RNAi as a new therapeutic strategy against HCV

Biotechnology Advances

Volumn 28, Issue 1, 2010, Pages 27-34

  Khaliq, Saba ^a   Khaliq, Sadaf A ^b   Zahur, Muzna ^a   Ijaz, Bushra ^a   Jahan, Shah ^a   Ansar, Muhammad ^a   Riazuddin, Sheikh ^a   Hassan, Sajida ^a  

^a UNIVERSITY OF THE PUNJAB   (Pakistan)

^b GC UNIVERSITY   (Pakistan)

Author keywords

Hepatitis C Virus; RNAi; siRNA delivery; siRNA design

Indexed keywords

AUTOIMMUNE DISORDER; ENCODED PROTEINS; GENE PRODUCTS; HEPATITIS C VIRUS; NEW TECHNOLOGIES; POST-TRANSCRIPTIONAL; RNA INTERFERENCE; SIRNA DELIVERY; SIRNA DESIGN; SMALL INTERFERING RNA (SIRNA); THERAPEUTIC STRATEGY; VIRAL INFECTIONS;

DRUG THERAPY; GENETIC ENGINEERING; NUCLEIC ACIDS;

RNA;

SMALL INTERFERING RNA;

CANCER; HEPATITIS; IMMUNE RESPONSE; PATHOTYPE; RNA; VACCINE; VIRUS;

DRUG DELIVERY SYSTEM; GENETICS; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; METHODOLOGY; REVIEW; RNA INTERFERENCE; VIROLOGY; VIRUS GENE;

DRUG DELIVERY SYSTEMS; GENES, VIRAL; HEPACIVIRUS; HEPATITIS C; HUMANS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

HEPATITIS C VIRUS;

EID: 71249099403     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2009.08.004     Document Type: Review

References (105)

