RNA silencing is an established method for investigating gene function and has attracted particular interest because of the potential for generating RNA-based therapeutics. Using lentiviral vectors as an efficient delivery system that offers stable, long-term expression in postmitotic cells further enhances the applicability of an RNA-based gene therapy for the CNS. In this review we provide an overview of both lentiviral vectors and RNA silencing along with design considerations for generating lentiviral vectors capable of RNA silencing. We go on to describe the current preclinical data regarding lentiviral vector-mediated RNA silencing for CNS disorders and discuss the concerns of side effects associated with lentiviral vectors and small interfering RNAs and how these might be mitigated.
Get full access to this article
View all access options for this article.
References
1.
Abordo-AdesidaE., FollenziA., BarciaC., et al. (2005). Stability of lentiviral vector-mediated transgene expression in the brain in the presence of systemic antivector immune responses. Hum. Gene Ther., 16, 741–751.
2.
AhmedZ., DentR.G., SuggateE.L., et al. (2005). Disinhibition of neurotrophin-induced dorsal root ganglion cell neurite outgrowth on CNS myelin by siRNA-mediated knockdown of NgR, p75NTR and Rho-A. Mol. Cell Neurosci., 28, 509–523.
3.
AlexopoulouL., HoltA.C., MedzhitovR., et al. (2001). Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature, 413, 732–738.
4.
AlvesS., Nascimento-FerreiraI., AureganG., et al. (2008). Allele-specific RNA silencing of mutant ataxin-3 mediates neuroprotection in a rat model of Machado-Joseph disease. PLoS One, 3, e3341.
5.
AmarzguiouiM., and PrydzH. (2004). An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun., 316, 1050–1058.
6.
AnD.S., QinF.X., AuyeungV.C., et al. (2006). Optimization and functional effects of stable short hairpin RNA expression in primary human lymphocytes via lentiviral vectors. Mol. Ther., 14, 494–504.
7.
AndersonE.M., BirminghamA., BaskervilleS., et al. (2008). Experimental validation of the importance of seed complement frequency to siRNA specificity. RNA. 704–708.
8.
BaeuerleP.A., and HenkelT. (1994). Function and activation of NF-κB in the immune system. Annu. Rev. Immunol., 12, 141–179.
9.
BaoL., GuoH., HuangX., et al. (2009). High-titer lentiviral vectors stimulate fetal calf serum-specific human CD4 T-cell responses: Implications in human gene therapy. Gene Ther., 16, 788–795.
10.
BarksJ.D., NairM.P., SchwartzS.A., et al. (1993). Potentiation of N-methyl-d-aspartate-mediated brain injury by a human immunodeficiency virus-1-derived peptide in perinatal rodents. Pediatr. Res., 34, 192–198.
11.
BauerM., KinklN., MeixnerA., et al. (2008). Prevention of interferon-stimulated gene expression using microRNA-designed hairpins. Gene Ther., 16, 142–147.
12.
BaumC., and FehseB. (2003). Mutagenesis by retroviral transgene insertion: Risk assessment and potential alternatives. Curr. Opin. Mol. Ther., 5, 458–462.
13.
BaumC., KustikovaO., ModlichU., et al. (2006). Mutagenesis and oncogenesis by chromosomal insertion of gene transfer vectors. Hum. Gene Ther., 17, 253–263.
14.
Behm-AnsmantI., RehwinkelJ., DoerksT., et al. (2006). mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev., 20, 1885–1898.
15.
BentwichI., AvnielA., KarovY., et al. (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet., 37, 766–770.
16.
BernsteinE., CaudyA.A., HammondS.M., et al. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366.
17.
BilangesB., and StokoeD. (2005). Direct comparison of the specificity of gene silencing using antisense oligonucleotides and RNAi. Biochem. J., 388, 573–583.
18.
BirminghamA., AndersonE.M., ReynoldsA., et al. (2006). 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods, 3, 199–204.
19.
BlomerU., NaldiniL., KafriT., et al. (1997). Highly efficient and sustained gene transfer in adult neurons with a lentivirus vector. J. Virol., 71, 6641–6649.
20.
BoudreauR.L., MonteysA.M., and DavidsonB.L. (2008). Minimizing variables among hairpin-based RNAi vectors reveals the potency of shRNAs. RNA, 14, 1834–1844.
21.
BoudreauR.L., MartinsI., and DavidsonB.L. (2009). Artificial microRNAs as siRNA shuttles: Improved safety as compared with shRNAs in vitro and in vivo. Mol. Ther., 17, 169–175.
22.
BraaschD.A., and CoreyD.R. (2001). Locked nucleic acid (LNA): Fine-tuning the recognition of DNA and RNA. Chem. Biol., 8, 1–7.
23.
BraunJ.E., HuntzingerE., FauserM., et al. (2011). GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. Mol. Cell, 44, 120–133.
24.
BridgeA.J., PebernardS., DucrauxA., et al. (2003). Induction of an interferon response by RNAi vectors in mammalian cells. Nat. Genet., 34, 263–264.
25.
