Characterization of an HIV-targeted transcriptional gene-silencing RNA in primary cells

Human Gene Therapy

Volumn 23, Issue 5, 2012, Pages 473-483

  Turner, Anne Marie W ^a   Ackley, Amanda M ^a   Matrone, Michael A ^a   Morris, Kevin V ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN P53; VIRUS RNA;

ARTICLE; CD4+ T LYMPHOCYTE; CONTROLLED STUDY; GENE SILENCING; HUMAN IMMUNODEFICIENCY VIRUS; PROTEIN EXPRESSION; RNA ANALYSIS; TRANSCRIPTIONAL GENE SILENCING;

CD4-POSITIVE T-LYMPHOCYTES; CHROMATIN; GENE SILENCING; GENETIC VECTORS; HEK293 CELLS; HIV-1; HUMANS; JURKAT CELLS; PROMOTER REGIONS, GENETIC; RNA, ANTISENSE; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION; TUMOR SUPPRESSOR PROTEIN P53;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84861670544     PISSN: 10430342     EISSN: 15577422     Source Type: Journal    
DOI: 10.1089/hum.2011.165     Document Type: Article

References (46)

1. Allison, A.C., and Eugui, E.M. (2000). Mycophenolate mofetil and its mechanisms of action. Immunopharmacology 47, 85-118. (Pubitemid 30394534)
2. Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B Stat. Methodol. 57, 289-300.
3. Bhat, K.P., Itahana, K., Jin, A., and Zhang, Y. (2004). Essential role of ribosomal protein L11 in mediating growth inhibitioninduced p53 activation. EMBO J. 23, 2402-2412. (Pubitemid 38954847)
4. Bolstad, B.M., Irizarry, R.A., Astrand, M., and Speed, T.P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193. (Pubitemid 36181903)
5. Castanotto, D., Tommasi, S., Li, M.J., et al. (2005). Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol. Ther. 12, 179-183. (Pubitemid 40862370)
6. Chapuis, A.G., Rizzardi, G.P., D'Agostino, C., et al. (2000). Effects of mycophenolic acid on human immunodeficiency virus infection in vitro and in vivo. Nat. Med. 6, 762-768. (Pubitemid 30469424)
7. Coull, J.J., Turner, D., Melby, T., et al. (2001). A pilot study of the use of mycophenolate mofetil as a component of therapy for multidrug-resistant HIV-1 infection. J. Acquir. Immune Defic. Syndr. 26, 423-434. (Pubitemid 32489020)
8. Dai, M.-S., Zeng, S.X., Jin, Y., et al. (2004). Ribosomal protein L23 activates p53 by inhibiting MDM2 function in response to ribosomal perturbation but not to translation inhibition. Mol. Cell. Biol. 24, 7654-7668. (Pubitemid 39121491)
9. DiGiusto, D.L., Krishnan, A., Li, L., et al. (2010). RNA-based gene therapy for HIV with lentiviral vector-modified CD34 + cells in patients undergoing transplantation for AIDS-related lymphoma. Sci. Transl. Med. 2, 36-43.
10. El-Deiry, W.S., Tokino, T., Velculescu, V.E., et al. (1993). WAF1, a potential mediator of p53 tumor suppression. Cell 75, 817-825. (Pubitemid 23346378)
11. Gilkes, D.M., Chen, L., and Chen, J. (2006). MDMX regulation of p53 response to ribosomal stress. EMBO J. 25, 5614-5625. (Pubitemid 44847201)
12. 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, 537-541. (Pubitemid 44050158)
13. Hawkins, P.G., Santoso, S., Adams, C., et al. (2009). Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res. 37, 2984-2995.
14. Hö lzel, M., Orban, M., Hochstatter, J., et al. (2010). Defects in 18 S or 28 S rRNA processing activate the p53 pathway. J. Biol. Chem. 285, 6364-6370.
15. Hossain, M.M., Coull, J.J., Drusano, G.L., and Margolis, D.M. (2002). Dose proportional inhibition of HIV-1 replication by mycophenolic acid and synergistic inhibition in combination with abacavir, didanosine, and tenofovir. Antiviral Res. 55, 41-52. (Pubitemid 34655641)
16. Huang, C., and Yu, Y.-T. (2010). Targeted 2¢-O methylation at a nucleotide within the pseudoknot of telomerase RNA reduces telomerase activity in vivo. Mol. Cell. Biol. 30, 4368-4378.
17. Huang, C., Karijolich, J., and Yu, Y.-T. (2011). Post-transcriptional modification of RNAs by artificial box H/ACA and box C/D RNPs. Methods Mol. Biol. 718, 227-244.
18. Irizarry, R.A., Bolstad, B.M., Collin, F., et al. (2003). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15.
19. Jin, A., Itahana, K., O'Keefe, K., and Zhang, Y. (2004). Inhibition of HDM2 and activation of p53 by ribosomal protein L23. Mol. Cell. Biol. 24, 7669-7680. (Pubitemid 39121492)
20. Kim, D.H., Villeneuve, L.M., Morris, K.V., and Rossi, J.J. (2006). Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol. 13, 793-797. (Pubitemid 44338773)
21. Kim, D.H., Saetrom, P., Snove, O., and Rossi, J.J. (2008). Micro-RNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 105, 16230-16235.
