Toward a durable treatment of HIV-1 infection using RNA interference

Progress in Molecular Biology and Translational Science

Volumn 102, Issue , 2011, Pages 141-163

  Eekels, Julia J M ^a   Berkhout, Ben ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Cofactors; Gene therapy; HIV 1; Lentivirus; RNA interference; Therapeutics; Therapy; Viral escape

Indexed keywords

EID: 80051882660     PISSN: 18771173     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-415795-8.00001-5     Document Type: Chapter

References (171)

1. A.P. McCaffrey, H. Nakai, K. Pandey, Z. Huang, F.H. Salazar, and H. Xu Inhibition of hepatitis B virus in mice by RNA interference Nat Biotechnol 21 2003 639 644 (Pubitemid 36638090)
2. S.B. Kapadia, A. Brideau-Andersen, and F.V. Chisari Interference of hepatitis C virus RNA replication by short interfering RNAs Proc Natl Acad Sci USA 100 2003 2014 2018 (Pubitemid 36254565)
3. A. Banerjea, M.J. Li, G. Bauer, L. Remling, N.S. Lee, and J. Rossi Inhibition of HIV-1 by lentiviral vector-transduced siRNAs in T lymphocytes differentiated in SCID-hu mice and CD34+ progenitor cell-derived macrophages Mol Ther 8 2003 62 71 (Pubitemid 36939297)
4. O. Ter Brake, N. Legrand, K.J. von Eije, M. Centlivre, H. Spits, and K. Weijer Evaluation of safety and efficacy of RNAi against HIV-1 in the human immune system (Rag-2(-/-)(c)(-/-)) mouse model Gene Ther 16 2009 148 153
5. H. Ding, D.S. Schwarz, A. Keene, E.B. Affar, L. Fenton, and X. Xia Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis Aging Cell 2 2003 209 217
6. F. Takeshita, and T. Ochiya Therapeutic potential of RNA interference against cancer Cancer Sci 97 2006 689 696 (Pubitemid 43983779)
7. B.L. Davidson, and H.L. Paulson Molecular medicine for the brain: silencing of disease genes with RNA interference Lancet Neurol 3 2004 145 149 (Pubitemid 38229948)
8. J.C. Carrington, and V. Ambros Role of microRNAs in plant and animal development Science 301 2003 336 338 (Pubitemid 36877060)
9. V. Ambros The functions of animal microRNAs Nature 431 2004 350 355 (Pubitemid 39265675)
10. V. Ambros microRNAs: tiny regulators with great potential Cell 107 2001 823 826 (Pubitemid 34084973)
11. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
12. E.H. Baehrecke miRNAs: micro managers of programmed cell death Curr Biol 13 2003 R473 R475
13. M.T. McManus Small RNAs and immunity Immunity 21 2004 747 756 (Pubitemid 39626666)
14. Y. Lee, K. Jeon, J.T. Lee, S. Kim, and V.N. Kim MicroRNA maturation: stepwise processing and subcellular localization EMBO J 21 2002 4663 4670 (Pubitemid 34984353)
15. E. Bernstein, A.A. Caudy, S.M. Hammond, and G.J. Hannon Role for a bidentate ribonuclease in the initiation step of RNA interference Nature 409 2001 363 366 (Pubitemid 32151243)
16. A.M. Denli, B.B. Tops, R.H. Plasterk, R.F. Ketting, and G.J. Hannon Processing of primary microRNAs by the microprocessor complex Nature 432 2004 231 235 (Pubitemid 39545854)
17. R.I. Gregory, K.P. Yan, G. Amuthan, T. Chendrimada, B. Doratotaj, and N. Cooch The microprocessor complex mediates the genesis of microRNAs Nature 432 2004 235 240 (Pubitemid 39545855)
18. J. Han, Y. Lee, K.H. Yeom, Y.K. Kim, H. Jin, and V.N. Kim The Drosha-DGCR8 complex in primary microRNA processing Genes Dev 18 2004 3016 3027 (Pubitemid 39658171)
19. M. Landthaler, A. Yalcin, and T. Tuschl The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis Curr Biol 14 2004 2162 2167 (Pubitemid 39623200)
20. Y. Lee, C. Ahn, J. Han, H. Choi, J. Kim, and J. Yim The nuclear RNase III Drosha initiates microRNA processing Nature 425 2003 415 419 (Pubitemid 37187272)
21. J.G. Ruby, C.H. Jan, and D.P. Bartel Intronic microRNA precursors that bypass Drosha processing Nature 448 2007 83 86 (Pubitemid 47037009)
22. S.P. Chan, and F.J. Slack And now introducing mammalian mirtrons Dev Cell 13 2007 605 607 (Pubitemid 350011994)