BrownH.E., ChenH., and EngelmanA. (1999). Structure based mutagenesis of the human immunodeficiency virus type 1 DNA attachment site: Effects on integration and cDNA synthesis. J. Virol., 73, 9011–9020.
26.
BrummelkampT.R., BernardsR., and AgamiR. (2002). A system for stable expression of short interfering RNAs in mammalian cells. Science, 296, 550–553.
27.
BurnsJ.C., FriedmannT., DrieverW., et al. (1993). Vesicular stomatitis virus G glycoprotein pseudotyped retroviral vectors: Concentration to very high titer and efficient gene transfer into mammalian and nonmammalian cells. Proc. Natl. Acad. Sci. U.S.A., 90, 8033–8037.
28.
CaraA., CeresetoA., LoriF., et al. (1996). HIV-1 protein expression from synthetic circles of DNA mimicking the extrachromosomal forms of viral DNA. J. Biol. Chem., 271, 5393–5397.
29.
CastanottoD., SakuraiK., LingemanR., et al. (2007). Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC. Nucleic Acids Res., 35, 5154–5164.
30.
CekaiteL., FursetG., HovigE., et al. (2007). Gene expression analysis in blood cells in response to unmodified and 2′-modified siRNAs reveals TLR-dependent and independent effects. J. Mol. Biol., 365, 90–108.
31.
ChalkA.M., WahlestedtC., and SonnhammerE.L. (2004). Improved and automated prediction of effective siRNA. Biochem. Biophys. Res. Commun., 319, 264–274.
32.
CharneauP., AlizonM., and ClavelF. (1992). A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication. J. Virol., 66, 2814–2820.
33.
ChekulaevaM., MathysH., ZipprichJ.T., et al. (2011). miRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifs. Nat. Struct. Mol. Biol., 18, 1218–1226.
34.
ChendrimadaT.P., GregoryR.I., KumaraswamyE., et al. (2005). TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 436, 740–744.
35.
ChristensenM., and SchrattG.M. (2009). microRNA involvement in developmental and functional aspects of the nervous system and in neurological diseases. Neurosci. Lett., 466, 55–62.
36.
CraigieR. (2001). HIV integrase, a brief overview from chemistry to therapeutics. J. Biol. Chem., 276, 23213–23216.
CullenB.R. (2005). RNAi the natural way. Nat. Genet., 37, 1163–1165.
39.
CullenB.R. (2006). Induction of stable RNA interference in mammalian cells. Gene Ther., 13, 503–508.
40.
DalyT.J., CookK.S., GrayG.S., et al. (1989). Specific binding of HIV-1 recombinant Rev protein to the Rev-responsive element in vitro. Nature, 342, 816–819.
41.
DasA.T., KokenS.E., EssinkB.B., et al. (1994). Human immunodeficiency virus uses tRNALys,3 as primer for reverse transcription in HeLa-CD4+ cells. FEBS Lett., 341, 49–53.
42.
DavidsonB.L., and BoudreauR.L. (2007). RNA interference: A tool for querying nervous system function and an emerging therapy. Neuron, 53, 781–788.
43.
DebouckC. (1991). Substrate specificity of the human (type 1) and simian immunodeficiency virus proteases. Adv. Exp. Med. Biol., 306, 407–415.
44.
DelhayeS., PaulS., BlakqoriG., et al. (2006). Neurons produce type I interferon during viral encephalitis. Proc. Natl. Acad. Sci. U.S.A., 103, 7835–7840.
45.
DenliA.M., TopsB.B., PlasterkR.H., et al. (2004). Processing of primary microRNAs by the Microprocessor complex. Nature, 432, 231–235.
46.
DickinsR.A., HemannM.T., ZilfouJ.T., et al. (2005). Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat. Genet., 37, 1289–1295.
47.
DieboldS.S., MassacrierC., AkiraS., et al. (2006). Nucleic acid agonists for Toll-like receptor 7 are defined by the presence of uridine ribonucleotides. Eur. J. Immunol., 36, 3256–3267.
48.
DoenchJ.G., and SharpP.A. (2004). Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504–511.
49.
DoenchJ.G., PetersenC.P., and SharpP.A. (2003). siRNAs can function as miRNAs. Genes Dev., 17, 438–442.
50.
Doss-PepeE.W., StenroosE.S., JohnsonW.G., et al. (2003). Ataxin-3 interactions with rad23 and valosin-containing protein and its associations with ubiquitin chains and the proteasome are consistent with a role in ubiquitin-mediated proteolysis. Mol. Cell. Biol., 23, 6469–6483.
51.
DullT., ZuffereyR., KellyM., et al. (1998). A third-generation lentivirus vector with a conditional packaging system. J. Virol., 72, 8463–8471.
52.
EackerS.M., DawsonT.M., and DawsonV.L. (2009). Understanding microRNAs in neurodegeneration. Nat. Rev. Neurosci., 10, 837–841.
53.
EberleF., GiesslerK., DeckC., et al. (2008). Modifications in small interfering RNA that separate immunostimulation from RNA interference. J. Immunol., 180, 3229–3237.
54.
EhlertE.M., EggersR., NiclouS.P., et al. (2010). Cellular toxicity following application of adeno-associated viral vector-mediated RNA interference in the nervous system. BMC Neurosci., 18, 11–20.
