RNA interference: On the road to an alternate therapeutic strategy!

Reviews in Medical Virology

Volumn 13, Issue 6, 2003, Pages 373-385

  Dave, Rajnish S ^a   Pomerantz, Roger J ^a,b  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

^b Jefferson Alumni Hall ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRUS VECTOR; ALPHA INTERFERON; ANTISENSE OLIGONUCLEOTIDE; DOUBLE STRANDED DNA; DOUBLE STRANDED RNA BINDING DOMAIN; GREEN FLUORESCENT PROTEIN; INFLUENZA VACCINE; LENTIVIRUS VECTOR; PROTEIN SERINE THREONINE KINASE; RETROVIRUS VECTOR; RIBAVIRIN; RNA DERIVATIVE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; VIRUS PROTEIN; VIRUS RNA;

ANTIVIRAL ACTIVITY; CELL GROWTH; DIMERIZATION; DRUG ACTIVITY; DRUG DELIVERY SYSTEM; DRUG MECHANISM; DRUG TARGETING; ENZYME ACTIVATION; GENETIC CODE; HEPATITIS C; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNOTHERAPY; INFLUENZA VIRUS A; NONHUMAN; PROTEIN FUNCTION; REVIEW; RNA DEGRADATION; RNA INTERFERENCE; RNA TRANSCRIPTION; SIDE EFFECT; VIRUS GENE; VIRUS REPLICATION;

ACQUIRED IMMUNODEFICIENCY SYNDROME; GENE SILENCING; HEPATITIS C; HUMANS; INFLUENZA, HUMAN; RNA INTERFERENCE; RNA, DOUBLE-STRANDED; RNA, SMALL INTERFERING;

EID: 0242526935     PISSN: 10529276     EISSN: None     Source Type: Journal    
DOI: 10.1002/rmv.407     Document Type: Review

References (96)