23. M.T. Bohnsack, K. Czaplinski, and D. Gorlich Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs RNA 10 2004 185 191 (Pubitemid 38129823)
24. E. Lund, S. Guttinger, A. Calado, J.E. Dahlberg, and U. Kutay Nuclear export of microRNA precursors Science 303 2004 95 98 (Pubitemid 38055779)
25. R. Yi, Y. Qin, I.G. Macara, and B.R. Cullen Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs Genes Dev 17 2003 3011 3016 (Pubitemid 38040764)
26. H. Zhang, F.A. Kolb, L. Jaskiewicz, E. Westhof, and W. Filipowicz Single processing center models for human Dicer and bacterial RNase III Cell 118 2004 57 68 (Pubitemid 38902814)
27. T.P. Chendrimada, R.I. Gregory, E. Kumaraswamy, J. Norman, N. Cooch, and K. Nishikura TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing Nature 436 2005 740 744 (Pubitemid 41117280)
28. R.I. Gregory, T.P. Chendrimada, N. Cooch, and R. Shiekhattar Human RISC couples microRNA biogenesis and posttranscriptional gene silencing Cell 123 2005 631 640 (Pubitemid 41608466)
29. E. Maniataki, and Z. Mourelatos A human, ATP-independent, RISC assembly machine fueled by pre-miRNA Genes Dev 19 2005 2979 2990 (Pubitemid 41798114)
30. S.M. Hammond, S. Boettcher, A.A. Caudy, R. Kobayashi, and G.J. Hannon Argonaute2, a link between genetic and biochemical analyses of RNAi Science 293 2001 1146 1150 (Pubitemid 32758097)
31. Y. Tomari, C. Matranga, B. Haley, N. Martinez, and P.D. Zamore A protein sensor for siRNA asymmetry Science 306 2004 1377 1380 (Pubitemid 39532515)
32. Y. Tomari, and P.D. Zamore Perspective: machines for RNAi Genes Dev 19 2005 517 529 (Pubitemid 40314984)
33. H.L. Guo, N.T. Ingolia, J.S. Weissman, and D.P. Bartel Mammalian microRNAs predominantly act to decrease target mRNA levels Nature 466 2010 835 840
34. J. Brennecke, D.R. Hipfner, A. Stark, R.B. Russell, and S.M. Cohen Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila Cell 113 2003 25 36 (Pubitemid 36411957)
35. J.G. Doench, and P.A. Sharp Specificity of microRNA target selection in translational repression Genes Dev 18 2004 504 511 (Pubitemid 38372808)
36. B.P. Lewis, I.H. Shih, M.W. Jones-Rhoades, D.P. Bartel, and C.B. Burge Prediction of mammalian microRNA targets Cell 115 2003 787 798 (Pubitemid 38058492)
37. M. Kiriakidou, P.T. Nelson, A. Kouranov, P. Fitziev, C. Bouyioukos, and Z. Mourelatos A combined computational-experimental approach predicts human microRNA targets Genes Dev 18 2004 1165 1178 (Pubitemid 38669037)
38. E.C. Lai Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation Nat Genet 30 2002 363 364
39. P. Saetrom, B.S. Heale, O. Snove Jr., L. Aagaard, J. Alluin, and J.J. Rossi Distance constraints between microRNA target sites dictate efficacy and cooperativity Nucleic Acids Res 35 2007 2333 2342 (Pubitemid 47073716)
40. S. Yekta, I.H. Shih, and D.P. Bartel MicroRNA-directed cleavage of HOXB8 mRNA Science 304 2004 594 596 (Pubitemid 38541919)
41. S.M. Elbashir, J. Harborth, W. Lendeckel, A. Yalcin, K. Weber, and T. Tuschl Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells Nature 411 2001 494 498 (Pubitemid 32494397)
42. T.R. Brummelkamp, R. Bernards, and R. Agami A system for stable expression of short interfering RNAs in mammalian cells Science 296 2002 550 553 (Pubitemid 34408678)
43. P.J. Paddison, A.A. Caudy, E. Bernstein, G.J. Hannon, and D.S. Conklin Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells Genes Dev 16 2002 948 958 (Pubitemid 34408544)
44. Y. Zeng, E.J. Wagner, and B.R. Cullen Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells Mol Cell 9 2002 1327 1333 (Pubitemid 34722311)
45. N.C. Schopman, Y.P. Liu, P. Konstantinova, O. Ter Brake, and B. Berkhout Optimization of shRNA inhibitors by variation of the terminal loop sequence Antiviral Res 86 2010 204 211
46. Y.P. Liu, K.J. von Eije, N.C. Schopman, J.T. Westerink, O. Ter Brake, and J. Haasnoot Combinatorial RNAi against HIV-1 using extended short hairpin RNAs Mol Ther 17 2009 1712 1723
