RNAi as a potential new therapy for HIV infection

Future HIV Therapy

Volumn 2, Issue 6, 2008, Pages 567-577

  Wheeler, Lee A ^a   Dykxhoorn, Derek M ^b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

Antiviral therapy; Genetic therapy; HIV 1; RNAi; Sirna

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; APTAMER; CHEMOKINE RECEPTOR CCR5; CHEMOKINE RECEPTOR CXCR4; DICER; RIBOZYME; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; TOLL LIKE RECEPTOR;

AMINO ACID SEQUENCE; APOPTOSIS; BASE MISPAIRING; CD4 LYMPHOCYTE COUNT; CD4+ T LYMPHOCYTE; DRUG DESIGN; GENE EXPRESSION; GENE SILENCING; GENE TARGETING; HOST CELL; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOSTIMULATION; INFECTION CONTROL; INNATE IMMUNITY; LONG TERMINAL REPEAT; MACROPHAGE; MICROARRAY ANALYSIS; NONHUMAN; REVIEW; RNA INTERFERENCE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; T LYMPHOCYTE; VIRUS INHIBITION; VIRUS REPLICATION;

EID: 67149131702     PISSN: 17469600     EISSN: None     Source Type: Journal    
DOI: 10.2217/17469600.2.6.567     Document Type: Review

References (77)