1. Aleku M., Schulz P., Keil O., Santel U., Schaeper U., Dieckhoff B., et al. Atu027, a liposomal small interfering RNA formulation targeting protein kinase N3, inhibits cancer progression. Cancer Res 68 (2008) 9788-9798
2. Bartenschlager R., Ahlborn-Laake L., Mous J., and Jacobsen H. Kinetic and structural analyses of hepatitis C virus polyprotein processing. J Virol 68 (1994) 5045-5055
3. Bertrand J.R., Pottier M., Vekris A., Opolon P., Maksimenko A., and Malvy C. Comparison of antisense oligonucleotides and siRNAs in cell culture and in vivo. Biochem Biophys Res Commun 296 (2002) 1000-1004
4. Bridge A.J., Pebernard S., Ducraus A., Nicoulaz A.L., and Iggo R. Induction of an interferon response by RNAi vectors in mammalian cells. Nat Genet 34 (2003) 263-264
5. Brown K.M., Chu C.Y., and Rana T.M. Target accessibility dictates the potency of Human RISC. Nat Struct Mol Biol 12 (2005) 469-470
6. Burncrot D., Manoharan M., Koteliansky V., and Sah D.W. RNAi therapeutics: a potential new class of pharmaceutical drugs. Nat Chem Biol 2 (2006) 711-719
7. Caplen N.J., Parrish S., Imani F., Fire A., and Morgan R.A. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 98 (2001) 9742-9747
8. Cho I.S., Kim J., Lim do H., Ahn H.C., Kim H., Lee K.B., and Lee Y.S. Improved serum stability and biophysical properties of siRNAs following chemical modifications. Biotechnol Lett 30 11 (2008) 1901-1908
9. Choo Q.L., Richman J.H., Berger K., et al. Genetic organization and diversity of hepatitis C virus. Proc Natl Acad Sci USA 88 (1991) 2451-2455
10. Clayton J. RNA interference: the silent treatment. Nature 431 (2004) 371-378
11. Couzin J. Breakthrough of the year: Small RNAs make big splash. Science 298 (2002) 2296-2297
12. De Francesco R., and Migliaccio G. Challenges and successes in developing new therapies for hepatitis C virus. Nature 436 (2005) 953-960
13. Dimitrova M., Affolter C., Meyer F., Nguyen I., Richard D.G., Schuster C., et al. Sustained delivery of siRNAs targeting viral infection by cell degradable multilayered polyelectrolyte films. PNAS 105 (2008) 16320-16325
14. Elbashir S.M., Harborth J., Lendeekel W., Yalcin A., Weber K., and Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411 (2001) 494-498
15. Feld J.J., and Hoofnagle J.H. Mechanism of action of interferon and ribavirin in treatment of hepatitis C. Nature 436 (2005) 967-972
16. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
17. Fluiter K., Mook O.R., and Baas F. the therapeutic potential of LNA-modified siRNAs: reduction of off-target effects by chemical modification of the siRNA sequence. Methods Mol Biol 487 (2009) 187-203
18. Giannini C., and Brechot C. Hepatitis C virus biology. Cell Death Differ 10 (2003) S27-S38
19. Golzio M., Mazzolini L., Moller P., Rols M.P., and Teissie J. Inhibition of gene expression in mice muscles by in vivo electrically mediated siRNA delivery. Gene Ther 12 (2005) 246-251
20. Goodchild A., Nopper N., King A., Doan T., Tanudji M., Arndt G.M., et al. Sequence determinants of innate immune activation by short interfering RNAs. BMC Immunol 10 (2009) 40
21. Grimm D., Streetz K.L., Jopling C.L., Storm T.A., Pandey K., Davis C.R., et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441 (2006) 537-541
22. Gupta S., Schoer R.A., Egan J.E., Hannon G.J., and Mittal V. Inducible, reversible and stable RNA interference in mammalian cells. Natl Acad Sci USA 101 (2004) 1927-1932
23. Hannan G.J. RNA interference. Nature 418 (2002) 244-251
24. Heale B.S.E., Soifer H.S., Bowers C., and Rossi J.J. siRNA target site secondary structure predictions using local stable substructures. Nucleic Acids Res 33 3 (2005) e30