47. Y.P. Liu, J. Haasnoot, O. Ter Brake, B. Berkhout, and P. Konstantinova Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron Nucleic Acids Res 36 2008 2811 2824 (Pubitemid 351737175)
48. S. Barichievy, S. Saayman, K.J. von Eije, K.V. Morris, P. Arbuthnot, and M.S. Weinberg The inhibitory efficacy of RNA POL III-expressed long hairpin RNAs targeted to untranslated regions of the HIV-1 5′ long terminal repeat Oligonucleotides 17 2007 419 431
49. S.M. Saayman, P. Arbuthnot, and M.S. Weinberg Effective Pol III-expressed long hairpin RNAs targeted to multiple unique sites of HIV-1 Methods Mol Biol 629 2010 159 174
50. R.M. O'Connell, A.A. Chaudhuri, D.S. Rao, W.S. Gibson, A.B. Balazs, and D. Baltimore MicroRNAs enriched in hematopoietic stem cells differentially regulate long-term hematopoietic output Proc Natl Acad Sci USA 107 2010 14235 14240
51. D. Grimm, K.L. Streetz, C.L. Jopling, T.A. Storm, K. Pandey, and C.R. Davis Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways Nature 441 2006 537 541 (Pubitemid 44050158)
52. J.L. McBride, R.L. Boudreau, S.Q. Harper, P.D. Staber, A.M. Monteys, and I. Martins Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: implications for the therapeutic development of RNAi Proc Natl Acad Sci USA 105 2008 5868 5873 (Pubitemid 351758464)
53. R.L. Boudreau, A.M. Monteys, and B.L. Davidson Minimizing variables among hairpin-based RNAi vectors reveals the potency of shRNAs RNA 14 2008 1834 1844
54. T.A. Vickers, W.F. Lima, J.G. Nichols, and S.T. Crooke Reduced levels of Ago2 expression result in increased siRNA competition in mammalian cells Nucleic Acids Res 35 2007 6598 6610 (Pubitemid 350111625)
55. D. Castanotto, K. Sakurai, R. Lingeman, H. Li, L. Shively, and L. Aagaard Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC Nucleic Acids Res 35 2007 5154 5164 (Pubitemid 47394199)
56. J. Brennecke, A. Stark, R.B. Russell, and S.M. Cohen Principles of microRNA-target recognition PLoS Biol 3 2005 e85
57. A.L. Jackson, S.R. Bartz, J. Schelter, S.V. Kobayashi, J. Burchard, and M. Mao Expression profiling reveals off-target gene regulation by RNAi Nat Biotechnol 21 2003 635 637 (Pubitemid 36638089)
58. Y. Fedorov, E.M. Anderson, A. Birmingham, A. Reynolds, J. Karpilow, and K. Robinson Off-target effects by siRNA can induce toxic phenotype RNA 12 2006 1188 1196 (Pubitemid 43990544)
59. A.L. Jackson, J. Burchard, J. Schelter, B.N. Chau, M. Cleary, and L. Lim Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity RNA 12 2006 1179 1187 (Pubitemid 43990543)
60. A.J. Bridge, S. Pebernard, A. Ducraux, A.L. Nicoulaz, and R. Iggo Induction of an interferon response by RNAi vectors in mammalian cells Nat Genet 34 2003 263 264 (Pubitemid 36792856)
61. C.A. Sledz, M. Holko, M.J. de Veer, R.H. Silverman, and B.R. Williams Activation of the interferon system by short-interfering RNAs Nat Cell Biol 5 2003 834 839 (Pubitemid 37087172)
62. J.T. Marques, and B.R. Williams Activation of the mammalian immune system by siRNAs Nat Biotechnol 23 2005 1399 1405 (Pubitemid 41679392)
63. P. Kumar, H.S. Ban, S.S. Kim, H. Wu, T. Pearson, and D.L. Greiner T cell-specific siRNA delivery suppresses HIV-1 infection in humanized mice Cell 134 2008 577 586
64. M.E. Davis, J.E. Zuckerman, C.H. Choi, D. Seligson, A. Tolcher, and C.A. Alabi Evidence of RNAi in humans from systemically administered siRNA via targeted nanoparticles Nature 464 2010 1067 1070
65. L. Naldini, U. Blomer, P. Gallay, D. Ory, R. Mulligan, and F.H. Gage In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector Science 272 1996 263 267 (Pubitemid 26119138)
66. B. Berkhout HIV-based lentiviral vectors for anti-HIV gene therapy Future Virol 5 2010 367 369
67. O. Ter Brake, and B. Berkhout Lentiviral vectors that carry anti-HIV shRNAs: problems and solutions J Gene Med 9 2007 743 750 (Pubitemid 47386859)
