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Strategies in Designing Multigene Expression Units to Downregulate HIV-1

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RNA Interference

Part of the book series: Methods in Molecular Biology ((MIMB,volume 623))

Abstract

The treatment of viral diseases such as HIV and HCV is limited by the genetic diversity of the viruses, especially when they are under the selective pressure of drugs. This problem holds true for gene-based therapies using RNAi in which there is evolution of drug-resistant strains under the discriminating pressure of treatment (1, 2). In a gene therapy setting for treatment of HIV, the incorporation of multiple effector molecules, targeting different viral and cellular sequences, can improve viral inhibition by substantially delaying the emergence of escape mutants (3-8). However, for short hairpin RNA triggers of RNAi, high levels of expression by strong Pol III promoters has led to cell toxicity, and even death in experimental animals (9, 10). Here, we describe a new combinatorial anti-HIV gene expression system allowing simultaneous expression of multiple RNAi effector units from a single Pol II polycistronic transcript. Our platform is suitable for the inclusion of any shRNA sequence and can be combined with other types of small RNA antiviral inhibitors.

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References

  1. Dykxhoorn, D.M. and Lieberman, J. (2006) Silencing viral infection. PLoS Med 3(7):e242.

    Article  PubMed  Google Scholar 

  2. Grimm, D. and Kay, M.A. (2007) Combinatorial RNAi: A Winning Strategy for the Race Against Evolving Targets? Mol. Ther. 15(5): 878–888.

    CAS  PubMed  Google Scholar 

  3. Andersson, M.G., Haasnoot, P.C., Xu, N., Berenjian, S., Berkhout, B. and Akusjarvi, G. (2005) Suppression of RNA interference by adenovirus virus-associated RNA. J. Virol. 79(15):9556–9565.

    Article  CAS  PubMed  Google Scholar 

  4. Chang, L.J., Liu, X. and He, J. (2005) Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1. Gene Ther. 12(14):1133–1144.

    Article  CAS  PubMed  Google Scholar 

  5. Henry, S.D., van der Wegen, P., Metselaar, H.J., Tilanus, H.W., Scholte, B.J. and van der Laan, L.J. (2006) Simultaneous targeting of HCV replication and viral binding with a single lentiviral vector containing multiple RNA interference expression cassettes. Mol. Ther. 14(4):485–493.

    Article  CAS  PubMed  Google Scholar 

  6. Li, M. and Rossi, J.J. (2005) Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells. Methods Mol. Biol. 309:261–272.

    CAS  PubMed  Google Scholar 

  7. ter Brake, O., Konstantinova, P., Ceylan, M. and Berkhout, B. (2006) Silencing of HIV-1 with RNA interference: a multiple shRNA approach. Mol. Ther. 14(6):883–892.

    Article  PubMed  Google Scholar 

  8. ter Brake, O., t Hooft, K., Liu, Y.P., Centlivre, M., von Eije, K.J. and Berkhout, B. (2008) Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition. Mol. Ther. 16(3):557–564.

    Article  PubMed  Google Scholar 

  9. An, D.S., Qin, F.X., Auyeung, V.C., et al. (2006) Optimization and functional effects of stable short hairpin RNA expression in primary human lymphocytes via lentiviral vectors. Mol. Ther. 14(4):494–504.

    Article  CAS  PubMed  Google Scholar 

  10. Grimm, D., Streetz, K.L., Jopling, C.L., et al. (2006) Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441(7092):537–541.

    Article  CAS  PubMed  Google Scholar 

  11. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411(6836):494–498.

    Article  CAS  PubMed  Google Scholar 

  12. Brummelkamp, T.R., Bernards, R., and Agami, R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296(5567):550–553.

    Article  CAS  PubMed  Google Scholar 

  13. Paddison, P.J., Caudy, A.A., Bernstein, E., Hannon, G.J., and Conklin, D.S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16(8):948–958.

    Article  CAS  PubMed  Google Scholar 

  14. Bartel, D.P. and Chen, C.Z. (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5(5):396–400.

    Article  CAS  PubMed  Google Scholar 

  15. Zeng, Y., Wagner, E.J. and Cullen, B.R. (2002) Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell 9(6):1327–1333.

    Article  CAS  PubMed  Google Scholar 

  16. Li, M.J., Bauer, G., Michienzi, A., et al. (2003) Inhibition of HIV-1 infection by lentiviral vectors expressing Pol III-promoted anti-HIV RNAs. Mol. Ther. 8(2):196–206.

    Article  CAS  PubMed  Google Scholar 

  17. Rubinson, D.A., Dillon, C.P., Kwiatkowski, A.V., et al. (2003) A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat. Genet. 33(3): 401–406.

    Article  CAS  PubMed  Google Scholar 

  18. Snove, O., Jr. and Rossi, J.J. (2006) Expressing short hairpin RNAs in vivo. Nat. Methods 3(9):689–695.

    Article  CAS  PubMed  Google Scholar 

  19. Song, E., Lee, S.K., Dykxhoorn, D.M., et al. (2003) Sustained small interfering RNA-mediated human immunodeficiency virus type 1 inhibition in primary macrophages. J. Virol. 77(13):7174–1781.

    Article  CAS  PubMed  Google Scholar 

  20. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297.

    Article  CAS  PubMed  Google Scholar 

  21. Kim, V.N. (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6(5):376–385.

    Article  CAS  PubMed  Google Scholar 

  22. Kim, V.N. (2005) Small RNAs: classification, biogenesis, and function. Mol. Cells 19 (1):1–15.

    Article  CAS  PubMed  Google Scholar 

  23. Aagaard, L.A., Zhang, J., von Eije, K.J., et al. (2008) Engineering and optimization of the miR-106b cluster for ectopic expression of multiplexed anti-HIV RNAs. Gene Ther. 15(23):1536–1549.

    Article  CAS  PubMed  Google Scholar 

  24. Chendrimada, T.P., Gregory, R.I., Kumaraswamy, E., et al. (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436(7051):740-744

    Article  CAS  PubMed  Google Scholar 

  25. Gregory, R.I., Chendrimada, T.P., Cooch, N. and Shiekhattar, R. (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123(4):631–640.

    Article  CAS  PubMed  Google Scholar 

  26. Lee, Y., Jeon, K., Lee, J.T., Kim, S. and Kim, V.N. (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21(17):4663–4670.

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Jane Zhang .

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Zhang, J., Rossi, J.J. (2010). Strategies in Designing Multigene Expression Units to Downregulate HIV-1. In: Min, WP., Ichim, T. (eds) RNA Interference. Methods in Molecular Biology, vol 623. Humana Press. https://doi.org/10.1007/978-1-60761-588-0_8

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  • DOI: https://doi.org/10.1007/978-1-60761-588-0_8

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-587-3

  • Online ISBN: 978-1-60761-588-0

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