Advertisement

Design and Evaluation of Clinically Relevant SOFA-HDV Ribozymes Targeting HIV RNA

  • Robert J. Scarborough
  • Michel V. Lévesque
  • Jean-Pierre Perreault
  • Anne Gatignol
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1103)

Abstract

Nucleic acid therapies targeting HIV replication have the potential to be used in conjunction with or in place of the standard small-molecule therapies. Among the different classes of nucleic acid therapies, several ribozymes (Rzs, RNA enzymes) have been developed to target HIV RNA. The design of Rzs targeting HIV RNA is complicated by the sequence diversity of viral strains and the structural diversity of their target sites. Using the SOFA-HDV Rz as an example, this chapter describes methods that can be used to design Rzs for controlling HIV replication. We describe how to (1) identify highly conserved Rz target sites in HIV RNA; (2) generate a set of Rzs with the potential to be used as therapeutics; and (3) screen these Rzs for activity against HIV production.

Key words

HIV Ribozymes Sequence conservation Antisense RNA therapeutics 

References

  1. 1.
    De Clercq E (2010) Antiretroviral drugs. Curr Opin Pharmacol 10(5):507–515PubMedCrossRefGoogle Scholar
  2. 2.
    Tsibris AM, Hirsch MS (2010) Antiretroviral therapy in the clinic. J Virol 84(11):5458–5464PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Taiwo B, Hicks C, Eron J (2010) Unmet therapeutic needs in the new era of combination antiretroviral therapy for HIV-1. J Antimicrob Chemother 65(6):1100–1107PubMedCrossRefGoogle Scholar
  4. 4.
    Scherer LJ, Rossi JJ (2011) Ex vivo gene therapy for HIV-1 treatment. Hum Mol Genet 20(R1):R100–R107PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Burnett JC, Rossi JJ (2012) RNA-based therapeutics: current progress and future prospects. Chem Biol 19(1):60–71PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Serganov A, Patel DJ (2007) Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet 8(10):776–790PubMedCrossRefGoogle Scholar
  7. 7.
    Haasnoot J, Berkhout B (2009) Nucleic acids-based therapeutics in the battle against pathogenic viruses. Handb Exp Pharmacol 189:243–263PubMedCrossRefGoogle Scholar
  8. 8.
    Lainé S, Scarborough RJ, Lévesque D, Didierlaurent L, Soye KJ, Mougel M, Perreault JP, Gatignol A (2011) In vitro and in vivo cleavage of HIV-1 RNA by new SOFA-HDV ribozymes and their potential to inhibit viral replication. RNA Biol 8(2):343–353Google Scholar
  9. 9.
    Reyes-Darias JA, Sánchez-Luque FJ, Berzal-Herranz A (2008) Inhibition of HIV-1 replication by RNA-based strategies. Curr HIV Res 6(6):500–514PubMedCrossRefGoogle Scholar
  10. 10.
    Taylor JM (2006) Hepatitis delta virus. Virology 344(1):71–76PubMedCrossRefGoogle Scholar
  11. 11.
    Bergeron LJ, Perreault JP (2005) Target-dependent on/off switch increases ribozyme fidelity. Nucleic Acids Res 33(4): 1240–1248PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Bergeron LJ, Reymond C, Perreault JP (2005) Functional characterization of the SOFA delta ribozyme. RNA 11(12):1858–1868PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Asif-Ullah M, Lévesque M, Robichaud G, Perreault JP (2007) Development of ribozyme-based gene-inactivations; the example of the hepatitis delta virus ribozyme. Curr Gene Ther 7(3):205–216PubMedCrossRefGoogle Scholar
  14. 14.
    Lévesque MV, Lévesque D, Brière FP, Perreault JP (2010) Investigating a new generation of ribozymes in order to target HCV. PLoS One 5(3):e9627PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Motard J, Rouxel R, Paun A, von Messling V, Bisaillon M, Perreault JP (2011) A novel ribozyme-based prophylaxis inhibits influenza A virus replication and protects from severe disease. PLoS One 6(11):e27327PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Robichaud GA, Perreault JP, Ouellette RJ (2008) Development of an isoform-specific gene suppression system: the study of the human Pax-5B transcriptional element. Nucleic Acids Res 36(14):4609–4620PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Ben Aissa M, April MC, Bergeron LJ, Perreault JP, Levesque G (2012) Silencing of amyloid precursor protein expression using a new engineered delta ribozyme. Int J Alzheimers Dis 2012:947147PubMedCentralPubMedGoogle Scholar
