Dual gene targeted multimeric siRNA for combinatorial gene silencing

Biomaterials

Volumn 32, Issue 9, 2011, Pages 2359-2368

  Lee, Soo Hyeon ^a   Mok, Hyejung ^a   Jo, Sungduk ^a   Hong, Cheol Am ^a   Park, Tae Gwan ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

Co RNAi; Dual gene targeting; Gene delivery; Multimerization; SiRNA

Indexed keywords

CO-RNAI; DUAL GENE TARGETING; GENE DELIVERY; MULTIMERIZATION; SIRNA;

GENE EXPRESSION; GENE TRANSFER; RNA;

GENE THERAPY;

ANTISENSE OLIGODEOXYNUCLEOTIDE; GREEN FLUORESCENT PROTEIN; MESSENGER RNA; PROTEIN BCL 2; SMALL INTERFERING RNA; SURVIVIN; VASCULOTROPIN;

ARTICLE; CONJUGATION; DISULFIDE BOND; DRUG SYNTHESIS; GENE SILENCING; GENE TARGETING; HUMAN; HUMAN CELL; IMMUNE RESPONSE; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN EXPRESSION; PROTEIN MULTIMERIZATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA STRUCTURE;

APOPTOSIS; ELECTROLYTES; GENE EXPRESSION REGULATION; GENE SILENCING; GENE TRANSFER TECHNIQUES; GREEN FLUORESCENT PROTEINS; HELA CELLS; HUMANS; INHIBITOR OF APOPTOSIS PROTEINS; INTRACELLULAR SPACE; MICROSCOPY, ATOMIC FORCE; PROTO-ONCOGENE PROTEINS C-BCL-2; RNA, SMALL INTERFERING; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 78751701558     PISSN: 01429612     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biomaterials.2010.11.062     Document Type: Article

References (64)

1. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
2. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001, 411:494-498.
3. Bumcrot D., Manoharan M., Koteliansky V., Sah D.W.Y. RNAi therapeutics: a potential new class of pharmaceutical drugs. Nat Chem Biol 2006, 2:711-719.
4. Whitehead K.A., Langer R., Anderson D.G. Knocking down barriers: advances in siRNA delivery. Nat Rev Drug Discov 2009, 8:129-138.
5. Oh Y.K., Park T.G. siRNA delivery systems for cancer treatment. Adv Drug Deliv Rev 2009, 61:850-862.
6. De Fougerolles A., Vornlocher H.P., Maraganore J., Lieberman J. Interfering with disease: a progress report on siRNA-based therapeutics. Nat Rev Drug Discov 2007, 6:443-453.
7. Kim D.H., Rossi J.J. Strategies for silencing human disease using RNA interference. Nat Rev Genet 2007, 8:173-184.
8. Hornung V., Guenthner-Biller M., Bourquin C., Ablasser A., Schlee M., Uematsu S., et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med 2005, 11:263-270.
9. Judge A.D., Sood V., Shaw J.R., Fang D., McClintock K., MacLachlan I. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol 2005, 23:457-462.
10. Judge A.D., Bola G., Lee A.C., MacLachlan I. Design of noninflammatory synthetic siRNA mediating potent gene silencing in vivo. Mol Ther 2006, 13:494-505.
11. Allerson C.R., Sioufi N., Jarres R., Prakash T.P., Naik N., Berdeja A., et al. Fully 2'-modified oligonucleotide duplexes with improved in vitro potency and stability compared to unmodified small interfering RNA. J Med Chem 2005, 48:901-904.
12. Kim S.H., Jeong J.H., Lee S.H., Kim S.W., Park T.G. Local and systemic delivery of VEGF siRNA using polyelectrolyte complex micelles for effective treatment of cancer. J Control Release 2008, 129:107-116.
13. Elmén J., Thonberg H., Ljungberg K., Frieden M., Westergaard M., Xu Y., et al. Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality. Nucleic Acids Res 2005, 33:439-447.
14. Braasch D.A., Jensen S., Liu Y., Kaur K., Arar K., White M.A., et al. RNA interference in mammalian cells by chemically-modified RNA. Biochemistry 2003, 42:7967-7975.
15. Wolfrum C., Shi S., Jayaprakash K.N., Jayaraman M., Wang G., Pandey R.K., et al. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nat Biotechnol 2007, 25:1149-1157.
16. Kim S.H., Jeong J.H., Lee S.H., Kim S.W., Park T.G. PEG conjugated VEGF siRNA for anti-angiogenic gene therapy. J Control Release 2006, 116:123-129.
17. Kim S.H., Jeong J.H., Lee S.H., Kim S.W., Park T.G. LHRH receptor-mediated delivery of siRNA using polyelectrolyte complex micelles self-assembled from siRNA-PEG-LHRH conjugate and PEI. Bioconjug Chem 2008, 10:2156-2162.
18. Choi S.W., Lee S.H., Mok H., Park T.G. Multifunctional siRNA delivery system: polyelectrolyte complex micelles of six-arm PEG conjugate of siRNA and cell penetrating peptide with crosslinked fusogenic peptide. Biotechnol Prog 2010, 26:57-63.
19. Muratovska A., Eccles M.R. Conjugate for efficient delivery of short interfering RNA (siRNA) into mammalian cells. FEBS Lett 2004, 558:63-68.
20. Mok H., Lee S.H., Park J.W., Park T.G. Multimeric small interfering ribonucleic acid for highly efficient sequence-specific gene silencing. Nat Mater 2010, 9:272-278.
21. Bolcato-Bellemin A.L., Bonnet M.E., Creusat G., Erbacher P., Behr J.P. Sticky overhangs enhance siRNA-mediated gene silencing. Proc Natl Acad Sci U S A 2007, 104:16050-16055.
22. Grimm D., Kay M.A. Combinatorial RNAi: a winning strategy for the race against evolving targets?. Mol Ther 2007, 15:878-888.
23. Tai W., Qin B., Cheng K. Inhibition of breast cancer cell growth and invasiveness by dual silencing of HER-2 and VEGF. Mol Pharm 2010, 7:543-556.
24. Liu Y.P., von Eije K.J., Schopman N.C., Westerink J.T., ter Brake O., Haasnoot J., et al. Combinatorial RNAi against HIV-1 using extended short hairpin RNAs. Mol Ther 2009, 17:1712-1723.
25. Liu Y.P., Haasnoot J., Berkhout B. Design of extended short hairpin RNAs for HIV-1 inhibition. Nucleic Acids Res 2007, 35:5683-5693.
26. ter Brake O., 't Hooft K., Liu Y.P., Centlivre M., von Eije K.J., Berkhout B. Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition. Mol Ther 2008, 16:557-564.
27. Schuck S., Manninen A., Honsho M., Füllekrug J., Simons K. Generation of single and double knockdowns in polarized epithelial cells by retrovirus-mediated RNA interference. Proc Natl Acad Sci U S A 2004, 101:4912-4917.
28. Song E., Zhu P., Lee S.K., Chowdhury D., Kussman S., Dykxhoorn D.M., et al. Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors. Nat Biotechnol 2005, 23:709-717.
29. Love K.T., Mahon K.P., Levins C.G., Whitehead K.A., Querbes W., Dorkin J.R., et al. Lipid-like materials for low-dose, in vivo gene silencing. Proc Natl Acad Sci U S A 2010, 107:1864-1869.
30. Yu J.Y., Taylor J., DeRuiter S.L., Vojtek A.B., Turner D.L. Simultaneous inhibition of GSK3alpha and GSK3beta using hairpin siRNA expression vectors. Mol Ther 2003, 7:228-236.
31. Sun D., Melegari M., Sridhar S., Rogler C.E., Zhu L. Multi-miRNA hairpin method that improves gene knockdown efficiency and provides linked multi-gene knockdown. Biotechniques 2006, 41:59-63.
32. Cheng A., Li M., Liang Y., Wang Y., Wong L., Chen C., et al. Stem-loop RT-PCR quantification of siRNAs in vitro and in vivo. Oligonucleotides 2009, 19:203-208.
33. Kim D.H., Behlke M.A., Rose S.D., Chang M.S., Choi S., Rossi J.J. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 2005, 23:222-226.
34. Rose S.D., Kim D.H., Amarzguioui M., Heidel J.D., Collingwood M.A., Davis M.E., et al. Functional polarity is introduced by dicer processing of short substrate RNAs. Nucleic Acids Res 2005, 33:4140-4156.