55.
ElbashirS.M., HarborthJ., LendeckelW., et al. (2001a). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494–498
56.
ElbashirS.M., LendeckelW., and TuschlT. (2001b). RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev., 15, 188–200
57.
ElbashirS.M., MartinezJ., PatkaniowskaA., et al. (2001c). Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J., 20, 6877–6888
58.
ElbashirS.M., HarborthJ., WeberK., et al. (2002). Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods, 26, 199–213.
59.
EngelmanA. (1999). In vivo analysis of retroviral integrase structure and function. Adv. Virus Res., 52, 411–426.
60.
EngelsB.M., and HutvagnerG. (2006). Principles and effects of microRNA-mediated post-transcriptional gene regulation. Oncogene, 25, 6163–6169.
61.
EulalioA., HuntzingerE., NishiharaT., et al. (2009a). Deadenylation is a widespread effect of miRNA regulation. RNA, 15, 21–32
62.
EulalioA., TritschlerF., and IzaurraldeE. (2009b). The GW182 protein family in animal cells: New insights into domains required for miRNA-mediated gene silencing. RNA, 15, 1433–1442
63.
FabianM.R., CieplakM.K., FrankF., et al. (2011). miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. Nat. Struct. Mol. Biol., 18, 1211–1217.
64.
FarnetC.M., and HaseltineW.A. (1991). Determination of viral proteins present in the human immunodeficiency virus type 1 preintegration complex. J. Virol., 65, 1910–1915.
65.
FedorovY., AndersonE.M., BirminghamA., et al. (2006). Off-target effects by siRNA can induce toxic phenotype. RNA, 12, 1188–1196.
66.
FilipowiczW., BhattacharyyaS.N., and SonenbergN. (2008). Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight?. Nat. Rev. Genet., 9, 102–114.
67.
FischerU., HuberJ., BoelensW.C., et al. (1995). The HIV-1 Rev activation domain is a nuclear export signal that accesses an export pathway used by specific cellular RNAs. Cell, 82, 475–483.
68.
FishR.J., and KruithofE.K. (2004). Short-term cytotoxic effects and long-term instability of RNAi delivered using lentiviral vectors. BMC Mol. Biol., 5, 9.
69.
FiszerA., MykowskaA., KrzyzosiakW. J. (2011). Inhibition of mutant huntingtin expression by RNA duplex targeting expanded CAG repeats. Nucleic Acids Res., 39, 5578–5585.
70.
ForbachA., NemorinJ.G., MontinoC., et al. (2008). Identification of RNA sequence motifs stimulating sequence-specific TLR8-dependent immune responses. J. Immunol., 180, 3729–3738.
71.
GeQ., DallasA., IlvesH., et al. (2010a). Effects of chemical modification on the potency, serum stability, and immunostimulatory properties of short shRNAs. RNA, 16, 118–130
72.
GeQ., IlvesH., DallasA., et al. (2010b). Minimal-length short hairpin RNAs: The relationship of structure and RNAi activity. RNA, 16, 106–117
73.
GiraldezA.J., MishimaY., RihelJ., et al. (2006). Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science, 312, 75–79.
74.
Gonzalez-AlegreP., BodeN., DavidsonB.L., et al. (2005). Silencing primary dystonia: Lentiviral-mediated RNA interference therapy for DYT1 dystonia. J. Neurosci., 25, 10502–10509.
75.
GrimmD. (2011). The dose can make the poison: Lessons learned from adverse in vivo toxicities caused by RNAi overexpression. Silence, 2, 8.
76.
GrimmD., StreetzK.L., JoplingC.L., et al. (2006). Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature, 441, 537–541.
77.
GrimmD., WangL., LeeJ.S., et al. (2010). Argonaute proteins are key determinants of RNAi efficacy, toxicity, and persistence in the adult mouse liver. J. Clin. Invest., 120, 3109.
78.
Hacein-Bey-AbinaS., Von KalleC., SchmidtM., et al. (2003). LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science, 302, 415–419.
79.
HammondS.M., BoettcherS., CaudyA.A., et al. (2001). Argonaute2, a link between genetic and biochemical analyses of RNAi. Science, 293, 1146–1150.
80.
HanJ., LeeY., YeomK.-H., et al. (2006). Molecular basis for the recognition of primary microRNAs by the Drosha–DGCR8 complex. Cell, 125, 887–901.
81.
HornungV., Guenthner-BillerM., BourquinC., et al. (2005). Sequence-specific potent induction of IFN-α by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat. Med., 11, 263–270.
82.
HornungV., EllegastJ., KimS., et al. (2006). 5′-Triphosphate RNA is the ligand for RIG-I. Science, 314, 994–997.
83.
HorvathL., VanMarion, I., TaiK., et al. (2011). Knockdown of GAD67 protein levels normalizes neuronal activity in a rat model of Parkinson's disease. J. Gene Med., 13, 188–197.
84.
HuJ., MatsuiM., GagnonK.T., et al. (2009). Allele-specific silencing of mutant huntingtin and ataxin-3 genes by targeting expanded CAG repeats in mRNAs. Nat. Biotechnol., 27, 478–484.
