Advanced search
Publication Cover
Expert Opinion on Biological Therapy Volume 9, 2009 - Issue 2
Submit an article Journal homepage
238
Views
20
CrossRef citations to date
0
Altmetric
Reviews

Towards a durable RNAi gene therapy for HIV-AIDS

Ben Berkhout Academic Medical Center of the University of Amsterdam, Center for Infection and Immunity Amsterdam (CINIMA), Department of Medical Microbiology, Laboratory of Experimental Virology, K3-110, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands +31 20 566 4822; +31 20 691 6531; [email protected]
&
Olivier ter Brake Academic Medical Center of the University of Amsterdam, Center for Infection and Immunity Amsterdam (CINIMA), Department of Medical Microbiology, Laboratory of Experimental Virology, K3-110, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands +31 20 566 4822; +31 20 691 6531; [email protected]
Pages 161-170 | Published online: 19 Dec 2008

Bibliography

  • He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004;5:522-31
  • Elbashir SM, Harborth J, Lendeckel W, et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001;411:494-8
  • Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 2002;296:550-3
  • Hammond SM, Bernstein E, Beach D, Hannon GJ. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000;404:293-6
  • Bitko V, Musiyenko A, Shulyayeva O, Barik S. Inhibition of respiratory viruses by nasally administered siRNA. Nat Med 2005;11:29350293-55
  • Ge Q, Filip L, Bai A, et al. Inhibition of influenza virus production in virus-infected mice by RNA interference. Proc Natl Acad Sci USA 2004;101:8676-81
  • Li BJ, Tang Q, Cheng D, et al. Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque. Nat Med 2005;11:944-51
  • Zhang W, Yang H, Kong X, et al. Inhibition of respiratory syncytial virus infection with intranasal siRNA nanoparticles targeting the viral NS1 gene. Nat Med 2005;11:56-62
  • Kleinman ME, Yamada K, Takeda A, et al. Sequence- and target-independent angiogenesis suppression by siRNA via TLR3. Nature 2008;452:591-7
  • Reich SJ, Fosnot J, Kuroki A, et al. Small interfering RNA (siRNA) targeting VEGF effectively inhibits ocular neovascularization in a mouse model. Molecular vision 2003;9:210-16
  • Shen J, Samul R, Silva RL, et al. Suppression of ocular neovascularization with siRNA targeting VEGF receptor 1. Gene Ther 2005;13:225-34
  • Robbins M, Judge A, Ambegia E, et al. Misinterpreting the therapeutic effects of siRNA caused by immune stimulation. Hum Gene Ther 2008: published online 19 August 2008, doi:10.1089/hgt.2008.131
  • Berkhout B. RNA interference as an antiviral approach: targeting HIV-1. Curr Opin Mol Ther 2004;6:141-5
  • Lee NS, Rossi JJ. Control of HIV-1 replication by RNA interference. Virus Res 2004;6:141-5
  • Anderson J, Li MJ, Palmer B, et al. Safety and efficacy of a lentiviral vector containing three anti-HIV genes-CCR5 Ribozyme, Tat-rev siRNA, and TAR decoy-in SCID-hu mouse-derived T cells. Mol Ther 2007;14:1182-8
  • Grimm D, Kay MA. Therapeutic application of RNAi: is mRNA targeting finally ready for prime time? J Clin Invest 2007;117:3633-41
  • Kumar P, Ban HS, Kim SS, et al. T cell-specific siRNA delivery suppresses HIV-1 infection in humanized mice. Cell 2008;134:577-86
  • Goffinet C, Keppler OT. Efficient nonviral gene delivery into primary lymphocytes from rats and mice. FASEB J 2006;20:500-2
  • Ter Brake O, Berkhout. A novel approach for inhibition of HIV-1 by RNA interference: counteracting viral escape with a second generation of siRNAs. Journal of RNAi and Gene Silencing 2005;1:56-65
  • Ter Brake O, ‘t Hooft K, et al. Lentiviral vector design for multiple shRNA expression and durable HIV-1 Inhibition. Mol Ther 2008;16:557-64
  • Haasnoot J, Westerhout EM, Berkhout B. RNA interference against viruses: strike and counterstrike. Nat Biotechnol 2007;25:1435-43
  • Boden D, Pusch O, Lee F, et al. Human immunodeficiency virus type 1 escape from RNA interference. J Virol 2003;77:11531-5