68. Y.P. Liu, M.A. Vink, J.T. Westerink, A.E. Ramirez de, P. Konstantinova, and O. Ter Brake Titers of lentiviral vectors encoding shRNAs and miRNAs are reduced by different mechanisms that require distinct repair strategies RNA 16 2010 1328 1339
69. T. Nguyen, E.M. Menocal, J. Harborth, and J.H. Fruehauf RNAi therapeutics: an update on delivery Curr Opin Mol Ther 10 2008 158 167 (Pubitemid 351498878)
70. A.R. de Fougerolles Delivery vehicles for small interfering RNA in vivo Hum Gene Ther 19 2008 125 132 (Pubitemid 351278372)
71. R.G. Amado, R.T. Mitsuyasu, J.D. Rosenblatt, F.K. Ngok, A. Bakker, and S. Cole Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a phase I study: myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients Hum Gene Ther 15 2004 251 262 (Pubitemid 38365914)
72. R.T. Mitsuyasu, T.C. Merigan, A. Carr, J.A. Zack, M.A. Winters, and C. Workman Phase 2 gene therapy trial of an anti-HIV ribozyme in autologous CD34(+) cells Nat Med 15 2009 285 292
73. N. Cartier, S. Hacein-Bey-Abina, C.C. Bartholomae, G. Veres, M. Schmidt, and I. Kutschera Hematopoietic stem cell gene therapy with a lentiviral vector in X-linked adrenoleukodystrophy Science 326 2009 818 823
74. B. Dropulic Lentivirus in the clinic Mol Ther 4 2001 511 512
75. D. Boden, O. Pusch, F. Lee, L. Tucker, and B. Ramratnam Human immunodeficiency virus type 1 escape from RNA interference J Virol 77 2003 11531 11535 (Pubitemid 37271651)
76. A.T. Das, T.R. Brummelkamp, E.M. Westerhout, M. Vink, M. Madiredjo, and R. Bernards Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition J Virol 78 2004 2601 2605 (Pubitemid 38228957)
77. H. Nishitsuji, M. Kohara, M. Kannagi, and T. Masuda Effective suppression of human immunodeficiency virus type 1 through a combination of short- or long-hairpin RNAs targeting essential sequences for retroviral integration J Virol 80 2006 7658 7666 (Pubitemid 44092586)
78. R. Sabariegos, M. Gimenez-Barcons, N. Tapia, B. Clotet, and M.A. Martinez Sequence homology required by human immunodeficiency virus type 1 to escape from short interfering RNAs J Virol 80 2006 571 577 (Pubitemid 43062869)
79. O. Ter Brake, P. Konstantinova, M. Ceylan, and B. Berkhout Silencing of HIV-1 with RNA interference: a multiple shRNA approach Mol Ther 14 2006 883 892 (Pubitemid 44743127)
80. H.J. Unwalla, H.T. Li, I. Bahner, M.J. Li, D. Kohn, and J.J. Rossi Novel Pol II fusion promoter directs human immunodeficiency virus type 1-inducible coexpression of a short hairpin RNA and protein J Virol 80 2006 1863 1873 (Pubitemid 43228726)
81. E.M. Westerhout, M. Ooms, M. Vink, A.T. Das, and B. Berkhout HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome Nucleic Acids Res 33 2005 796 804 (Pubitemid 40361009)
82. O. Ter Brake, K. 't Hooft, Y.P. Liu, M. Centlivre, K.J. von Eije, and B. Berkhout Lentiviral vector design for multiple shRNA expression and durable HIV-1 Inhibition Mol Ther 16 2008 557 564 (Pubitemid 351314996)
83. Y.P. Liu, and B. Berkhout Lentiviral delivery of RNAi effectors against HIV-1 Curr Top Med Chem 9 2009 1130 1143
84. D. Grimm, and M.A. Kay Combinatorial RNAi: a winning strategy for the race against evolving targets? Mol Ther 15 2007 878 888 (Pubitemid 46621646)
85. M.J. Li, J. Kim, S. Li, J. Zaia, J.K. Yee, and J. Anderson Long-term inhibition of HIV-1 infection in primary hematopoietic cells by lentiviral vector delivery of a triple combination of anti-HIV shRNA, anti-CCR5 ribozyme, and a nucleolar-localizing TAR decoy Mol Ther 12 2005 900 909 (Pubitemid 41614486)
86. D.L. DiGiusto, A. Krishnan, L. Li, H. Li, S. Li, and A. Rao RNA-based gene therapy for HIV with lentiviral vector-modified CD34(+) cells in patients undergoing transplantation for AIDS-related lymphoma Sci Transl Med 2 2010 36ra43
87. J. Zhou, P. Swiderski, H. Li, J. Zhang, C.P. Neff, and R. Akkina Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells Nucleic Acids Res 37 2009 3094 3109
88. C.P. Neff, J. Zhou, L. Remling, J. Kuruvilla, J. Zhang, and H. Li An aptamer-siRNA chimera suppresses HIV-1 viral loads and protects from helper CD4(+) T cell decline in humanized mice Sci Transl Med 3 2011 66ra6