85.
HuJ., LiuJ., and CoreyD.R. (2010). Allele-selective inhibition of huntingtin expression by switching to an miRNA-like RNAi mechanism. Chem. Biol., 17, 1183–1188.
86.
HutsonT.H., FosterE., DawesJ.M., et al. (2012a). Lentiviral vectors encoding short hairpin RNAs efficiently transduce and knockdown LINGO-1 but induce an interferon response and cytotoxicity in central nervous system neurones. J. Gene Med., 14, 299–315
87.
HutsonT.H., VerhaagenJ., Yáñez-MuñozR.J., et al. (2012b). Corticospinal tract transduction: A comparison of seven adeno-associated viral vector serotypes and a non-integrating lentiviral vector. Gene Ther., 19, 49–60
88.
HutvagnerG., and SimardM.J. (2008). Argonaute proteins: Key players in RNA silencing. Nat. Rev. Mol. Cell Biol., 9, 22–32.
89.
JacksonA.L., and LinsleyP.S. (2010). Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat. Rev. Drug Discov., 9, 57–67.
90.
JacksonA.L., BartzS.R., SchelterJ., et al. (2003). Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol., 21, 635–637.
91.
JacksonA.L., BurchardJ., LeakeD., et al. (2006a). Position-specific chemical modification of siRNAs reduces “off-target” transcript silencing. RNA, 12, 1197–1205
92.
JacksonA.L., BurchardJ., SchelterJ., et al. (2006b). Widespread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity. RNA, 12, 1179–1187.
93.
JakymiwA., LianS., EystathioyT., et al. (2005). Disruption of GW bodies impairs mammalian RNA interference. Nat. Cell Biol., 7, 1267–1274.
94.
JankowskiM.P., CornuetP.K., McilwrathS., et al. (2006). SRY-box containing gene 11 (Sox11) transcription factor is required for neuron survival and neurite growth. Neuroscience, 143, 501–514.
95.
JankowskiM.P., McilwrathS.L., JingX., et al. (2009). Sox11 transcription factor modulates peripheral nerve regeneration in adult mice. Brain Res., 1256, 43–54.
96.
JudgeA., and MacLachlanI. (2008). Overcoming the innate immune response to small interfering RNA. Hum. Gene Ther., 19, 111–124.
97.
JudgeA.D., SoodV., ShawJ.R., et al. (2005). Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat. Biotechnol., 23, 457–462.
98.
JudgeA.D., BolaG., LeeA.C., et al. (2006). Design of noninflammatory synthetic siRNA mediating potent gene silencing. Mol. Ther., 13, 494–505.
99.
JuliusD., and BasbaumA.I. (2001). Molecular mechanisms of nociception. Nature, 413, 203–210.
100.
KarikóK., BhuyanP., CapodiciJ., et al. (2004). Exogenous siRNA mediates sequence-independent gene suppression by signaling through Toll-like receptor 3. Cells Tissues Organs, 177, 132–138.
101.
KarikóK., BucksteinM., NiH., et al. (2005). Suppression of RNA recognition by Toll-like receptors: The impact of nucleoside modification and the evolutionary origin of RNA. Immunity, 23, 165–175.
102.
KatzeM.G., HeY., and GaleM. (2002). Viruses and interferon: A fight for supremacy. Nat. Rev. Immunol., 2, 675–687.
103.
KayM.A., GloriosoJ.C., and NaldiniL. (2001). Viral vectors for gene therapy: The art of turning infectious agents into vehicles of therapeutics. Nat. Med., 7, 33–40.
104.
KayeJ.F., RichardsonJ.H., and LeverA.M. (1995). Cis-acting sequences involved in human immunodeficiency virus type 1 RNA packaging. J. Virol., 69, 6588–6592.
105.
KeenN.J., GaitM.J., and KarnJ. (1996). Human immunodeficiency virus type-1 Tat is an integral component of the activated transcription–elongation complex. Proc. Natl. Acad. Sci. U.S.A., 93, 2505–2510.
106.
KhanA.A., BetelD., MillerM.L., et al. (2009). Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat. Biotechnol., 27, 549–555.
107.
KhodrC.E., SapruM.K., PedapatiJ., et al. (2011). An α-synuclein AAV gene silencing vector ameliorates a behavioral deficit in a rat model of Parkinson's disease, but displays toxicity in dopamine neurons. Brain Res., 1395, 94–107.
108.
KhvorovaA., ReynoldsA., and JayasenaS.D. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209–216.
109.
KimA.H., and BonniA. (2007). Thinking within the D box: Initial identification of Cdh1-APC substrates in the nervous system. Mol. Cell. Neurosci., 34, 281–287.
110.
KimD.-H., BehlkeM.A., RoseS.D., et al. (2005). Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat. Biotechnol., 23, 222–226.
111.
KimV.N., MitrophanousK., KingsmanS.M., et al. (1998). Minimal requirement for a lentivirus vector based on human immunodeficiency virus type 1. J. Virol., 72, 811–816.
112.