  • Boden D, Pusch O, Lee F, et al. Efficient gene transfer of HIV-1-specific short hairpin RNA into human lymphocytic cells using recombinant adeno-associated virus vectors. Mol Ther 2004;9:396-402
  • Boden D, Pusch O, Silbermann R, et al. Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins. Nucleic Acids Res 2004;32:1154-8
  • Das AT, Brummelkamp TR, Westerhout EM, et al. Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J Virol 2004;78:2601-5
  • Westerhout EM, Ooms M, Vink M, et al. HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res 2005;33:796-804
  • Westerhout EM, Vink M, Haasnoot PC, et al. A conditionally replicating HIV-based vector that stably expresses an antiviral shRNA against HIV-1 replication. Mol Ther 2006;14:268-75
  • Liu YP, Haasnoot J, Ter Brake, et al. Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron. Nucleic Acids Res 2008;36:2811-24
  • Ter Brake, O Konstantinova, P Ceylan, M Berkhout. Silencing of HIV-1 with RNA interference: a multiple shRNA approach. Mol Ther 2006;14:883-92
  • von Eije KJ, Ter Brake O, Berkhout B. Human immunodeficiency virus type 1 escape is restricted when conserved genome sequences are targeted by RNA interference. J Virol 2008;82:2895-903
  • Martinez MA, Clotet B, Este JA. RNA interference of HIV replication. Trends Immunol 2002;23:559-61
  • 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;16:2385-90
  • Sabariegos R, Gimenez-barcons M, Tapia N, et al. Sequence homology required by human immunodeficiency virus type 1 to escape from short interfering RNAs. J Virol 2006;80:571-7
  • Anderson J, Banerjea A, Akkina R. Bispecific short hairpin siRNA constructs targeted to CD4, CXCR4, and CCR5 confer HIV-1 resistance. Oligonucleotides 2003;13:303-12
  • Barichievy S, Saayman S, von Eije KJ, et al. The inhibitory efficacy of RNA POL III-expressed long hairpin RNAs targeted to untranslated regions of the HIV-1 5′ long terminal repeat. Oligonucleotides 2007;17:419-31
  • Boden D, Pusch O, Lee F, et al. Promoter choice affects the potency of HIV-1 specific RNA interference. Nucleic Acids Res 2003;31:5033-8
  • Capodici J, Kariko K, Weissman D. Inhibition of HIV-1 infection by small interfering RNA-mediated RNA interference. J Immunol 2002;169:5196-201
  • Chiu YL, Cao H, Jacque JM, et al. Inhibition of human immunodeficiency virus type 1 replication by RNA interference directed against human transcription elongation factor P-TEFb (CDK9/CyclinT1). J Virol 2004;78:2517-29
  • Huff B. News from the bench. Assay for less-fit phenotype? GMHC Treat Issues 2004;18:14
  • Konstantinova P, Ter Brake, O Haasnoot, et al. Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome. Retrovirology 2007;4:15: published online March 1 2007, doi:10.1186/1742-4690-4-15
  • Lawrence D. RNAi could hold promise in the treatment of HIV. Lancet 2002;359:2007.
  • Li Z, Xiong Y, Peng Y, et al. Specific inhibition of HIV-1 replication by short hairpin RNAs targeting human cyclin T1 without inducing apoptosis. FEBS Lett 2005;579:3100-6
  • Liu YP, Haasnoot J, Berkhout B. Design of extended short hairpin RNAs for HIV-1 inhibition. Nucleic Acids Res 2007;35:5683-93.
  • Nishitsuji H, Ikeda T, Miyoshi H, et al. Expression of small hairpin RNA by lentivirus-based vector confers efficient and stable gene-suppression of HIV-1 on human cells including primary non-dividing cells. Microbes Infect 2004;6:76-85
  • Omoto S, Ito M, Tsutsumi Y, et al. HIV-1 nef suppression by virally encoded microRNA. Retrovirology 2004;1:44: published online 15 December 2004, doi:10.1186/1742-4690-1-44
  • Ping YH, Chu CY, Cao H, et al. Modulating HIV-1 replication by RNA interference directed against human transcription elongation factor SPT5. Retrovirology 2004;1:46: published online 27 December 2004, doi:10.1186/1742-4690-1-46
  • Rossi JJ. RNAi as a treatment for HIV-1 infection. Biotechn 2006;Suppl:25-9.