89. O.t. Brake, and B. Berkhout A novel approach for inhibition of HIV-1 by RNA interference: counteracting viral escape with a second generation of siRNAs J RNAi Gene Silencing 1 2005 56 65
90. K.J. von Eije, O. Ter Brake, and B. Berkhout Human immunodeficiency virus type 1 escape is restricted when conserved genome sequences are targeted by RNA interference J Virol 82 2008 2895 2903 (Pubitemid 351329179)
91. N.C. Schopman, O. Ter Brake, and B. Berkhout Anticipating and blocking HIV-1 escape by second generation antiviral shRNAs Retrovirology 7 2010 52
92. M.A. Muesing, D.H. Smith, C.D. Cabradilla, C.V. Benton, L.A. Lasky, and D.J. Capon Nucleic acid structure and expression of the human AIDS/lymphadenopathy retrovirus Nature 313 1985 450 458 (Pubitemid 15153157)
93. E.M. Westerhout, and B. Berkhout A systematic analysis of the effect of target RNA structure on RNA interference Nucleic Acids Res 35 2007 4322 4330 (Pubitemid 47244586)
94. J.M. Watts, K.K. Dang, R.J. Gorelick, C.W. Leonard, J.W. Bess Jr., and R. Swanstrom Architecture and secondary structure of an entire HIV-1 RNA genome Nature 460 2009 711 716
95. O. Ter Brake, K.J. von Eije, and B. Berkhout Probing the sequence space available for HIV-1 evolution AIDS 22 2008 1875 1877
96. K.J. von Eije, B.O. Ter Brake, and B. Berkhout Stringent testing identifies highly potent and escape-proof anti-HIV short hairpin RNAs J Gene Med 11 2009 459 467
97. G.J. McIntyre, J.L. Groneman, Y.H. Yu, A. Jaramillo, S. Shen, and T.L. Applegate 96 shRNAs designed for maximal coverage of HIV-1 variants Retrovirology 6 2009 55
98. J.M. Jacque, K. Triques, and M. Stevenson Modulation of HIV-1 replication by RNA interference Nature 418 2002 435 438 (Pubitemid 34826845)
99. L.J. Chang, X. Liu, and J. He Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1 Gene Ther 12 2005 1133 1144 (Pubitemid 41030619)
100. C.D. Novina, M.F. Murray, D.M. Dykxhoorn, P.J. Beresford, J. Riess, and S.K. Lee siRNA-directed inhibition of HIV-1 infection Nat Med 8 2002 681 686 (Pubitemid 34778720)
101. W.S. Park, N. Miyano-Kurosaki, M. Hayafune, E. Nakajima, T. Matsuzaki, and F. Shimada Prevention of HIV-1 infection in human peripheral blood mononuclear cells by specific RNA interference Nucleic Acids Res 30 2002 4830 4835 (Pubitemid 35414642)
102. B. Berkhout, and O.t. Brake Towards an RNAi-based gene therapy Bioforum Eur 4 2008 35 37
103. R.M. Surabhi, and R.B. Gaynor RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type 1 replication J Virol 76 2002 12963 12973 (Pubitemid 35386980)
104. G.A. Coburn, and B.R. Cullen Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference J Virol 76 2002 9225 9231 (Pubitemid 34919881)
105. N.S. Lee, T. Dohjima, G. Bauer, H. Li, M.J. Li, and A. Ehsani Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells Nat Biotechnol 20 2002 500 505 (Pubitemid 34495938)
106. Y.P. Liu, J. Haasnoot, and B. Berkhout Design of extended short hairpin RNAs for HIV-1 inhibition Nucleic Acids Res 35 2007 5683 5693 (Pubitemid 47506286)
107. M. Sano, H. Li, M. Nakanishi, and J.J. Rossi Expression of long anti-HIV-1 hairpin RNAs for the generation of multiple siRNAs: advantages and limitations Mol Ther 16 2008 170 177
108. P. Konstantinova, W. de Vries, J. Haasnoot, O. Ter Brake, P. de Haan, and B. Berkhout Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA Gene Ther 13 2006 1403 1413 (Pubitemid 44420635)
109. L.A. Aagaard, J. Zhang, K.J. von Eije, H. Li, P. Saetrom, and M. Amarzguioui Engineering and optimization of the miR-106b cluster for ectopic expression of multiplexed anti-HIV RNAs Gene Ther 15 2008 1536 1549
110. L.L. Snyder, J.M. Esser, C.J. Pachuk, and L.F. Steel Vector design for liver-specific expression of multiple interfering RNAs that target hepatitis B virus transcripts Antiviral Res 80 2008 36 44