KirchnerR., VogtherrM., LimmerS., et al. (1998). Secondary structure dimorphism and interconversion between hairpin and duplex form of oligoribonucleotides. Antisense Nucleic Acid Drug Dev., 8, 507–516.
113.
KittlerR., SurendranathV., HeningerA.K., et al. (2007). Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. Nat. Methods, 4, 337–344.
114.
KleinmanM.E., YamadaK., TakedaA., et al. (2008). Sequence- and target-independent angiogenesis suppression by siRNA via TLR3. Nature, 452, 591–597.
115.
KonishiY., StegmullerJ., MatsudaT., et al. (2004). Cdh1-APC controls axonal growth and patterning in the mammalian brain. Science, 303, 1026–1030.
KrichevskyA.M., KingK.S., DonahueC.P., et al. (2003). A microRNA array reveals extensive regulation of microRNAs during brain development. RNA, 9, 1274–1281.
118.
KrolJ., LoedigeI., and FilipowiczW. (2010). The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet., 11, 597–610.
119.
KruegerU., BergauerT., KaufmannB., et al. (2007). Insights into effective RNAi gained from large-scale siRNA validation screening. Oligonucleotides, 17, 237–250.
120.
KulkarniM., OzgurS., and StoecklinG. (2010). On track with P-bodies. Biochem. Soc. Trans., 38, 242–251.
121.
KwonB.K., LiuJ., LamC., et al. (2007). Brain-derived neurotrophic factor gene transfer with adeno-associated viral and lentiviral vectors prevents rubrospinal neuronal atrophy and stimulates regeneration-associated gene expression after acute cervical spinal cord injury. Spine, 32, 1164–1173.
122.
LeavittA.D., RoblesG., AlesandroN., et al. (1996). Human immunodeficiency virus type 1 integrase mutants retain in vitro integrase activity yet fail to integrate viral DNA efficiently during infection. J. Virol., 70, 721–728.
123.
LeeY., AhnC., HanJ., et al. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415–419.
124.
LeeY., KimM., HanJ., et al. (2004). MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051–4060.
125.
LeeY., HurI., ParkS.-Y., et al. (2006). The role of PACT in the RNA silencing pathway. EMBO J., 25, 522–532.
126.
LerchJ.K., KuoF., MottiD., et al. (2012). Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq. PLoS One, 7, e30417.
127.
LeverA., GottlingerH., HaseltineW., et al. (1989). Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions. J. Virol., 63, 4085–4087.
128.
LewisB.P., ShihI.H., Jones-RhoadesM.W., et al. (2003). Prediction of mammalian microRNA targets. Cell, 115, 787–798.
129.
LewisB.P., BurgeC.B., and BartelD.P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15–20.
130.
LiL., OlveraJ.M., YoderK.E., et al. (2001). Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection. EMBO J., 20, 3272–3281.
131.
LiL., LinX., KhvorovaA., et al. (2007). Defining the optimal parameters for hairpin-based knockdown constructs. RNA, 13, 1765–1774.
132.
LiZ., DullmannJ., SchiedlmeierB., et al. (2002). Murine leukemia induced by retroviral gene marking. Science, 296, 497.
133.
LingelA., SimonB., IzaurraldeE., et al. (2003). Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature, 426, 465–469.
134.
LiuJ., CarmellM.A., RivasF.V., et al. (2004). Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437–1441.
135.
LiuJ., Valencia-SanchezM.A., HannonG.J., et al. (2005). MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol., 7, 719–723.
136.
LoewenN., LeskeD.A., ChenY., et al. (2003). Comparison of wild-type and class I integrase mutant-FIV vectors in retina demonstrates sustained expression of integrated transgenes in retinal pigment epithelium. J. Gene Med., 5, 1009–1017.
137.
LombardiM.S., JaspersL., SpronkmansC., et al. (2009). A majority of Huntington's disease patients may be treatable by individualized allele-specific RNA interference. Exp. Neurol., 217, 312–319.
138.
LvB., YuanW., XuS., et al. (2012). Lentivirus-siNgR199 promotes axonal regeneration and functional recovery in rats. Int. J. Neurosci., 122, 133–139.
139.
MaW., and BisbyM.A. (1998). Increased activation of nuclear factor κB in rat lumbar dorsal root ganglion neurons following partial sciatic nerve injuries. Brain Res., 797, 243–254.
140.
MaczugaP., LubelskiJ., van LogtensteinR., et al. (2013) Embedding siRNA sequences targeting Apolipoprotein B100 in shRNA and miRNA scaffolds results in differential processing and in vivo efficacy. Mol. Ther., 21, 217–227.
141.
MakarovS.S. (2000). NF-κB as a therapeutic target in chronic inflammation: Recent advances. Mol. Med Today, 6, 441–448.
142.
MalmbergA.B., ChenC., TonegawaS., et al. (1997). Preserved acute pain and reduced neuropathic pain in mice lacking PKCγ. Science, 278, 279–283.
143.
MartinJ.N., WolkenN., BrownT., et al. (2011). Lethal toxicity caused by expression of shRNA in the mouse striatum: Implications for therapeutic design. Gene Ther., 18, 666–673.
144.