1. Fauci AS, Johnston MI, Dieffenbach CW et al.: HIV vaccine research: the way forward. Science 321, 530-532 (2008).
2. Jorgensen R: Altered gene expression in plants due to trans interactions between homologous genes. Trends Biotechnol. 8, 340-344 (1990).
3. Wightman B, Ha I, Ruvkun G: Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855-862 (1993).
4. Lee RC, Feinbaum RL, Ambros V: The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854 (1993).
5. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC: Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998).
6. + progenitor cell-derived macrophages. Mol. Ther. 8, 62-71 (2003).
7. Novina CD, Murray MF, Dykxhoorn DM et al.: siRNA-directed inhibition of HIV-1 infection. Nat. Med. 8, 681-686 (2002).
8. Lee SK, Dykxhoorn DM, Kumar P et al.: Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV. Blood 106, 818-826 (2005).
9. Kumar P, Ban HS, Kim SS et al.: T cell-specific siRNA delivery suppresses HIV-1 infection in humanized mice. Cell 134, 577-586 (2008).
10. Song E, Lee SK, Dykxhoorn DM et al.: Sustained small interfering RNA-mediated human immunodeficiency virus type 1 inhibition in primary macrophages. J. Virol. 77, 7174-7181 (2003).
11. Song E, Zhu P, Lee SK et al.: Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors. Nat. Biotechnol. 23, 709-717 (2005).
12. Bitko V, Musiyenko A, Shulyayeva O, Barik S: Inhibition of respiratory viruses by nasally administered siRNA. Nat. Med. 11, 50-55 (2005).
13. Palliser D, Chowdhury D, Wang QY et al.: An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection. Nature 439, 89-94 (2006).
14. Peer D, Park EJ, Morishita Y, Carman CV, Shimaoka M: Systemic leukocyte-directed siRNA delivery revealing cyclin D1 as an anti-inflammatory target. Science 319, 627-630 (2008).
15. Hamar P, Song E, Kokeny G, Chen A, Ouyang N, Lieberman J: Small interfering RNA targeting Fas protects mice against renal ischemia-reperfusion injury. Proc. Natl Acad. Sci. USA 101, 14883-14888 (2004).
16. Song E, Lee SK, Wang J et al.: RNA interference targeting Fas protects mice from fulminant hepatitis. Nat. Med. 9, 347-351 (2003).
17. Dykxhoorn DM, Chowdhury D, Lieberman J: RNA interference and cancer: endogenous pathways and therapeutic approaches. Adv. Exp. Med. Biol. 615, 299-329 (2008).
18. Pai SI, Lin YY, Macaes B, Meneshian A, Hung CF, Wu TC: Prospects of RNA interference therapy for cancer. Gene Ther. 13, 464-477 (2006).
19. Masiero M, Nardo G, Indraccolo S, Favaro E: RNA interference: implications for cancer treatment. Mol. Aspects Med. 28, 143-166 (2007).
20. Meister G, Tuschl T: Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343-349 (2004).
21. Stefani G, Slack FJ: Small non-coding RNAs in animal development. Nat. Rev. Mol. Cell Biol. 9, 219-230 (2008).
22. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
23. Lee Y, Han J, Yeom KH, Jin H, Kim VN: Drosha in primary microRNA processing. Cold Spring Harb. Symp. Quant. Biol. 71, 51-57 (2006).
24. Kim DH, Rossi JJ: Strategies for silencing human disease using RNA interference. Nat. Rev. Genet. 8, 173-184 (2007).
25. Lee Y, Jeon K, Lee JT, Kim S, Kim VN: MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663-4670 (2002).
26. Kim VN: MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol. 14, 156-159 (2004).
27. Dykxhoorn DM, Novina CD, Sharp PA: Killing the messenger: short RNAs that silence gene expression. Nat. Rev. Mol. Cell Biol. 4, 457-467 (2003).
28. Zamore PD, Tuschl T, Sharp PA, Bartel DP: RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25-33 (2000).
29. Elbashir SM, Lendeckel W, Tuschl T: RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188-200 (2001).
30. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T: Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498 (2001).
31. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD: Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208 (2003).
32. Matranga C, Tomari Y, Shin C, Bartel DP, Zamore PD: Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607-620 (2005).
33. Dykxhoorn DM, Lieberman J: Running interference: prospects and obstacles to using small interfering RNAs as small molecule drugs. Annu. Rev. Biomed. Eng. 8, 377-402 (2006).
34. Wu L, Belasco JG: Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs. Mol. Cell 29, 1-7 (2008).
35. Dykxhoorn DM, Lieberman J: Silencing viral infection. PLoS Med. 3, e242 (2006).
36. Rossi JJ, June CH, Kohn DB: Genetic therapies against HIV. Nat. Biotechnol. 25, 1444-1454 (2007).
37. Sarver N: Ribozymes: a new frontier in anti-HIV strategy. Antisense Res. Dev. 1, 373-378 (1991).
38. Sarver N, Cantin EM, Chang PS et al.: Ribozymes as potential anti-HIV-1 therapeutic agents. Science 247, 1222-1225 (1990).
39. Held DM, Kissel JD, Saran D, Michalowski D, Burke DH: Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication. J. Biol. Chem. 281, 25712-25722 (2006).
40. Held DM, Kissel JD, Patterson JT, Nickens DG, Burke DH: HIV-1 inactivation by nucleic acid aptamers. Front. Biosci. 11, 89-112 (2006).
41. Chatterjee S, Johnson PR, Wong KK Jr: Dual-target inhibition of HIV-1 in vitro by means of an adeno-associated virus antisense vector. Science 258, 1485-1488 (1992).