111. M. Wiznerowicz, and D. Trono Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference J Virol 77 2003 8957 8961 (Pubitemid 36936105)
112. X. Zhou, J. Symons, R. Hoppes, C. Krueger, C. Berens, and W. Hillen Improved single-chain transactivators of the Tet-On gene expression system BMC Biotechnol 7 2007 6
113. Y.P. Liu, and B. Berkhout Combinatorial RNAi strategies against HIV-1 and other escape-prone viruses Int J BioSci Technol 1 2008 1 10
114. J. Lisziewicz, D. Sun, J. Smythe, P. Lusso, F. Lori, and A. Louie Inhibition of human immunodeficiency virus type 1 replication by regulated expression of a polymeric Tat activation response RNA decoy as a strategy for gene therapy in AIDS Proc Natl Acad Sci USA 90 1993 8000 8004 (Pubitemid 23260842)
115. N. Sarver, E.M. Cantin, P.S. Chang, J.A. Zaia, P.A. Ladne, and D.A. Stephens Ribozymes as potential anti-HIV-1 therapeutic agents Science 247 1990 1222 1225
116. S. Chatterjee, P.R. Johnson, and K.K. Wong Jr. Dual-target inhibition of HIV-1 in vitro by means of an adeno-associated virus antisense vector Science 258 1992 1485 1488
117. B.L. Levine, L.M. Humeau, J. Boyer, R.R. MacGregor, T. Rebello, and X. Lu Gene transfer in humans using a conditionally replicating lentiviral vector Proc Natl Acad Sci USA 103 2006 17372 17377 (Pubitemid 44788976)
118. D.B. Kohn, G. Bauer, C.R. Rice, J.C. Rothschild, D.A. Carbonaro, and P. Valdez A clinical trial of retroviral-mediated transfer of a rev-responsive element decoy gene into CD34(+) cells from the bone marrow of human immunodeficiency virus-1-infected children Blood 94 1999 368 371 (Pubitemid 29300172)
119. T.L. Symensma, L. Giver, M. Zapp, G.B. Takle, and A.D. Ellington RNA aptamers selected to bind human immunodeficiency virus type 1 Rev in vitro are Rev responsive in vivo J Virol 70 1996 179 187 (Pubitemid 126508784)
120. M.S. Weinberg, L.M. Villeneuve, A. Ehsani, M. Amarzguioui, L. Aagaard, and Z.X. Chen The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells RNA 12 2006 256 262 (Pubitemid 43121930)
121. X. Abad, M. Vera, S.P. Jung, E. Oswald, I. Romero, and V. Amin Requirements for gene silencing mediated by U1 snRNA binding to a target sequence Nucleic Acids Res 36 2008 2338 2352 (Pubitemid 351567007)
122. J. Anderson, A. Banerjea, and R. Akkina Bispecific short hairpin siRNA constructs targeted to CD4, CXCR4, and CCR5 confer HIV-1 resistance Oligonucleotides 13 2003 303 312 (Pubitemid 38404815)
123. J. Martinez, A. Patkaniowska, H. Urlaub, R. Luhrmann, and T. Tuschl Single-stranded antisense siRNAs guide target RNA cleavage in RNAi Cell 110 2002 563 574 (Pubitemid 35247837)
124. J. Anderson, and R. Akkina CXCR4 and CCR5 shRNA transgenic CD34+ cell derived macrophages are functionally normal and resist HIV-1 infection Retrovirology 2 2005 53
125. J. Anderson, A. Banerjea, V. Planelles, and R. Akkina Potent suppression of HIV type 1 infection by a short hairpin anti-CXCR4 siRNA AIDS Res Hum Retroviruses 19 2003 699 706 (Pubitemid 37047095)
126. M. Ishaq, J. Hu, X. Wu, Q. Fu, Y. Yang, and Q. Liu Knockdown of cellular RNA helicase DDX3 by short hairpin RNAs suppresses HIV-1 viral replication without inducing apoptosis Mol Biotechnol 39 2008 231 238
127. L. Vandekerckhove, F. Christ, B. Van Maele, J. De Rijck, R. Gijsbers, and H.C. Van den Transient and stable knockdown of the integrase cofactor LEDGF/p75 reveals its role in the replication cycle of human immunodeficiency virus J Virol 80 2006 1886 1896 (Pubitemid 43228728)
128. D.S. An, R.E. Donahue, M. Kamata, B. Poon, M. Metzger, and S.H. Mao Stable reduction of CCR5 by RNAi through hematopoietic stem cell transplant in non-human primates Proc Natl Acad Sci USA 104 2007 13110 13115 (Pubitemid 351737601)
129. J.J. Eekels, D. Geerts, R.E. Jeeninga, and B. Berkhout Long-term inhibition of HIV-1 replication with RNA interference against cellular co-factors Antiviral Res 89 2011 43 53