25. Heidel J.D., Liu J.Y., Yen Y., Zhou B., Heale B.S., Rossi J.J., et al. Potent siRNA inhibitors of ribonucleotide reductase subunit RRM2 reduce cell proliferation in vitro and in vivo. Clin Cancer Res 13 (2007) 2207-2215
26. Henry S.D., van der Wegen P., Metselaar H.J., Tilanus H.W., Scholte B.J., and van der Laan L.J. Simultaneous targeting of HCV replication and viral binding with a single lentiviral vector containing multiple RNA interference expression cassettes. Mol Ther 14 (2006) 485-493
27. Hijikata M., Kato N., Ootsuyama Y., Nakagawa M., and Shimotohno K. Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis. Proc Natl Acad Sci USA 88 (1991) 5547-5551
28. Huang H., Sun F., Owen D.M., Li W., Chen Y., Gale M., et al. Hepatitis C virus production by human hepatocytes dependent on assembly and secretion of very low-density lipoproteins. PNAS 104 (2007) 5848-5853
29. Hughes J.A., and Rao G.A. Targeted polymers for gene delivery. Expert Opin Drug Deliv 2 (2005) 145-157
30. Hutvagner G., and Zamore P.D. RNAi: Nature abhors a double-strand. Curr Opin Genet Dev 12 (2002) 225-232
31. Jarczak D., Korf M., Beger C., Manns M.P., and Kruger M. Hairpin ribozymes in combination with siRNA against highly conserved hepatitis C virus sequence inhibit RNA replication and protein translation from hepatitis C virus subgenomic replicons. FEBS J 272 (2005) 5910-5922
32. Jiang G., Park K., Kim J., Kim K.S., and Hahn S.K. Target specific intracellular delivery of siRNA/PEI-HA complex by receptor mediated endocytosis. Mol Pharmacol 6 (2009) 727-737
33. Judge A., and MacLachlan I. Overcoming the innate immune response to small interfering RNA. Hum Gene Ther 19 (2008) 111-124
34. Kanda T., Kusov Y., Yokosuka O., and Gauss-Miller V. Interference of hepatitis A virus replication by small interfering RNAs. Biochem Biophys Res Commun 318 2 (2004) 314-315
35. Kanda T., Steele R., Ray R., and Ray R.B. Small interfering RNA targeted to hepatitis C virus 5′ nontranslated regions exerts potent antiviral effect. J Virol 81 (2007) 669-676
36. Kapadia S.B., Brideau-Andersen A., and Chisari F.V. Interference of hepatitis C virus RNA replication by short interfering RNAs. Proc Natl Acad Sci USA 100 (2003) 2014-2018
37. Kariko K., Buckstein M., Ni H., and Weissman D. Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and evolutionary origin of RNA. Immunity 23 (2005) 165-175
38. Kennerdell J.R., and Caerthew R.W. Heritable gene silencing in Drossophila using double stranded RNA. Nat Biotechnol 18 (2000) 896-898
39. Kim D.H., Behlke M.A., Rose S.D., Chang M.S., Choi S., and Rossi J.J. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 23 (2005) 222-226
40. Kim M., Shin D., Kim S.I., and Park M. Inhibition of hepatitis C virus gene expression by small interfering RNAs using a tri-cistronic full length viral replicon and a transient mouse model. Virus Res 122 (2006) 1-10
41. Kim E.J., Shim G., Kim K., Kwon I.C., Oh Y.K., and Shim C.K. Hyaluronic acid complexed to biodegradable poly L-arginine for targeted delivery of siRNAs. J Gene Med 11 9 (2009) 791-803
42. Kim S.I., Shin D., Lee H., Ahn B.Y., Yoon Y., and Kim M. targeted delivery of siRNA against hepatitis C virus by apolipoprotein A-I bound cationic liposomes. J Hepatol 50 (2009) 479-488
43. Kim Y., Tewari M., Pajerowski J.D., Cai S., Sen S., Williams J., et al. Polymersome delivery of siRNA and antisense oligonucleotides. J Control Release 134 (2009) 132-140
44. Klein C., Bock C.T., Wedemeyer H., et al. Inhibition of Hepatitis B virus replication in vivo by nucleoside analogues and siRNA. Gastroenterology 125 (2003) 9-18