22. Kim, J.-W., Zhang, Y.-H., Zern, M.A., et al. (2007). Short hairpin RNA causes the methylation of transforming growth factorbeta receptor II promoter and silencing of the target gene in rat hepatic stellate cells. Biochem. Biophys. Res. Commun. 359, 292-297. (Pubitemid 46880504)
23. Kiss-László, Z., Henry, Y., Bachellerie, J.-P., et al. (1996). Sitespecific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077-1088. (Pubitemid 26231174)
24. Knowling, S., Turner, A.M., Uhlmann, E., et al. (2011). Chemically modified antisense oligonucleotide modulate transcription gene silencing in human cells. Manuscript in submission.
25. Levine, B.L., Humeau, L.M., Boyer, J., et al. (2006). Gene transfer in humans using a conditionally replicating lentiviral vector. Proc. Natl. Acad. Sci. U.S.A. 103, 17372-17377. (Pubitemid 44788976)
26. Marks, P.W., Arai, M., Bandura, J.L., and Kwiatkowski, D.J. (1998). Advillin (p92): a new member of the gelsolin/villin family of actin regulatory proteins. J. Cell Sci. 111, 2129-2136. (Pubitemid 28403518)
27. Morris, K.V. (2011). The emerging role of RNA in the regulation of gene transcription in human cells. Semin. Cell Dev. Biol. 22, 351-358.
28. Morris, K.V., and Looney, D.J. (2005). Characterization of human immunodeficiency virus (HIV)-2 vector mobilization by HIV-1. Hum. Gene Ther. 16, 1463-1472. (Pubitemid 41829021)
29. Morris, K.V., Chan, S.W., Jacobsen, S.E., and Looney, D.J. (2004a). Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305, 1289-1292. (Pubitemid 39129233)
30. Morris, K.V., Gilbert, J., Wong-Staal, F., et al. (2004b). Transduction of cell lines and primary cells by FIV-packaged HIV vectors. Mol. Ther. 10, 181-190. (Pubitemid 38878160)
31. Moses, J., Goodchild, A., and Rivory, L.P. (2010). Intended transcriptional silencing with siRNA results in gene repression through sequence-specific off-targeting. RNA 16, 430-441.
32. Rebane, A., Roomere, H., and Metspalu, A. (2002). Locations of several novel 2¢-O-methylated nucleotides in human 28S rRNA. BMC Mol. Biol. 3, 1.
33. Rossi, J.J., June, C.H., and Kohn, D.B. (2007). Genetic therapies against HIV. Nat. Biotechnol. 25, 1444-1454. (Pubitemid 350233141)
34. Smith, S.D., Shatsky, M., Cohen, P.S., et al. (1984). Monoclonal antibody and enzymatic profiles of human malignant Tlymphoid cells and derived cell lines. Cancer Res. 44, 5657-5660. (Pubitemid 15183573)
35. Smyth, G.K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 3.
36. Sun, X.-X., Dai, M.-S., and Lu, H. (2008). Mycophenolic acid activation of p53 requires ribosomal proteins L5 and L11. J. Biol. Chem. 283, 12387-12392.
37. Suzuki, K., Shijuuku, T., Fukamachi, T., et al. (2005). Prolonged transcriptional silencing and CpG methylation induced by dsRNAs targeted to the HIV-1 promoter region. J. RNAi Gene Silencing 1, 66-78.
38. Suzuki, K., Juelich, T., Lim, H., et al. (2008). Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J. Biol. Chem. 283, 23353-23363.
39. 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, 883-892. (Pubitemid 44743127)
40. Turner, A.M., and Morris, K.V. (2010). Controlling transcription with noncoding RNAs in mammalian cells. Biotechniques 48, ix-xvi.
41. Turner, A.-M.W., De La Cruz, J., and Morris, K.V. (2008). Mobilization-competent lentiviral vector-mediated sustained transcriptional modulation of HIV-1 expression. Mol. Ther. 17, 360-368.
42. Unwalla, H.J., Li, M.-J., Kim, J.D., et al. (2004). Negative feedback inhibition of HIV-1 by TAT-inducible expression of siRNA. Nat. Biotechnol. 22, 1573-1578. (Pubitemid 40039461)
43. Weinberg, M.S., Villeneuve, L.M., Ehsani, A., et al. (2006). The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12, 256-262. (Pubitemid 43121930)
44. Weinberg, M.S., Barichievy, S., Schaffer, L., et al. (2007). An RNA targeted to the HIV-1 LTR promoter modulates indiscriminate off-target gene activation. Nucleic Acids Res. 35, 7303-7312.
45. Yam, P., Jensen, M., Akkina, R., et al. (2006). Ex vivo selection and expansion of cells based on expression of a mutated inosine monophosphate dehydrogenase 2 after HIV vector transduction: effects on lymphocytes, monocytes, and CD34 + stem cells. Mol. Ther. 14, 236-244. (Pubitemid 43942347)
46. Yamagishi, M., Ishida, T., Miyake, A., et al. (2009). Retroviral delivery of promoter-targeted shRNA induces long-term silencing of HIV-1 transcription. Microbes Infect. 11, 500-508.