MartinW.J., MalmbergA.B., and BasbaumA.I. (2001). PKCγ contributes to a subset of the NMDA-dependent spinal circuits that underlie injury-induced persistent pain. J. Neurosci., 21, 5321–5327.
145.
MasudaT., PlanellesV., KrogstadP., et al. (1995). Genetic analysis of human immunodeficiency virus type 1 integrase and the U3 att site: Unusual phenotype of mutants in the zinc finger-like domain. J. Virol., 69, 6687–6696.
146.
MasudaT., KurodaM.J., and HaradaS. (1998). Specific and independent recognition of U3 and U5 att sites by human immunodeficiency virus type 1 integrase in vivo. J. Virol., 72, 8396–8402.
147.
McBrideJ.L., BoudreauR.L., HarperS.Q., et al. (2008). Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: Implications for the therapeutic development of RNAi. Proc. Natl. Acad. Sci. U.S.A., 105, 5868–5873.
148.
MichelsS., Schmidt-ErfurthU., and RosenfeldP.J. (2006). Promising new treatments for neovascular age-related macular degeneration. Expert Opin. Investig. Drugs, 15, 779–793.
149.
MiyoshiH., BlomerU., TakahashiM., et al. (1998). Development of a self-inactivating lentivirus vector. J. Virol., 72, 8150–8157.
150.
MooreD.L., BlackmoreM.G., HuY., et al. (2009). KLF family members regulate intrinsic axon regeneration ability. Science, 326, 298–301.
151.
MorrisseyD.V., LockridgeJ.A., ShawL., et al. (2005). Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs. Nat. Biotechnol., 23, 1002–1007.
152.
NaldiniL. (2011). Ex vivo gene transfer and correction for cell based therapies. Nat. Rev. Genet., 12, 301–315.
153.
NaldiniL., BlomerU., GageF.H., et al. (1996a). Efficient transfer, integration, and sustained long-term expression of the transgene in adult rat brains injected with a lentiviral vector. Proc. Natl. Acad. Sci. U.S.A., 93, 11382–11388
154.
NaldiniL., BlomerU., GallayP., et al. (1996b). In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science, 272, 263–267
155.
NightingaleS.J., HollisR.P., PepperK.A., et al. (2006). Transient gene expression by nonintegrating lentiviral vectors. Mol. Ther., 13, 1121–1132.
156.
PaddisonP.J., CaudyA.A., BernsteinE., et al. (2002). Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev., 16, 948–958.
157.
PebernardS., and IggoR.D. (2004). Determinants of interferon-stimulated gene induction by RNAi vectors. Differentiation, 72, 103–111.
158.
PeluffoH., FosterE., AhmedS.G., et al. (2013). Efficient gene expression from integration-deficient lentiviral vectors in the spinal cord. Gene Ther., 20, 645–657.
159.
PengC., HoB.K., ChangT.W., et al. (1989). Role of human immunodeficiency virus type 1-specific protease in core protein maturation and viral infectivity. J. Virol., 63, 2550–2556.
160.
PersengievS.P., ZhuX., and GreenM.R. (2004). Non-specific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA, 10, 12–18.
161.
PfisterE.L., KenningtonL., StaubhaarJ., et al. (2009). Five siRNAs targeting three SNPs may provide therapy for three-quarters of Huntington's disease patients. Curr. Biol., 19, 774–778.
162.
PhilippeS., SarkisC., BarkatsM., et al. (2006). Lentiviral vectors with a defective integrase allow efficient and sustained transgene expression in vitro and in vivo. Proc. Natl. Acad. Sci. U.S.A., 103, 17684–17689.
163.
PhilpottN.J., and ThrasherA.J. (2007) Use of nonintegrating lentiviral vectors for gene therapy. Hum. Gene Ther., 18, 483–489.
164.
PiedrahitaD., HernandezI., Lopez-TobonA., et al. (2010). Silencing of CDK5 reduces neurofibrillary tangles in transgenic Alzheimer's mice. J. Neurosci., 30, 13966–13976.
165.
RahimA.A., WongA.M.S., HoweS.J., et al. (2009). Efficient gene delivery to the adult and fetal CNS using pseudotyped non-integrating lentiviral vectors. Gene Ther., 16, 509–520.
166.
RalphG.S., RadcliffeP.A., DayD.M., et al. (2005). Silencing mutant SOD1 using RNAi protects against neurodegeneration and extends survival in an ALS model. Nat. Med., 11, 429–433.
167.
RamezaniA., and HawleyR.G. (2002). Overview of the HIV-1 lentiviral vector system. Curr. Protoc. Mol. Biol. Chapter 16, Unit 16.21.
168.
RaoM.K., and WilkinsonM.F. (2006). Tissue-specific and cell type-specific RNA interference in vivo. Nat. Protoc., 1, 1494–1501.
169.
RaoulC., Abbas-TerkiT., BensadounJ.C., et al. (2005). Lentiviral-mediated silencing of SOD1 through RNA interference retards disease onset and progression in a mouse model of ALS. Nat. Med., 11, 423–428.
170.