  • Saayman S, Barichievy S, Capovilla A, et al. The efficacy of generating three independent anti-HIV-1 siRNAs from a single U6 RNA Pol III-expressed long hairpin RNA. PLoS One 2008;3:e2602: published online July 2 2008, doi:10.1371/journal.pone.0002602
  • Son J, Uchil PD, Kim YB, et al. Effective suppression of HIV-1 by artificial bispecific miRNA targeting conserved sequences with tolerance for wobble base-pairing. Biochem Biophys Res Commun 2008;374:214-18
  • Yamamoto T, Omoto S, Mizuguchi M, et al. Double-stranded nef RNA interferes with human immunodeficiency virus type 1 replication. Microbiol Immunol 2002;46:809-17
  • Yamamoto T, Miyoshi H, Yamamoto N, et al. Lentivirus vectors expressing short hairpin RNAs against the U3-overlapping region of HIV nef inhibit HIV replication and infectivity in primary macrophages. Blood 2006;108:3305-12
  • Zhou N, Fang J, Mukhtar M, et al. Inhibition of HIV-1 fusion with small interfering RNAs targeting the chemokine coreceptor CXCR4. Gene Ther 2004;11:1703-12
  • Ter BO, Haasnoot J, Kurreck J, Berkhout B. ESF-EMBO symposium: antiviral applications of RNA interference. Retrovirology 2008;5:81: published online 18 September 2008, doi:10.1186/1742-5-81
  • Naito Y, Nohtomi K, Onogi T, et al. Optimal design and validation of antiviral siRNA for targeting HIV-1. Retrovirology 2007;4:80. published online 8 November 2007, doi:10.1186/1742-4690-4-80
  • Coburn GA, Cullen BR. Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J Virol 2002;76:9225-31
  • Jacque JM, Triques K, Stevenson M. Modulation of HIV-1 replication by RNA interference. Nature 2002;418:435-8
  • Joshi PJ, North TW, Prasad VR. Aptamers directed to HIV-1 reverse transcriptase display greater efficacy over small hairpin RNAs targeted to viral RNA in blocking HIV-1 replication. Mol Ther 2005;11:677-86
  • Nishitsuji H, Kohara M, Kannagi M, Masuda T. 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 2006;80:7658-66
  • Surabhi RM, Gaynor RB. RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type 1 replication. J Virol 2002;76:12963-73
  • Hu WY, Myers CP, Kilzer JM, et al. Inhibition of retroviral pathogenesis by RNA interference. Curr Biol 2002;12:1301-11
  • Westerhout EM, Ter Brake O, Berkhout B. The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference. Retrovirology 2006;3:57-65.
  • Gao Y, Lobritz MA, Roth J, et al. Targets of small interfering RNA restriction during human immunodeficiency virus type 1 replication. J Virol 2008;82:2938-51
  • 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 2005;106:818-26
  • Unwalla HJ, Li HT, Bahner I, et al. Novel Pol II fusion promoter directs human immunodeficiency virus type 1-inducible coexpression of a short hairpin RNA and protein. J Virol 2006;80:1863-73
  • Ter Brake O, von Eije KJ, Berkhout B. Probing the sequence space available for HIV-1 evolution. AIDS 2008;22:1875-7
  • Liu YP, Berkhout B. Combinatorial RNAi strategies against HIV-1 and other escape-prone viruses. Int J BioSci Technol 2008;1:1-10
  • Grimm D, Kay MA. Combinatorial RNAi: a winning strategy for the race against evolving targets? Mol Ther 2007;15:878-88
  • Hannon GJ, Rossi JJ. Unlocking the potential of the human genome with RNA interference. Nature 2004;431:371-8
  • Shankar P, Manjunath N, Lieberman J. The prospect of silencing disease using RNA interference. JAMA (2005);293:1367-1373
  • Stevenson M. Dissecting HIV-1 through RNA interference. Nat Rev Immunol 2003;3:851-8
  • Mansky LM. The mutation rate of human immunodeficiency virus type 1 is influenced by the vpr gene. Virol 1996;222:391-400
  • Anderson J, Akkina R. HIV-1 resistance conferred by siRNA cosuppression of CXCR4 and CCR5 coreceptors by a bispecific lentiviral vector. AIDS Res Ther 2005;2:1: published online 13 January 2005, doi:10.1186/1742-6405-2-1
  • Llano M, Saenz DT, Meehan A, et al. An essential role for LEDGF/p75 in HIV integration. Science 2006;314:461-4
  • Maertens G, Cherepanov P, Pluymers W, et al. LEDGF/p75 is essential for nuclear and chromosomal targeting of HIV-1 integrase in human cells. J Biol Chem 2003;278:33528-39
  • Jacque JM, Stevenson M. The inner-nuclear-envelope protein emerin regulates HIV-1 infectivity. Nature 2006;441:641-5
  • Nguyen DG, Wolff KC, Yin H, et al. “UnPAKing” human immunodeficiency virus (HIV) replication: using small interfering RNA screening to identify novel cofactors and elucidate the role of group I PAKs in HIV Infection. J Virol 2006;80:130-7
  • Liu R, Paxton WA, Choe S, et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 1996;86:367-77
  • de Roda Husman AM, Blaak H, Brouwer M, Schuitemaker H. CC chemokine receptor 5 cell-surface expression in relation to CC chemokine receptor 5 genotype and the clinical course of HIV-1 infection. J Immunol 1999;163:4597-603
  • 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 2007;104:13110-15