1. Wilson JA, Jayasena S, Khvorova A, et al. RNA interference blocks gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells. Proc Natl Acad Sci USA 2003; 100: 2783-2788.
2. Randall G, Grakoui A, Rice CM. Clearance of replicating hepatitis C virus replicon RNAs in cell culture by small interfering RNAs. Proc Natl Acad Sci USA 2003; 100: 235-240.
3. Ge Q, McManus MT, Nguyen T, et al. RNA interference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription. Proc Natl Acad Sci USA 2003; 100: 2718-2723.
4. Gitlin L, Karelsky S, Andino R. Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 2002; 418: 430-434.
5. Hu WY, Myers CP, Kilzer JM, et al. Inhibition of retroviral pathogenesis by RNA interference. Curr Biol 2002; 12: 1301-1311.
6. Li H, Li WX, Ding SW. Induction and suppression of RNA silencing by an animal virus. Science 2002; 296: 1319-1321.
7. Jia Q, Sun R. Inhibition of gammaherpesvirus replication by RNA interference. J Virol 2003; 77: 3301-3306.
8. Olson KE, Adelman ZN, Travanty EA, et al. Developing arbovirus resistance in mosquitoes. Insect Biochem Mol Biol 2002; 32: 1333-1343.
9. Jiang M, Milner J. Selective silencing of viral gene expression in HPV-positive human cervical carcinoma cells treated with siRNA, a primer of RNA interference. Oncogene 2002; 21: 6041-6048.
10. Jacque JM, Triques K, Stevenson M. Modulation of HIV-1 replication by RNA interference. Nature 2002; 418: 435-438.
11. Novina CD, Murray MF, Dykxhoorn DM, et al. siRNA-directed inhibition of HIV-1 infection. Nat Med 2002; 8: 681-686.
12. Montaner JS, Mellors JW. Effective salvage therapy for HIV-1 infection-an unmet challenge. Antivir Ther 1999; 4: 59-60.
13. Kim WR. The burden of hepatitis C in the United States. Hepatology 2002; 36: S30-S34.
14. Christie JM, Chapman RW. Combination therapy for chronic hepatitis C: interferon and ribavirin. Hosp Med 1999; 60: 357-361.
15. Davis GL, Esteban-Mur R, Rustgi V, et al. Interferon alfa-2b alone or in combination with ribavirin for the treatment of relapse of chronic hepatitis C. International Hepatitis Interventional Therapy Group. N Engl J Med 1998; 339: 1493-1499.
16. Manns MP, McHutchison JG, Gordon SC, et al. Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial. Lancet 2001; 358: 958-965.
17. Fried MW, Shiffman ML, Reddy KR, et al. Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N Engl J Med 2002; 347: 975-982.
18. Webby RJ, Webster RG. Emergence of influenza A viruses. Philos Trans R Soc Lond B Biol Sci 2001; 356: 1817-1828.
19. Webster RG, Bean WJ, Gorman OT, et al. Evolution and ecology of influenza A viruses. Microbiol Rev 1992; 56: 152-179.
20. Zambon MC. The pathogenesis of influenza in humans. Rev Med Virol 2001; 11: 227-241.
21. Marcus PI, Sekellick MJ. Defective interfering particles with covalently linked [+/-]RNA induce interferon. Nature 1977; 266: 815-819.
22. Lee JY, Marshall JA, Bowden DS. Characterization of rubella virus replication complexes using antibodies to double-stranded RNA. Virology 1994; 200: 307-312.
23. Dasgupta S, Fernandez L, Kameyama L, et al. Genetic uncoupling of the dsRNA-binding and RNA cleavage activities of the Escherichia coli endoribonuclease RNase III-the effect of dsRNA binding on gene expression. Mol Microbiol 1998; 28: 629-640.
24. Denzler KL, Jacobs BL. Site-directed mutagenic analysis of reovirus sigma 3 protein binding to dsRNA. Virology 1994; 204: 190-199.
25. Lichner Z, Silhavy D, Burgyan J. Double-stranded RNA-binding proteins could suppress RNA interference-mediated antiviral defences. J Gen Virol 2003; 84: 975-980.
26. Kaufman RJ. Double-stranded RNA-activated protein kinase mediates virus-induced apoptosis: a new role for an old actor. Proc Natl Acad Sci USA 1999; 96: 11693-11695.
27. Garcia MA, Guerra S, Gil J, et al. Anti-apoptotic and oncogenic properties of the dsRNA-binding protein of vaccinia virus, E3L. Oncogene 2002; 21: 8379-8387.
28. Park H, Davies MV, Langland JO, et al. TAR RNA-binding protein is an inhibitor of the interferon-induced protein kinase PKR. Proc Natl Acad Sci USA 1994; 91: 4713-4717.
29. Yeung MC, Chang DL, Camantigue RE, et al. Inhibitory role of the host apoptogenic gene PKR in the establishment of persistent infection by encephalomyocarditis virus in U937 cells. Proc Natl Acad Sci USA 1999; 96: 11860-11865.
30. Yuan W, Aramini JM, Montelione GT, et al. Structural basis for ubiquitin-like ISG 15 protein binding to the NS1 protein of influenza B virus: a protein-protein interaction function that is not shared by the corresponding N-terminal domain of the NS1 protein of influenza A virus. Virology 2002; 304: 291-301.
31. Noah DL, Twu KY, Krug RM. Cellular antiviral responses against influenza A virus are countered at the posttranscriptional level by the viral NS1A protein via its binding to a cellular protein required for the 3′-end processing of cellular pre-mRNAS. Virology 2003; 307: 386-395.