ReadM.L., MirS., SpiceR., et al. (2009). Profiling RNA interference (RNAi)-mediated toxicity in neural cultures for effective short interfering RNA design. J. Gene Med., 11, 523–534.
171.
ReynoldsA., LeakeD., BoeseQ., et al. (2004). Rational siRNA design for RNA interference. Nat. Biotechnol., 22, 326–330.
172.
ReynoldsA., AndersonE.M., VermeulenA., et al. (2006). Induction of the interferon response by siRNA is cell type- and duplex length-dependent. RNA, 12, 988–993.
173.
RobbinsM., JudgeA., LiangL., et al. (2007). 2′-O-Methyl-modified RNAs act as TLR7 antagonists. Mol. Ther., 15, 1663–1669.
174.
RossiJ.J. (2009). Innate Immunity confounds the clinical efficacy of small interfering RNAs (siRNAs). Gene Ther., 16, 579–580.
175.
SaenzD.T., LoewenN., PeretzM., et al. (2004). Unintegrated lentivirus DNA persistence and accessibility to expression in nondividing cells: Analysis with class I integrase mutants. J. Virol., 78, 2906–2920.
SapruM.K., YatesJ.W., HoganS., et al. (2006). Silencing of human α-synuclein in vitro and in rat brain using lentiviral-mediated RNAi. Exp. Neurol., 198, 382–390.
178.
SaxenaS., JonssonZ.O., and DuttaA. (2003). Small RNAs with imperfect match to endogenous mRNA repress translation: Implications for off-target activity of small inhibitory RNA in mammalian cells. J. Biol. Chem., 278, 44312–44319.
179.
ScacheriP.C., Rozenblatt-RosenO., CaplenN.J., et al. (2004). Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Proc. Natl. Acad. Sci. U.S.A., 101, 1892–1897.
180.
SchambachA., ZychlinskiD., EhrnstroemB., et al. (2013). Biosafety features of lentiviral vectors. Hum. Gene Ther., 24, 132–142.
181.
SchroderA.R., ShinnP., ChenH., et al. (2002). HIV-1 integration in the human genome favors active genes and local hotspots. Cell, 110, 521–529.
182.
SchwarzD.S., HutvagnerG., DuT., et al. (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199–208.
183.
SemizarovD., FrostL., SarthyA., et al. (2003). Specificity of short interfering RNA determined through gene expression signatures. Proc. Natl. Acad. Sci. U.S.A., 100, 6347–6352.
184.
SenG.L., and BlauH.M. (2005). Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat. Cell Biol., 7, 633–636.
185.
SeredeninaT., GokceO., and Luthi-CarterR. (2011). Decreased striatal RGS2 expression is neuroprotective in Huntington's disease (HD) and exemplifies a compensatory aspect of HD-induced gene regulation. PLoS One, 6, e22231.
186.
SilvaJ.M., LiM.Z., ChangK., et al. (2005). Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet., 37, 1281–1288.
187.
SingerO., MarrR.A., RockensteinE., et al. (2005). Targeting BACE1 with siRNAs ameliorates Alzheimer disease neuropathology in a transgenic model. Nat. Neurosci., 8, 1343–1349.
188.
SiolasD., LernerC., BurchardJ., et al. (2005). Synthetic shRNAs as potent RNAi triggers. Nat. Biotechnol., 23, 227–231.
189.
SioudM. (2005). Induction of inflammatory cytokines and interferon responses by double-stranded and single-stranded siRNAs is sequence-dependent and requires endosomal localization. J. Mol. Biol., 348, 1079–1090.
190.
SledzC.A., HolkoM., De VeerM.J., et al. (2003). Activation of the interferon system by short-interfering RNAs. Nat. Cell Biol., 5, 834–839.
191.
SledzC.A., and WilliamsB.R. (2004). RNA interference and double-stranded-RNA-activated pathways. Biochem. Soc. Trans., 32, 952–956.
192.
SongJ.J., SmithS.K., HannonG.J., et al. (2004). Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305, 1434–1437.
193.
StegmullerJ., KonishiY., HuynhM.A., et al. (2006). Cell-intrinsic regulation of axonal morphogenesis by the Cdh1-APC Target SnoN. Neuron, 50, 389–400.
194.
SteinB.S., and EnglemanE.G. (1990). Intracellular processing of the gp160 HIV-1 envelope precursor: Endoproteolytic cleavage occurs in a cis or medial compartment of the Golgi complex. J. Biol. Chem., 265, 2640–2649.
195.
StevensonM., HaggertyS., LamonicaC.A., et al. (1990). Integration is not necessary for expression of human immunodeficiency virus type 1 protein products. J. Virol., 64, 2421–2425.
SudarskyL., and CoutinhoP. (1995). Machado-Joseph disease. Clin. Neurosci., 3, 17–22.
198.
SuggateE.L., AhmedZ., ReadM.L., et al. (2009). Optimisation of siRNA-mediated RhoA silencing in neuronal cultures. Mol. Cell. Neurosci., 40, 451–462.
199.
SunT., LuoJ., JiaM., et al. (2012). Small interfering RNA-mediated knockdown of NF-κBp65 attenuates neuropathic pain following peripheral nerve injury in rats. Eur. J. Pharmacol., 682, 79–85.