45. Korf M., Jarczak D., Beger C., Manns M.P., and Kruger M. Inhibition of Hepatitis C virus translation and subgenomic replication by siRNAs directed against highly conserved HCV sequence and cellular HCV cofactors. J Hepatol 43 (2005) 225-234
46. Korf M., Meyer A., Jarczak D., Beger C., Manns M.P., and Kruger M. Inhibition of HCV subgenomic replicons by siRNAs derived from plasmids with opposing U6 and H1 promoters. J Virol Hepatitis 14 (2007) 122-132
47. Kusumoto K. Structural features of glutamate-based lipidic materials for small interfering RNA delivery system. J Biomed Mater Res A 89 (2009) 739-750
48. Layzer J.M., McCaffrey A.P., Tanner A.K., Huang Z., Kay M.A., and Sullenger B.A. In vivo activity of nuclease-resistant siRNAs. RNA 10 (2004) 766-771
49. Lee H., Kim S.I., Yoon Y., Choi T.H., Cheon G.J., and Kim M. Hepatic siRNA delivery using recombinant human apolipoprotein A-1 in mice. Biochem Biophys Res Commun 378 (2009) 192-196
50. Li Y.X., Farrell M.J., Liu R., Mohanty N., and Kirby M.L. Double-stranded RNA injection produces null phenotypes in zebrafish. Dev Biol 217 (2000) 394-405
51. Lin C., Lindenbach B.D., Pragai B.M., McCourt D.W., and Rice C.M. Processing in the hepatitis C virus E2- NS2 region: identification of p7 and two distinct E2-specific products with different C termini. J Virol 68 (1994) 5063-5073
52. Liu M., Ding H., Zhou P., Qin Z.L., Gao J., Cao M., et al. RNA interference effectively inhibits mRNA accumulation and protein expression of Hepatitis C virus Core and E2 genes in human cells. Biosci Biotechnol Biochem 70 (2006) 2049-2055
53. Lund E., Guttinger S., Calado A., Dahiberg J.E., and Kutay U. Nuclear export of microRNA precursors. Science 303 (2004) 95-98
54. Luten I., van Nostrum C.F., De Smedt S.C., and Hennink W.E. Biodegradable polymers as non-viral carriers for plasmid DNA delivery. J Control Release 126 (2008) 97-110
55. Mathupala S.P. Delivery of small interfering RNA (siRNA) to the brain. Expert Opin Ther Pat 19 (2009) 137-140
56. McAnuff M.A., Rettig G.R., and Rice K.G. Potency of siRNA versus shRNA mediated knockdown in vivo. J Pharm Sci 96 (2007) 2922-2930
57. McCaffrey A.P., Mause L., Pham T.T., Conklin D.S., Hannon G.J., and Kay M.A. RNA interference in adult mice. Nature 418 (2002) 38-39
58. Mittal V. Improving the efficacy of RNA interference in mammals. Nat Rev Genet 5 (2004) 355-365
59. Moreira J.N., Santos A., Moura V., Pedroso de Lima M.C., and Simoes S. Non-viral lipidbased nanoparticles for targeted cancer systemic gene silencing. J Nanosci Nanotechnol 8 (2008) 2187-2204
60. Morrissey D.V., Blanchard K., Shaw L., et al. Activity of stabilized short interfering RNA in a mouse model of hepatitis B virus replication. Hepatology 41 (2005) 1349-1356
61. Nakagawa S., Umehara T., Matsuda C., Kuge S., Sudoh M., and Kohara M. Hsp90 inhibitors suppress HCV replication in replicon cells and humanized liver mice. Biochem Biophys Res Com 353 (2007) 882-888
62. Okamoto H., Kojima M., Okada S., Yoshizawa H., Iizuka H., Tanaka T., et al. Genetic drift of hepatitis C virus during an 8.2 year infection in a chimpanzee: variability and stability. Virology 190 (1992) 894-899
63. Paddison P.J., Caudy A.A., Bernstein E., Hannon G.J., and Conklin D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16 (2002) 948-958
64. Prabhu R., Vittal Q., Yin Q., Flemington E., Garry R., Robichaus W.H., et al. Small interfering RNA effectively inhibits protein expression and negative strand RNA synthesis from a full length hepatitis C virus clone. J Med Virol B76 (2005) 511-519
65. Randall G., Grakoui A., and Rice C.M. Clearance of replicating hepatitis C virus replicon RNAs in cell culture by small interfering RNAs. Proc Natl Acad Sci USA 100 (2003) 235-240