130. J.K. Lim, W.G. Glass, D.H. McDermott, and P.M. Murphy CCR5: no longer a "good for nothing" gene-chemokine control of West Nile virus infection Trends Immunol 27 2006 308 312 (Pubitemid 43963479)
131. G. Hutter, D. Nowak, M. Mossner, S. Ganepola, A. Mussig, and K. Allers Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation N Engl J Med 360 2009 692 698
132. M. Westby, M. Lewis, J. Whitcomb, M. Youle, A.L. Pozniak, and I.T. James Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir J Virol 80 2006 4909 4920
133. T. Lapidot Mechanism of human stem cell migration and repopulation of NOD/SCID and B2mnull NOD/SCID mice. The role of SDF-1/CXCR4 interactions Ann N Y Acad Sci 938 2001 83 95 (Pubitemid 32620021)
134. A.L. Brass, D.M. Dykxhoorn, Y. Benita, N. Yan, A. Engelman, and R.J. Xavier Identification of host proteins required for HIV infection through a functional genomic screen Science 319 2008 921 926 (Pubitemid 351263756)
135. R. Konig, Y. Zhou, D. Elleder, T.L. Diamond, G.M. Bonamy, and J.T. Irelan Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication Cell 135 2008 49 60
136. H.L. Zhou, M. Xu, Q. Huang, A.T. Gates, X.H.D. Zhang, and J.C. Castle Genome-scale RNAi screen for host factors required for HIV replication Cell Host Microbe 4 2008 495 504
137. S.P. Goff Knockdown screens to knockout HIV-1 Cell 135 2008 417 420
138. F.D. Bushman, N. Malani, J. Fernandes, I. D'Orso, G. Cagney, and T.L. Diamond Host cell factors in HIV replication: meta-analysis of genome-wide studies PLoS Pathog 5 2009 e1000437
139. A. Karlas, N. Machuy, Y. Shin, K.P. Pleissner, A. Artarini, and D. Heuer Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication Nature 463 2010 818 822
140. R. Konig, S. Stertz, Y. Zhou, A. Inoue, H.H. Hoffmann, and S. Bhattacharyya Human host factors required for influenza virus replication Nature 463 2010 813 817
141. Q. Li, A.L. Brass, A. Ng, Z. Hu, R.J. Xavier, and T.J. Liang A genome-wide genetic screen for host factors required for hepatitis C virus propagation Proc Natl Acad Sci USA 106 2009 16410 16415
142. O.M. Sessions, N.J. Barrows, J.A. Souza-Neto, T.J. Robinson, C.L. Hershey, and M.A. Rodgers Discovery of insect and human dengue virus host factors Nature 458 2009 1047 1050
143. M.N. Krishnan, A. Ng, B. Sukumaran, F.D. Gilfoy, P.D. Uchil, and H. Sultana RNA interference screen for human genes associated with West Nile virus infection Nature 455 2008 242 245
144. A.A. Lackner, and R.S. Veazey Current concepts in AIDS pathogenesis: insights from the SIV/macaque model Annu Rev Med 58 2007 461 476 (Pubitemid 46706527)
145. M. Stremlau, C.M. Owens, M.J. Perron, M. Kiessling, P. Autissier, and J. Sodroski The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in old world monkeys Nature 427 2004 848 853 (Pubitemid 38297747)
146. T. Hatziioannou, Z. Ambrose, N.P. Chung, M. Piatak Jr., F. Yuan, and C.M. Trubey A macaque model of HIV-1 infection Proc Natl Acad Sci USA 106 2009 4425 4429
147. E. Traggiai, L. Chicha, L. Mazzucchelli, L. Bronz, J.C. Piffaretti, and A. Lanzavecchia Development of a human adaptive immune system in cord blood cell-transplanted mice Science 304 2004 104 107 (Pubitemid 38451466)
148. R. Gimeno, K. Weijer, A. Voordouw, C.H. Uittenbogaart, N. Legrand, and N.L. Alves Monitoring the effect of gene silencing by RNA interference in human CD34+ cells injected into newborn RAG2-/- gammac-/- mice: functional inactivation of p53 in developing T cells Blood 104 2004 3886 3893 (Pubitemid 39620134)
149. N. Legrand, K. Weijer, and H. Spits Experimental models to study development and function of the human immune system in vivo J Immunol 176 2006 2053 2058 (Pubitemid 43201649)
150. L.D. Shultz, F. Ishikawa, and D.L. Greiner Humanized mice in translational biomedical research Nat Rev Immunol 7 2007 118 130 (Pubitemid 46174859)
151. M.G. Manz Human-hemato-lymphoid-system mice: opportunities and challenges Immunity 26 2007 537 541 (Pubitemid 46756351)