200.
TegederI., CostiganM., GriffinR.S., et al. (2006). GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. Nat. Med., 12, 1269–1277.
201.
ThemisM., WaddingtonS.N., SchmidtM., et al. (2005). Oncogenesis following delivery of a nonprimate lentiviral gene therapy vector to fetal and neonatal mice. Mol. Ther., 12, 763–771.
202.
ThomasC.E., EhrhardtA., and KayM.A. (2003). Progress and problems with the use of viral vectors for gene therapy. Nat. Rev. Genet., 4, 346–358.
203.
TomariY., MatrangaC., HaleyB., et al. (2004). A protein sensor for siRNA asymmetry. Science, 306, 1377–1380.
204.
TuschlT., ZamoreP.D., LehmannR., et al. (1999). Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev., 13, 3191–3197.
205.
UlusoyA., SahinG., BjörklundT., et al. (2009). Dose optimization for long-term rAAV-mediated RNA interference in the nigrostriatal projection neurons. Mol. Ther., 17, 1574.
206.
ValsamakisA., ZeichnerS., CarswellS., et al. (1991). The human immunodeficiency virus type 1 polyadenylylation signal: A 3′ long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation. Proc. Natl. Acad. Sci. U.S.A., 88, 2108–2112.
207.
van BilsenP.H., JaspersL., LombardiM.S., et al. (2008). Identification and allele-specific silencing of the mutant huntingtin allele in Huntington's disease patient-derived fibroblasts. Hum. Gene Ther., 19, 710–719.
208.
WangH., SunH., Della PennaK., et al. (2002). Chronic neuropathic pain is accompanied by global changes in gene expression and shares pathobiology with neurodegenerative diseases. Neuroscience, 114, 529–546.
209.
WangY., ShengG., JuranekS., et al. (2008). Structure of the guide-strand-containing argonaute silencing complex. Nature, 456, 209–213.
210.
WanischK., and Yáñez-MuñozR.J. (2009). Integration-deficient lentiviral vectors: A slow coming of age. Mol. Ther., 17, 1316–1332.
211.
WatsonD.J., KobingerG.P., PassiniM.A., et al. (2002). Targeted transduction patterns in the mouse brain by lentivirus vectors pseudotyped with VSV, Ebola, Mokola, LCMV, or MuLV envelope proteins. Mol. Ther., 5, 528–537.
212.
WongL.F., AzzouzM., WalmsleyL.E., et al. (2004). Transduction patterns of pseudotyped lentiviral vectors in the nervous system. Mol. Ther., 9, 101–111.
213.
WuL., FanJ., and BelascoJ.G. (2006). MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl. Acad. Sci. U.S.A., 103, 4034–4039.
214.
WuY. (2004). HIV-1 gene expression: Lessons from provirus and non-integrated DNA. Retrovirology, 1, 13.
215.
WuY. (2008). The second chance story of HIV-1 DNA: Unintegrated? Not a problem!. Retrovirology, 5, 61.
216.
XiaoH.S., HuangQ.H., ZhangF.X., et al. (2002). Identification of gene expression profile of dorsal root ganglion in the rat peripheral axotomy model of neuropathic pain. Proc. Natl. Acad. Sci. U.S.A., 99, 8360–8365.
217.
YamadaT., and MorishitaS. (2005). Accelerated off-target search algorithm for siRNA. Bioinformatics, 21, 1316–1324.
218.
Yáñez-MuñozR.J., BalagganK.S., MacNeilA., et al. (2006). Effective gene therapy with nonintegrating lentiviral vectors. Nat. Med., 12, 348–353.
219.
YiR., QinY., MacaraI.G., et al. (2003). Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev., 17, 3011–3016.
220.
YiR., DoehleB.P., QinY., et al. (2005). Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA, 11, 220–226.
221.
ZamoreP.D. (2001). RNA interference: Listening to the sound of silence. Nat. Struct. Biol., 8, 746–750.
222.
ZengY., and CullenB.R. (2004). Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res., 32, 4776–4785.
223.
ZengY., and CullenB.R. (2005). Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J. Biol. Chem., 280, 27595–27603.
224.
ZengY., WagnerE.J., and CullenB.R. (2002). Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell, 9, 1327–1333.
225.
ZengY., YiR., and CullenB.R. (2003). MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Natl. Acad. Sci. U.S.A., 100, 9779–9784.
226.
ZengY., CaiX., and CullenB.R. (2005). Use of RNA polymerase II to transcribe artificial microRNAs. Methods Enzymol., 392, 371–380.
227.
ZennouV., PetitC., GuetardD., et al. (2000). HIV-1 genome nuclear import is mediated by a central DNA flap. Cell, 101, 173–185.
228.
ZouH., HoC., WongK., et al. (2009). Axotomy-induced Smad1 activation promotes axonal growth in adult sensory neurons. J. Neurosci., 29, 7116–7123.
ZuffereyR., DullT., MandelR.J., et al. (1998). Self-inactivating lentivirus vector for safe and efficient in vivo gene delivery. J. Virol., 72, 9873–9880.