42. Rayburn ER, Zhang R: Antisense, RNAi, and gene silencing strategies for therapy: mission possible or impossible? Drug Discov. Today 13, 513-521 (2008).
43. Michienzi A, Castanotto D, Lee N, Li S, Zaia JA, Rossi JJ: RNA-mediated inhibition of HIV in a gene therapy setting. Ann. NY Acad. Sci. 1002, 63-71 (2003).
44. Ngok FK, Mitsuyasu RT, Macpherson JL, Boyd MP, Symonds GP, Amado RG: Clinical gene therapy research utilizing ribozymes: application to the treatment of HIV/AIDS. Methods Mol. Biol. 252, 581-598 (2004).
45. Coburn GA, Cullen BR: Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J. Virol. 76, 9225-9231 (2002).
46. Lee NS, Dohjima T, Bauer G et al.: Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat. Biotechnol. 20, 500-505 (2002).
47. Lee NS, Rossi JJ: Control of HIV-1 replication by RNA interference. Virus Res. 102, 53-58 (2004).
48. Jacque JM, Triques K, Stevenson M: Modulation of HIV-1 replication by RNA interference. Nature 418, 435-438 (2002).
49. Anderson J, Banerjea A, Planelles V, Akkina R: Potent suppression of HIV type 1 infection by a short hairpin anti-CXCR4 siRNA. AIDS Res. Hum. Retroviruses 19, 699-706 (2003).
50. An DS, Donahue RE, Kamata M et al.: Stable reduction of CCR5 by RNAi through hematopoietic stem cell transplant in non-human primates. Proc. Natl Acad. Sci. USA 104, 13110-13115 (2007).
51. Unwalla HJ, Li MJ, Kim JD et al.: Negative feedback inhibition of HIV-1 by tat-inducible expression of siRNA. Nat. Biotechnol. 22, 1573-1578 (2004).
52. Grimm D, Streetz KL, Jopling CL et al.: Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441, 537-541 (2006).
53. An DS, Qin FX, Auyeung VC et al.: Optimization and functional effects of stable short hairpin RNA expression in primary human lymphocytes via lentiviral vectors. Mol. Ther. 14, 494-504 (2006).
54. Pyrc K, Berkhout B, van der Hoek L: The novel human coronaviruses NL63 and HKU1. J. Virol. 81, 3051-3057 (2007).
55. ter Brake O, 't Hooft K, Liu YP, Centlivre M, von Eije KJ, Berkhout B: Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition. Mol. Ther. 16, 557-564 (2008).
56. Westerhout EM, Ooms M, Vink M, Das AT, Berkhout B: HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res. 33, 796-804 (2005).
57. Boden D, Pusch O, Lee F, Tucker L, Ramratnam B: Human immunodeficiency virus type 1 escape from RNA interference. J. Virol. 77, 11531-11535 (2003).
58. Das AT, Brummelkamp TR, Westerhout EM et al.: Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J. Virol. 78, 2601-2605 (2004).
59. Brass AL, Dykxhoorn DM, Benita Y et al.: Identification of host proteins required for HIV infection through a functional genomic screen. Science 319, 921-926 (2008).
60. Christ F, Thys W, De Rijck J et al.: Transportin-SR2 imports HIV into the nucleus. Curr. Biol. 18, 1192-1202 (2008).
61. Dykxhoorn DM, Schlehuber LD, London IM, Lieberman J: Determinants of specific RNA interference-mediated silencing of human β-globin alleles differing by a single nucleotide polymorphism. Proc. Natl Acad. Sri. USA 103, 5953-5958 (2006).
62. Schwarz DS, Ding H, Kennington L et al.: Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genet. 2, e140 (2006).
63. Jackson AL, Bartz SR, Schelter J et al.: Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21, 635-637 (2003).
64. Jackson AL, Linsley PS: Noise amidst the silence: off-target effects of siRNAs? Trends Genet. 20, 521-524 (2004).
65. Birmingham A, Anderson EM, Reynolds A et al.: 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods 3, 199-204 (2006).
66. Jackson AL, Burchardv J, Leake D et al.: Position-specific chemical modification of siRNAs reduces 'off-target' transcript silencing. RNA 12, 1197-1205 (2006).
67. Fedorov Y, Anderson EM, Birmingham A et al.: Off-target effects by siRNA can induce toxic phenotype. RNA 12, 1188-1196 (2006).
68. Hornung V, Guenthner-Biller M, Bourquin C et al.: Sequence-specific potent induction of IFN-α by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat. Med. 11, 263-270 (2005).
69. Judge AD, Sood V, Shaw JR, Fang D, McClintock K, MacLachlan I: Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat. Biotechnol. 23, 457-462 (2005).
70. Judge AD, Bola G, Lee AC, MacLachlan I: Design of noninflammatory synthetic siRNA mediating potent gene silencing in vivo. Mol. Ther. 13, 494-505 (2006).
71. Judge A, MacLachlan I: Overcoming the innate immune response to small interfering RNA. Hum. Gene Ther. 19, 111-124 (2008).
72. Sioud M, Furset G, Cekaite L: Suppression of immunostimulatory siRNA-driven innate immune activation by 2′-modified RNAs. Biochem. Biophys. Res. Commun. 361, 122-126 (2007).
73. Sioud M: Does the understanding of immune activation by RNA predict the design of safe siRNAs? Front. Biosci. 13, 4379-4392 (2008).
74. Dykxhoorn DM, Lieberman J: Knocking down disease with siRNAs. Cell 126, 231-235 (2006).
75. Westerhout EM, ter Brake O, Berkhout B: The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference. Retrovirology 3, 57 (2006).
76. Gao Y, Lobritz MA, Roth J et al.: Targets of small interfering RNA restriction during human immunodeficiency virus type 1 replication. J. Virol. 82, 2938-2951 (2008).
77. Scherer L, Rossi JJ, Weinberg MS: Progress and prospects: RNA-based therapies for treatment of HIV infection. Gene Ther. 14, 1057-1064 (2007).