66. Randall G., Chen L., Panis M., Fischer A.K., Lindenbach B.D., Sun J., et al. Silencing of USP18 potentiates the antiviral activity of interferon against hepatitis C virus infection. Gastroenterology 131 (2006) 1584-1591
67. Rao D.D., Vorhies J.S., Senzer N., and Nemunaitis J. siRNA vs. shRNA: similarities and differences. Adv Drug Deliv Rev 61 (2009) 746-759
68. Ray R.B., and Kanda T. Inhibition of HCV replication by small interfering RNA. Methods Mol Biol 510 (2009) 251-262
69. Reid T., Warren R., and Kirn D. Intravascular adenoviral agents in cancer patients: lessons from clinical trials. Cancer Gen Ther 9 (2002) 979-986
70. Reynolds A., Leake D., Boese Q., Scaringe S., Marshall W.S., and Khvorova A. Rational siRNA design for RNA interference. Nat Biotechnol 22 (2004) 326-330
71. Reynolds A., Anderson E.M., Vermeulen A., Fedorov Y., et al. Induction of the interferon response by siRNA is cell type nad duplex length dependent. RNA 12 (2006) 988-993
72. Saito Y., and Dzik S. Gene knockdown: RNA-interference is coming of age. Transfusion 45 (2005) 111-114
73. Sano M., Li H., Nakanishi M., and Rossi J.J. Expression of Long Anti-HIV-I hairpin RNAs for the generation of multuple siRNAs: advantages and limitations. Mol Ther 16 (2007) 170-177
74. Sano M., Sierant M., Miyagishi M., nakanishi M., Takagi Y., and Sutou S. Effect of asymmetric terminal structures of short RNA duplexes on RNA interference activity and strand selection. Nucleic Acid Res 36 (2008) 5812-5821
75. Santel A., Aleku M., Keil O., Endruschat J., Esche V., Durieux B., et al. RNA interference in the mouse vascular endothelium by systemic administration of siRNA-lipoplexes for cancer therapy. Gene Ther 13 (2006) 1360-1370
76. Seo M.Y., Abrignani S., Houghton M., and Han J.H. Small interfering RNA-mediated inhibition of hepatitis C virus replication in the human hepatoma cell line Huh-7. J Virol 77 (2003) 810-812
77. Shin D., Lee H., Kim S.I., Yoon Y., and Kim M. Optimization of linear double-stranded RNA for the production of multiple siRNAs targeting hepatitis C virus. RNA 15 (2009) 898-910
78. Sioud M. Single-stranded small interfering RNA is more immunostimulatory than their double stranded counterparts: a central role for 2′-hydroxyl uridines in immune responses. Eur J Immunol 36 (2006) 1222-1230
79. Sledz C.A., Holko M., de Veer M.J., Silverman R.H., and Williams B.R. Activation of the interferon system by short interfering RNAs. Nat Cell Biol 5 (2003) 834-839
80. Song E., Lee S.K., Wang J., Ince N., Ouyang N., et al. RNA interference targeting Fas protects mice from fulminant hepatitis. Nat Med 9 (2003) 347-351
81. Szweykowska-kulinska Z., Jarmolowski A., and Figlerowicz M. RNA interference and its role in the regulation of eukaryotic gene expression. Acta Biochem Pol 50 (2003) 217-229
82. Takigawa Y., Nagano-Fujii M., Deng L., Hidajat R., Tanaka M., Mizuta H., et al. Suppression of hepatitis C virus replicon by RNA interference directed against the NS3 and NS5B regions of the viral genome. Microbiol Immunol 48 (2004) 591-598
83. Tanaka T., Lau J.Y., Mizokami M., Orito E., et al. Simple flouresecent enzyme immunoassay for detection and quantification of hepatitis C viremia. J Hepatol 23 (1995) 742-745
84. Thomas M., and Klibanov A.M. Enhancing polyethylenimine's delivery of plasmid DNA in mammalian cells. Proc Natl Acad Sci USA 99 (2002) 14640-14645
85. Tsukiyama-Kohara K., Iizuka N., Kohara M., and Nomoto A. Internal ribosome entry site within hepatitis C virus RNA. J Virol 66 (1992) 1476-1483
