer-independent, Ago2-mediated microRNA biogenesis in vertebrates. Cell Cycle 9: 4455-4460.
29. Yang, JS, Maurin, T, Robine, N, Rasmussen, KD, Jeffrey, KL, Chandwani, R et al. (2010). Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc Natl Acad Sci USA 107: 15163-15168.
30. Cheloufi, S, Dos Santos, CO, Chong, MM and Hannon, GJ (2010). A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 465: 584-589.
31. Yang, JS, Maurin, T and Lai, EC (2012). Functional parameters of Dicer-independent microRNA biogenesis. RNA 18: 945-957.
32. Liu, YP, Schopman, NC and Berkhout, B (2013). Dicer-independent processing of short hairpin RNAs. Nucleic Acids Res 41: 3723-3733.
33. Langenberger, D, akir, MV, Hoffmann, S and Stadler, PF (2013). Dicer-processed small RNAs: rules and exceptions. J Exp Zool B Mol Dev Evol 320: 35-46.
34. Ruan, Y and Wei, CL (2010). Multiplex parallel pair-end-ditag sequencing approaches in system biology. Wiley Interdiscip Rev Syst Biol Med 2: 224-234.
35. Snead, NM and Rossi, JJ (2010). Biogenesis and function of endogenous and exogenous siRNAs. Wiley Interdiscip Rev RNA 1: 117-131.
36. Moschos, SA, Frick, M, Taylor, B, Turnpenny, P, Graves, H, Spink, KG et al. (2011). Uptake, efficacy, and systemic distribution of naked, inhaled short interfering RNA (siRNA) and locked nucleic acid (LNA) antisense. Mol Ther 19: 2163-2168.
37. Chu, CY and Rana, TM (2006). Translation repression in human cells by microRNAinduced gene silencing requires RCK/p54. PLoS Biol 4: e210.
38. Chi, SW, Zang, JB, Mele, A and Darnell, RB (2009). Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
39. Brock, GJ, Moschos, S, Spivack, SD and Hurteau, GJ (2011). The 3 prime paradigm of the miR-200 family and other microRNAs. Epigenetics 6: 268-272.
40. Sakurai, K, Amarzguioui, M, Kim, DH, Alluin, J, Heale, B, Song, MS et al. (2011). A role for human Dicer in pre-RISC loading of siRNAs. Nucleic Acids Res 39: 1510-1525.
41. Tomari, Y, Du, T and Zamore, PD (2007). Sorting of Drosophila small silencing RNAs. Cell 130: 299-308. (Pubitemid 47086328)
42. Jaskiewicz, L and Filipowicz, W (2008). Role of Dicer in posttranscriptional RNA silencing. Curr Top Microbiol Immunol 320: 77-97.
43. Thomson, DW, Bracken, CP and Goodall, GJ (2011). Experimental strategies for microRNA target identification. Nucleic Acids Res 39: 6845-6853.
44. Rivas, FV, Tolia, NH, Song, JJ, Aragon, JP, Liu, J, Hannon, GJ et al. (2005). Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol 12: 340-349. (Pubitemid 43093089)
45. Martell, M, Esteban, JI, Quer, J, Genesc, J, Weiner, A, Esteban, R et al. (1992). Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J Virol 66: 3225-3229.
46. Lisowski, L, Elazar, M, Chu, K, Glenn, JS and Kay, MA (2013). The anti-genomic (negative) strand of Hepatitis C Virus is not targetable by shRNA. Nucleic Acids Res 41: 3688-3698.
47. Herzog, RW, Fields, PA, Arruda, VR, Brubaker, JO, Armstrong, E, McClintock, D et al. (2002). Influence of vector dose on factor IX-specific T and B cell responses in muscledirected gene therapy. Hum Gene Ther 13: 1281-1291. (Pubitemid 35034508)
48. Wilhelm, BT, Marguerat, S, Goodhead, I and Bhler, J (2010). Defining transcribed regions using RNA-seq. Nat Protoc 5: 255-266.
49. Langmead, B, Trapnell, C, Pop, M and Salzberg, SL (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.