152. N. Legrand, T. Cupedo, A.U. van Lent, M.J. Ebeli, K. Weijer, and T. Hanke Transient accumulation of human mature thymocytes and regulatory T cells with CD28 superagonist in "human immune system" Rag2(-/-)gammac(-/-) mice Blood 108 2006 238 245 (Pubitemid 43990634)
153. S. Baenziger, R. Tussiwand, E. Schlaepfer, L. Mazzucchelli, M. Heikenwalder, and M.O. Kurrer Disseminated and sustained HIV infection in CD34+ cord blood cell-transplanted Rag2-/-gamma c-/- mice Proc Natl Acad Sci USA 103 2006 15951 15956 (Pubitemid 44657573)
154. L. Zhang, G.I. Kovalev, and L. Su HIV-1 infection and pathogenesis in a novel humanized mouse model Blood 109 2007 2978 2981 (Pubitemid 46482096)
155. S. Watanabe, K. Terashima, S. Ohta, S. Horibata, M. Yajima, and Y. Shiozawa Hematopoietic stem cell-engrafted NOD/SCID/IL2Rgamma null mice develop human lymphoid systems and induce long-lasting HIV-1 infection with specific humoral immune responses Blood 109 2007 212 218 (Pubitemid 46070123)
156. B.K. Berges, W.H. Wheat, B.E. Palmer, E. Connick, and R. Akkina HIV-1 infection and CD4 T cell depletion in the humanized Rag2-/-gamma c-/- (RAG-hu) mouse model Retrovirology 3 2006 76
157. B.K. Berges, S.R. Akkina, J.M. Folkvord, E. Connick, and R. Akkina Mucosal transmission of R5 and X4 tropic HIV-1 via vaginal and rectal routes in humanized Rag2(-/-)gammac(-/-) (RAG-hu) mice Virology 373 2008 342 351
158. D.S. An, B. Poon, F.R. Ho Tsong, K. Weijer, B. Blom, and H. Spits Use of a novel chimeric mouse model with a functionally active human immune system to study human immunodeficiency virus type 1 infection Clin Vaccine Immunol 14 2007 391 396 (Pubitemid 46732549)
159. H. Goldstein Summary of presentations at the NIH/NIAID new humanized rodent models 2007 workshop AIDS Res Ther 5 2008 3
160. M. Robbins, A. Judge, E. Ambegia, C. Choi, E. Yaworski, and L. Palmer Misinterpreting the therapeutic effects of small interfering RNA caused by immune stimulation Hum Gene Ther 19 2008 991 999
161. M.E. Kleinman, K. Yamada, A. Takeda, V. Chandrasekaran, M. Nozaki, and J.Z. Baffi Sequence- and target-independent angiogenesis suppression by siRNA via TLR3 Nature 452 2008 591 597 (Pubitemid 351483358)
162. B.J. Culliton Gene therapy begins Science 249 1990 1372 (Pubitemid 20341896)
163. E. Marshall Gene therapy death prompts review of adenovirus vector Science 286 1999 2244 2245 (Pubitemid 30016842)
164. S. Hacein-Bey-Abina, F. Le Deist, F. Carlier, C. Bouneaud, C. Hue, and J.P. de Villartay Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy N Engl J Med 346 2002 1185 1193 (Pubitemid 34984579)
165. S. Hacein-Bey-Abina, C. von Kalle, M. Schmidt, M.P. McCormack, N. Wulffraat, and P. Leboulch LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1 Science 302 2003 415 419 (Pubitemid 37296260)
166. S. Hacein-Bey-Abina, J. Hauer, A. Lim, C. Picard, G.P. Wang, and C.C. Berry Efficacy of gene therapy for X-linked severe combined immunodeficiency N Engl J Med 363 2010 355 364
167. M.L. Edelstein, M.R. Abedi, and J. Wixon Gene therapy clinical trials worldwide to 2007 - an update J Gene Med 9 2007 833 842 (Pubitemid 47543250)
168. F. Bushman, M. Lewinski, A. Ciuffi, S. Barr, J. Leipzig, and S. Hannenhalli Genome-wide analysis of retroviral DNA integration Nat Rev Microbiol 3 2005 848 858 (Pubitemid 41693180)
169. E. Montini, D. Cesana, M. Schmidt, F. Sanvito, M. Ponzoni, and C. Bartholomae Hematopoietic stem cell gene transfer in a tumor-prone mouse model uncovers low genotoxicity of lentiviral vector integration Nat Biotechnol 24 2006 687 696 (Pubitemid 43882120)
170. P. Manilla, T. Rebello, C. Afable, X. Lu, V. Slepushkin, and L.M. Humeau Regulatory considerations for novel gene therapy products: a review of the process leading to the first clinical lentiviral vector Hum Gene Ther 16 2005 17 25 (Pubitemid 40250328)
171. J.J. Rossi, C.H. June, and D.B. Kohn Genetic therapies against HIV Nat Biotechnol 25 2007 1444 1454 (Pubitemid 350233141)