86. Ueno Y., Watanable Y., Shibata A., Yoshikawa K., Takano T., Kohara M., and Kitade Y. Synthesis of nuclease-resistant siRNAs possessing universal overhangs. Bioorg Med Chem 17 5 (2009) 1974-1981
87. Vlassov A.V., Korba B., Farrar K., Mukerjee S., Seyhan A.A., Ilves H., et al. shRNAs targeting hepatitis C: effects of sequence and structural features and comparison with siRNA. Oligonucleotides 17 (2007) 223-236
88. Von Eije K.J., tar Brake O., and Berkhout B. Human immunodeficiency virus type 1 escape is restricted when conserved genome sequences are targeted by RNA Interference. J Virol 82 (2008) 2895-2903
89. Vorhies J.S., and Nemunaitis J. Nonviral delivery vehicles for use in short hairpin RNA based cancer therapies. Expert Rev Anticancer Ther 7 (2007) 373-382
90. Wang Y., Kato N., Jazag A., Dharel N., et al. Hepatitis C virus core protein is a potent inhibitor of RNA silencing-based antiviral response. Gastroenterology 130 (2006) 883-892
91. Watanabe T., Umehara T., Yasui F., Nakagawa S., et al. Liver target delivery of small interfering RNA to the HCV gene by lactosylated cationic liposome. J Hepatol 47 (2007) 744-750
92. Wei B., Wei Y., Zhang K., Wang J., Xu R., Zhan S., et al. Development of an antisense RNA delivery system using conjugates of the MS2 bacteriophage capsids and HIV-1 TAT cell penetrating peptide. Biomed Pharmacother 63 (2009) 313-318
93. Westerhout E.M., and Berkhout B. A systematic analysis of the effect of target RNA structure on RNA interference. Nucleic Acid Res 35 (2007) 4322-4330
94. Wilson J.A., and Richardson C.D. Hepatitis C virus replicons escape RNA interference induced by a short interfering RNA directed against the NS5B coding region. J Virol 79 (2005) 7050-7058
95. Wilson J.A., Jayasena S., Khvorova A., Sabatinos S., et al. RNA interference blocks gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells. Proc Natl Acad Sci USA 100 (2003) 2783-2788
96. Xue Q., Ding H., Liu M., Zhao P., Gao J., Ren H., et al. Inhibition of hepatitis C virus replication and expression by small interfering RNA targeting host cellular genes. Arch Virol 152 (2007) 955-962
97. Yi Y., Qin Y., Macara I.G., and Cullen B.R. Exportin-5 mediate the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17 (2003) 3011-3016
98. Yokota T., Sakamoto N., Enomoto N., Tanabe Y M.M., Maekawa S., Yi L., et al. Inhibition of intracellular hepatitis C virus replication by synthetic and vector-derived small interfering RNAs. EMBO Rep 4 (2003) 602-608
99. Zamore P.D., Tuschl T., Sharp P.A., and Bartel D.P. RNAi: Double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21-23 nucleotide intervals. Cell 101 (2000) 25-33
100. Zeisel M.B., Koutsoudakis G., Schnober E.K., Haberstroh A., Blum H.E., Cosset F.L., et al. Scavenger receptor class B Type I is a key host factor for Hepatitis C virus infection required for an entry step closely linked to CD81. Hepatology 46 (2007) 1722-1731
101. Zekri A.R.N., Bahnassy A.A., Alam El Din H.M., and Salama H.M. Consensus siRNA for inhibition of HCV genotype-4 replication. Virol J 6 (2009) 13
102. Zender L., Hutker S., Leidtke C., et al. Caspase 8 small interfering RNA prevents acute liver failure in mice. Proc Natl Acad Sci USA 100 (2003) 7797-7802
103. Zhang X., Shan P., Jiang D., et al. Small interfering RNA targeting heme oxygenase-1 enhances ischemia-reperfusion-induced lung apoptosis. J Biol Chem 279 (2004) 10677-10684
104. Zhang S., Zhao B., Jiang H., Wang B., and Ma B. Cationic lipids and polymers mediated vectors for delivery of siRNA. J Control Release 123 (2007) 1-10
105. Zimmermann T.S., Lee A.C., Akinc A., Bramlage B., Bumcrot D., Fedoruk M.N., et al. RNAi-mediated gene silencing in non-human primates. Nature 44 (2006) 111-114