32. Moss B. Poxviridae: the viruses and their replication. In Virology, Fields BK, Knipe DM, Howley PM, et al. (eds). Lippincott-Raven: Philadelphia, 1996; 2637-2671.
33. Jacobs BL, Langland JO. When two strands are better than one: the mediators and modulators of the cellular responses to double-stranded RNA. Virology 1996; 219: 339-349.
34. Cullen BR. RNA interference: antiviral defense and genetic tool. Nat Immunol 2002; 3: 597-599.
35. Gale M, Jr, Blakely CM, Hopkins DA, et al. Regulation of interferon-induced protein kinase PKR: modulation of P58IPK inhibitory function by a novel protein, P52rIPK. Mol Cell Biol 1998; 18: 859-871.
36. Ryter JM, Schultz SC. Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA. Embo J 1998; 17: 7505-7513.
37. Patel RC, Sen GC. Requirement of PKR dimerization mediated by specific hydrophobic residues for its activation by double-stranded RNA and its antigrowth effects in yeast. Mol Cell Biol 1998; 18: 7009-7019.
38. Patel RC, Stanton P, Sen GC. Specific mutations near the amino terminus of double-stranded RNA-dependent protein kinase (PKR) differentially affect its double-stranded RNA binding and dimerization properties. J Biol Chem 1996; 271: 25657-25663.
39. Cosentino GP, Venkatesan S, Serluca FC, et al. Double-stranded-RNA-dependent protein kinase and TAR RNA-binding protein form homo- and heterodimers in vivo. Proc Natl Acad Sci USA 1995; 92: 9445-9449.
40. Gale M, Jr, Tan SL, Wambach M, et al. Interaction of the interferon-induced PKR protein kinase with inhibitory proteins P58IPK and vaccinia virus K3L is mediated by unique domains: implications for kinase regulation. Mol Cell Biol 1996; 16: 4172-4181.
41. Taylor DR, Shi ST, Romano PR, et al. Inhibition of the interferon-inducible protein kinase PKR by HCV E2 protein. Science 1999; 285: 107-110.
42. Gale MJ, Jr, Korth MJ, Tang NM, et al. Evidence that hepatitis C virus resistance to interferon is mediated through repression of the PKR protein kinase by the nonstructural 5A protein. Virology 1997; 230: 217-227.
43. Cogoni C, Macino G. Homology-dependent gene silencing in plants and fungi: a number of variations on the same theme. Curr Opin Microbiol 1999; 2: 657-662.
44. Sijen T, Kooter JM. Post-transcriptional gene-silencing: RNAs on the attack or on the defense? Bioessays 2000; 22: 520-531.
45. Yu JY, DeRuiter SL, Turner DL. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci USA 2002; 99: 6047-6052.
46. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 2002; 296: 550-553.
47. Sui G, Soohoo C, Affar el B, et al. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci USA 2002; 99: 5515-5520.
48. Bernstein E, Caudy AA, Hammond SM, et al. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001; 409: 363-366.
49. Hutvagner G, Zamore PD. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002; 297: 2056-2060.
50. Zeng Y, Cullen BR. RNA interference in human cells is restricted to the cytoplasm. Rna 2002; 8: 855-860.
51. Ahlquist P. RNA-dependent RNA polymerases, viruses, and RNA silencing. Science 2002; 296: 1270-1273.
52. Caplen NJ, Parrish S, Imani F, et al. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 2001; 98: 9742-9747.
53. Doi N, Zenno S, Ueda R, et al. Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Curr Biol 2003; 13: 41-46.
54. Martinez J, Patkaniowska A, Urlaub H, et al. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 2002; 110: 563-574.
55. Chiu YL, Rana TM. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol Cell 2002; 10: 549-561.
56. Ball LA, Li Y. Cis-acting requirements for the replication of flock house virus RNA2. J Virol 1993; 67: 3544-3551.
57. Elbashir SM, Harborth J, Lendeckel W, et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001; 411: 494-498.
58. Harborth J, Elbashir SM, Bechert K, et al. Identification of essential genes in cultured mammalian cells using small interfering RNAs. J Cell Sci 2001; 114: 4557-4565.
59. Nykanen A, Haley B, Zamore PD. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 2001; 107: 309-321.
60. Elbashir SM, Harborth J, Weber K, et al. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 2002; 26: 199-213.
61. Yu JY, Taylor J, DeRuiter SL, et al. Simultaneous inhibition of GSK3alpha and GSK3beta using hairpin siRNA expression vectors. Mol Ther 2003; 7: 228-236.
62. Bertrand JR, Pottier M, Vekris A, et al. Comparison of antisense oligonucleotides and siRNAs in cell culture and in vivo. Biochem Biophys Res Commun 2002; 296: 1000-1004.
63. Hohjoh H. RNA interference (RNA(i)) induction with various types of synthetic oligonucleotide duplexes in cultured human cells. FEBS Lett 2002; 521: 195-199.
64. Boutla A, Delidakis C, Livadaras I, et al. Short 5′-phosphorylated double-stranded RNAs induce RNA interference in Drosophila. Curr Biol 2001; 11: 1776-1780.