35. Zhang H., Kolb F.A., Brondani V., Billy E., Filipowicz W. Human dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 2002, 21:5875-5885.
36. Sioud M. Single-stranded small interfering RNA are more immunostimulatory than their double-stranded counterparts: a central role for 2'-hydroxyl uridines in immune responses. Eur J Immunol 2006, 36:1222-1230.
37. Zamanian-Daryoush M., Marques J.T., Gantier M.P., Behlke M.A., John M., Rayman P., et al. Determinants of cytokine induction by small interfering RNA in human peripheral blood mononuclear cells. J Interferon Cytokine Res 2008, 28:221-233.
38. Schlee M., Hornung V., Hartmann G. siRNA and isRNA: two edges of one sword. Mol Ther 2006, 14:463-470.
39. Yoneyama M., Kikuchi M., Natsukawa T., Shinobu N., Imaizumi T., Miyagishi M., et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat Immunol 2004, 5:730-737.
40. Boese Q., Leake D., Reynolds A., Read S., Scaringe S.A., Marshall W.S., et al. Mechanistic insights aid computational short interfering RNA design. Meth Enzymol 2005, 392:73-96.
41. Yuan B., Latek R., Hossbach M., Tuschl T., Lewitter F. siRNA selection server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res 2004, 32:W130-W134.
42. Kurreck J. siRNA efficiency: structure or sequence-that is the question. J Biomed Biotechnol 2006, 4:83757.
43. Chang C.I., Yoo J.W., Hong S.W., Lee S.E., Kang H.S., Sun X., et al. Asymmetric shorter-duplex siRNA structures trigger efficient gene silencing with reduced nonspecific effects. Mol Ther 2009, 17:725-732.
44. Koller E., Propp S., Murray H., Lima W., Bhat B., Prakash T.P., et al. Competition for RISC binding predicts in vitro potency of siRNA. Nucleic Acids Res 2006, 34:4467-4476.
45. Chithrani B.D., Ghazani A.A., Chan W.C. Determining the size and shape dependence of gold nanoparticle uptake into mammalian cells. Nano Lett 2006, 6:662-668.
46. Wang Z., Tiruppathi C., Minshall R.D., Malik A.B. Size and dynamics of caveolae studied using nanoparticles in living endothelial cells. ACS Nano 2009, 3:4110-4116.
47. He C., Hu Y., Yin L., Tang C., Yin C. Effects of particle size and surface charge on cellular uptake and biodistribution of polymeric nanoparticles. Biomaterials 2010, 31:3657-3666.
48. Ouyang D., Zhang H., Herten D.P., Parekh H.S., Smith S.C. Structure, dynamics, and energetics of siRNA-cationic vector complexation: a molecular dynamics study. J Phys Chem B 2010, 114:9220-9230.
49. Lam P.M., Levy J.C. Unzipping DNA from the condensed globule state-effects of unraveling. Biopolymers 2005, 79:287-291.
50. Pavan G.M., Albertazzi L., Danani A. Ability to adapt: different generations of PAMAM dendrimers show different behaviors in binding siRNA. J Phys Chem B 2010, 114:2667-2675.
51. Pavan G.M., Danani A., Pricl S., Smith D.K. Modeling the multivalent recognition between dendritic molecules and DNA: understanding how ligand "sacrifice" and screening can enhance binding. J Am Chem Soc 2009, 131:9686-9694.
52. Seibert E., Ross J.B., Osman R. Role of DNA flexibility in sequence-dependent activity of uracil DNA glycosylase. Biochemistry 2002, 41:10976-10984.
53. Scipioni A., Anselmi C., Zuccheri G., Samori B., De Santis P. Sequence-dependent DNA curvature and flexibility from scanning force microscopy images. Biophys J 2002, 83:2408-2418.
54. Wu L., Koudelka G.B. Sequence-dependent differences in DNA structure influence the affinity of P22 operator for P22 repressor. J Biol Chem 1993, 268:18975-18981.
55. Maiti P.K., Bagchi B. Structure and dynamics of DNA-dendrimer complexation: role of counterions, water, and base pair sequence. Nano Lett 2006, 6:2478-2485.
56. Travers A.A. The structural basis of DNA flexibility. Philos Transact A Math Phys Eng Sci 2004, 362:1423-1438.
57. Beh C.W., Seow W.Y., Wang Y., Zhang Y., Ong Z.Y., Ee P.L., et al. Efficient delivery of Bcl-2-targeted siRNA using cationic polymer nanoparticles: downregulating mRNA expression level and sensitizing cancer cells to anticancer drug. Biomacromolecules 2009, 10:41-48.
58. Lin Y., Fukuchi J., Hiipakka R.A., Kokontis J.M., Xiang J. Up-regulation of Bcl-2 is required for the progression of prostate cancer cells from an androgen-dependent to an androgen-independent growth stage. Cell Res 2007, 17:531-536.
59. Liu W.S., Yan H.J., Qin R.Y., Tian R., Wang M., Jiang J.X., et al. siRNA directed against survivin enhances pancreatic cancer cell gemcitabine chemosensitivity. Dig Dis Sci 2009, 54:89-96.
60. Yang C.T., Li J.M., Weng H.H., Li Y.C., Chen H.C., Chen M.F. Adenovirus-mediated transfer of siRNA against survivin enhances the radiosensitivity of human non-small cell lung cancer cells. Cancer Gene Ther 2010, 17:120-130.
61. Kappler M., Taubert H., Bartel F., Blümke K., Panian M., Schmidt H., et al. Radiosensitization, after a combined treatment of survivin siRNA and irradiation, is correlated with the activation of caspases 3 and 7 in a wt-p53 sarcoma cell line, but not in a mt-p53 sarcoma cell line. Oncol Rep 2005, 131:167-172.
62. Yonesaka K., Tamura K., Kurata T., Satoh T., Ikeda M., Fukuoka M., et al. Small interfering RNA targeting survivin sensitizes lung cancer cell with mutant p53 to adriamycin. Int J Cancer 2006, 1184:812-820.
63. Holcik M., Korneluk R.G. XIAP, the guardian angel. Nat Rev Mol Cell Biol 2001, 2:550-556.
64. Harlin H., Reffey S.B., Duckett C.S., Lindsten T., Thompson C.B. Characterization of XIAP-deficient mice. Mol Cell Biol 2001, 21:3604-3608.