  18. 18.
    D’Anjou F, Routhier S, Perreault JP, Latil A, Bonnel D, Fournier I, Salzet M, Day R (2011) Molecular validation of PACE4 as a target in prostate cancer. Transl Oncol 4(3):157–172PubMedCentralPubMedCrossRefGoogle Scholar
  19. 19.
    Lévesque MV, Perreault JP (2012) Target-induced SOFA-HDV ribozyme. Methods Mol Biol 848:369–384PubMedCrossRefGoogle Scholar
  20. 20.
    DeYoung MB, Hampel A (1997) Computer analysis of the conservation and uniqueness of ribozyme-targeted HIV sequences. Methods Mol Biol 74:27–36PubMedGoogle Scholar
  21. 21.
    Lee SK, Dykxhoorn DM, Kumar P, Ranjbar S, Song E, Maliszewski LE, François-Bongarçon V, Goldfeld A, Swamy NM, Lieberman J, Shankar P (2005) Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV. Blood 106(3):818–826PubMedCentralPubMedCrossRefGoogle Scholar
  22. 22.
    Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296(5567):550–553PubMedCrossRefGoogle Scholar
  24. 24.
    Good PD, Krikos AJ, Li SX, Bertrand E, Lee NS, Giver L, Ellington A, Zaia JA, Rossi JJ, Engelke DR (1997) Expression of small, therapeutic RNAs in human cell nuclei. Gene Ther 4(1):45–54PubMedCrossRefGoogle Scholar
  25. 25.
    Puerta-Fernández E, Barroso-del Jesus A, Romero-López C, Tapia N, Martínez MA, Berzal-Herranz A (2005) Inhibition of HIV-1 replication by RNA targeted against the LTR region. AIDS 19(9):863–870PubMedCrossRefGoogle Scholar
  26. 26.
    Unwalla HJ, Li H, Li SY, Abad D, Rossi JJ (2008) Use of a U16 snoRNA-containing ribozyme library to identify ribozyme targets in HIV-1. Mol Ther 16(6):1113–1119PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Chang LJ, Liu X, He J (2005) Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1. Gene Ther 12(14):1133–1144PubMedCrossRefGoogle Scholar
  28. 28.
    Peden KWC, Martin MA (1995) Virological and molecular genetic techniques for studies of established HIV isolates. In: Karn J (ed) HIV, a practical approach: virology and immunology. IRL Press, Oxford, pp 21–45Google Scholar
  29. 29.
    Clerzius G, Gélinas JF, Daher A, Bonnet M, Meurs EF, Gatignol A (2009) ADAR1 interacts with PKR during human immunodeficiency virus infection of lymphocytes and contributes to viral replication. J Virol 83(19):10119–10128PubMedCentralPubMedCrossRefGoogle Scholar
  30. 30.
    Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Lévesque MV, Rouleau SG, Perreault JP (2011) Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Ther 21(4):241–252PubMedCrossRefGoogle Scholar
  32. 32.
    Lucier JF, Bergeron LJ, Brière FP, Ouellette R, Elela SA, Perreault JP (2006) RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes. BMC Bioinformatics 7:480PubMedCentralPubMedCrossRefGoogle Scholar
  33. 33.
    Butler PJG (1995) Biological safety when working with HIV. In: Karn J (ed) HIV, a practical approach: virology and immunology. IRL Press, Oxford, pp 1–12Google Scholar

Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Robert J. Scarborough
    • 1
    • 2
    • 3
  • Michel V. Lévesque
    • 4
  • Jean-Pierre Perreault
    • 4
  • Anne Gatignol
    • 1
    • 2
    • 3
  1. 1.Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical ResearchMcGill UniversityMontréalCanada
  2. 2.Department of Microbiology & ImmunologyMcGill UniversityMontréalCanada
  3. 3.Department of Experimental MedicineMcGill UniversityMontréalCanada
  4. 4.RNA Group/Groupe ARN, Département de BiochimieUniversité de SherbrookeSherbrookeCanada

Personalised recommendations