65. Amarzguioui M, Holen T, Babaie E, et al. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res 2003; 31: 589-595.
66. Holen T, Amarzguioui M, Wiiger MT, et al. Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res 2002; 30: 1757-1766.
67. Hamada M, Ohtsuka T, Kawaida R, et al. Effects on RNA interference in gene expression (RNAi) in cultured mammalian cells of mismatches and the introduction of chemical modifications at the 3′-ends of siRNAs. Antisense Nucleic Acid Drug Dev 2002; 12: 301-309.
68. Elbashir SM, Martinez J, Patkaniowska A, et al. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. Embo J 2001; 20: 6877-6888.
69. Surig D, Bredow S, Benecke BJ. The seemingly identical 7SK and U6 core promoters depend on different transcription factor complexes. Gene Expr 1993; 3: 175-185.
70. Myslinski E, Ame JC, Krol A, et al. An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene. Nucleic Acids Res 2001; 29: 2502-2509.
71. Boyd DC, Turner PC, Watkins NJ, et al. Functional redundancy of promoter elements ensures efficient transcription of the human 7SK gene in vivo. J Mol Biol 1995; 253: 677-690.
72. Nguyen VT, Kiss T, Michels AA, et al. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 2001; 414: 322-325.
73. Noonberg SB, Scott GK, Benz CC. Evidence of post-transcriptional regulation of U6 small nuclear RNA. J Biol Chem 1996; 271: 10477-10481.
74. Connelly JC, Kirkham LA, Leach DR. The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA. Proc Natl Acad Sci USA 1998; 95: 7969-7974.
75. Castanotto D, Li H, Rossi JJ. Functional siRNA expression from transfected PCR products. Rna 2002; 8: 1454-1460.
76. Qin XF, An DS, Chen IS, et al. Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc Natl Acad Sci USA 2003; 100: 183-188.
77. Abbas-Terki T, Blanco-Bose W, Deglon N, et al. Lentiviral-mediated RNA interference. Hum Gene Ther 2002; 13: 2197-2201.
78. Devroe E, Silver PA. Retrovirus-dehvered siRNA. BMC Biotechnol 2002; 2: 15.
79. Barton GM, Medzhitov R. Retroviral delivery of small interfering RNA into primary cells. Proc Natl Acad Sci USA 2002; 99: 14943-14945.
80. Shen C, Buck AK, Liu X, et al. Gene silencing by adenovirus-delivered siRNA. FEBS Lett 2003; 539: 111-114.
81. Lewis DL, Hagstrom JE, Loomis AG, et al. Efficient delivery of siRNA for inhibition of gene expression in postnatal mice. Nat Genet 2002; 32: 107-108.
82. Song E, Lee SK, Wang J, et al. RNA interference targeting Fas protects mice from fulminant hepatitis. Nat Med 2003; 9: 347-351.
83. Sorensen DR, Leirdal M, Sioud M. Gene silencing by systemic delivery of synthetic siRNAs in adult mice. J Mol Biol 2003; 327: 761-766.
84. Calegari F, Haubensak W, Yang D, et al. Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNA. Proc Natl Acad Sci USA 2002; 99: 14236-14240.
85. Capodici J, Kariko K, Weissman D. Inhibition of HIV-1 infection by small interfering RNA-mediated RNA interference. J Immunol 2002; 169: 5196-5201.
86. Coburn GA, Cullen BR. Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J Virol 2002; 76: 9225-9231.
87. Martinez MA, Gutierrez A, Armand-Ugon M, et al. Suppression of chemokine receptor expression by RNA interference allows for inhibition of HIV-1 replication. Aids 2002; 16: 2385-2390.
88. McCaffrey AP, Meuse L, Pham TT, et al. RNA interference in adult mice. Nature 2002; 418: 38-39.
89. Martinez LA, Naguibneva I, Lehrmann H, et al. Synthetic small inhibiting RNAs: efficient tools to inactivate oncogenic mutations and restore p53 pathways. Proc Natl Acad Sci USA 2002; 99: 14849-14854.
90. Ramos A, Grunert S, Adams J, et al. RNA recognition by a Staufen double-stranded RNA-binding domain. Embo J 2000; 19: 997-1009.
91. Pettersson U, Philipson L. Synthesis of complementary RNA sequences during productive adenovirus infection. Proc Natl Acad Sci USA 1974; 71: 4887-4891.
92. Gribaudo G, Lembo D, Cavallo G, et al. Interferon action: binding of viral RNA to the 40-kilodalton 2′-5′-oligoadenylate synthetase in interferon-treated HeLa cells infected with encephalomyocarditis virus. J Virol 1991; 65: 1748-1757.
93. Jacquemont BR. B, RNA synthesis in cells infected with herpes simplex virus. X. Properties of viral symmetric transcripts and of double-stranded RNA. J Virol 1975; 15: 707-713.
94. Majde JA, Brown RK, Jones MW, et al. Detection of toxic viral-associated double-stranded RNA (dsRNA) in influenza-infected lung. Microb Pathog 1991; 10: 105-115.
95. Kimura-Takeuchi M, Majde JA, Toth LA, et al. The role of double-stranded RNA in induction of the acute-phase response in an abortive influenza virus infection model. J Infect Dis 1992; 166: 1266-1275.
96. Henry GL, McCormack SJ, Thomis DC, et al. Mechanism of interferon action. Translational control and the RNA-dependent protein kinase (PKR): antagonists of PKR enhance the translational activity of mRNAs that include a 161 nucleotide region from reovirus S1 mRNA. J Biol Regul Homeost Agents 1994; 8: 15-24.