  • Root DE, Hacohen N, Hahn WC, et al. Genome-scale loss-of-function screening with a lentiviral RNAi library. Nat Methods 2006;3:715-19
  • Huesken D, Lange J, Mickanin C, et al. Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol 2005;23:995-1001
  • Miyagishi M, Matsumoto S, Taira K. Generation of an shRNAi expression library against the whole human transcripts. Virus Res 2004;102:117-24
  • Paddison PJ, Silva JM, Conklin DS, et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 2004;428:427-431
  • Berns K, Hijmans EM, Mullenders J, et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 2004;428:431-7
  • Brass AL, Dykxhoorn DM, Benita Y, et al. Identification of host proteins required for HIV infection through a functional genomic screen. Science 2008;319:921-6
  • König R, Zhou Y, Elleder D, et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 2008;135:49-60
  • Ringrose J, Jeeninga RE, Berkhout B, Speijer D. Proteomic studies reveal coordinated changes in T cell expression patterns upon HIV-1 infection. J Virol 2008;82:4320-30
  • Berkhout B, Jeang KT. RISCy business: microRNAs, pathogenesis, and viruses. J Biol Chem 2007;282:26641-5
  • Berkhout B. A balancing act: Viruses and miRNAs. J Formos Med Assoc 2008;107:1-3
  • Huang J, Wang F, Argyris E, et al. Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med 2007;13:1241-7
  • Banerjea A, Li MJ, Bauer G, et al. 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 2003;8:62-71
  • Chang LJ, Liu X, He J. Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1. Gene Ther 2005;12:1133-44
  • Ter Brake, O Berkhout. Lentiviral vectors that carry anti-HIV shRNAs: problems and solutions. J Gene Med 2007;9:743-50
  • Westerhout EM, Berkhout B. A systematic analysis of the effect of target RNA structure on RNA interference. Nucleic Acids Res 2007;35:4322-30
  • An W, Telesnitsky A. Frequency of direct repeat deletion in a human immunodeficiency virus type 1 vector during reverse transcription in human cells. Virol 2001;286:475-82
  • Weinberg MS, Ely A, Barichievy S, et al. Specific inhibition of HBV replication in vitro and in vivo with expressed long hairpin RNA. Mol Ther 2007;15:534-41
  • Grimm D, Streetz KL, Jopling CL, et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006;441:537-41
  • Bridge AJ, Pebernard S, Ducraux A, et al. Induction of an interferon response by RNAi vectors in mammalian cells. Nat Genet 2003;34:263-64
  • 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 2005;11:263-70
  • Pebernard S, Iggo RD. Determinants of interferon-stimulated gene induction by RNAi vectors. Differentiation 2004;72:103-11
  • Robbins MA, Rossi JJ. Sensing the danger in RNA. Nat Med 2005;11:250-51
  • Sioud M. Induction of inflammatory cytokines and interferon responses by double-stranded and single-stranded siRNAs is sequence-dependent and requires endosomal localization. J Mol Biol 2005;348:1079-90
  • Birmingham A, Anderson EM, Reynolds A, et al. 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 2006;3:199-204
  • Jackson AL, Burchard J, Schelter J, et al. Widespread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity. RNA 2006;12:1179-87
  • Lin X, Ruan X, Anderson MG, et al. siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res 2005;33:4527-35
  • Legrand N, Weijer K, Spits H. Experimental models to study development and function of the human immune system in vivo. J Immunol 2006;176:2053-8
  • Ter Brake O, Legrand N, von Eije KJ, et al. Evaluation of safety and efficacy of RNAi against HIV-1 in the human immune system (Rag-2-/-γc-/-) mouse model. Gene Ther 2008; published online 31 July 2008, doi:10.1038/gt.2008.124
  • Baenziger S, Tussiwand R, Schlaepfer E, et al. Disseminated and sustained HIV infection in CD34+ cord blood cell-transplanted Rag2-/-γc-/- mice. Proc Natl Acad Sci USA 2006;103:15951-6
  • Berges BK, Wheat WH, Palmer BE, et al. HIV-1 infection and CD4 T cell depletion in the humanized Rag2-/-γc-/- (RAG-hu) mouse model. Retrovirology 2006;3:76: published online 1 November 2006, doi:10.1186/1742-4690-3-76
  • Zhang L, Kovalev GI, Su L. HIV-1 infection and pathogenesis in a novel humanized mouse model. Blood 2007;109:2978-81
  • Fire A, Xu S, Montgomery MK, et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998;391:806-11
  • Wilkinson KA, Merino EJ, Weeks KM. Selective 2¢-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc 2006;1:1610-16
  • Henry SD, van der Wegen P, Metselaar HJ, et al. Simultaneous targeting of HCV replication and viral binding with a single lentiviral vector containing multiple RNA interference expression cassettes. Mol Ther 2006;14:485-93
  • Birney E, Stamatoyannopoulos JA, Dutta A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799-816
  • Carninci P, Kasukawa T, Katayama S, et al. The transcriptional landscape of the mammalian genome. Science 2005;309:1559-63

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.