Antisense technology in molecular and cellular bioengineering

Current Opinion in Biotechnology

Volumn 14, Issue 5, 2003, Pages 505-511

  Lee, Li Kim ^a   Roth, Charles M ^a,b  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; COMPLEMENTARY RNA; ENZYME; RECOMBINANT RNA; RNA DERIVATIVE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

BASE PAIRING; BIOENGINEERING; CHEMICAL MODIFICATION; DOWN REGULATION; EXPRESSION VECTOR; GENE EXPRESSION REGULATION; GENE TARGETING; GENETIC ENGINEERING; HUMAN; METABOLIC ENGINEERING; MOLECULAR BIOLOGY; NONHUMAN; NUCLEIC ACID PROBE; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RNA INTERFERENCE; RNA PROCESSING; RNA TRANSLATION; TISSUE ENGINEERING; TRANSCRIPTION INITIATION;

VECTORS;

EID: 0142122307     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(03)00115-0     Document Type: Review

References (62)

1. Zamecnik P.C., Stephenson M.L. Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc. Natl. Acad Sci. USA. 75:1978;280-284.
2. Opalinska J.B., Gewirtz A.M. Nucleic-acid therapeutics: basic principles and recent applications. Nat. Rev. Drug Discov. 1:2002;503-514 This excellent review discusses in depth the mechanisms and design considerations of various antisense strategies (from oligonucleotides and ribozymes to RNAi), as well as current clinical applications (including oncology, inflammatory and cardiovascular diseases and immune activation) and technological problems.
3. Dias N., Stein C.A. Antisense oligonucleotides: basic concepts and mechanisms. Mol. Cancer Ther. 1:2002;347-355.
4. Sazani P., Vacek M.M., Kole R. Short-term and long-term modulation of gene expression by antisense therapeutics. Curr. Opin. Biotechnol. 13:2002;468-472.
5. Dean N.M. Functional genomics and target validation approaches using antisense oligonucleotide technology. Curr. Opin. Biotechnol. 12:2001;622-625.
6. Sohail M. Antisense technology: inaccessibility and non-specificity. Drug Discov. Today. 6:2001;1260-1261.
7. Kurreck J., Wyszko E., Gillen C., Erdmann V.A. Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 30:2002;1911-1918.
8. Koppelhus U., Nielsen P.E. Cellular delivery of peptide nucleic acid (PNA). Adv. Drug Deliv. Rev. 55:2003;267-280.
9. Vickers T.A., Koo S., Bennett C.F., Crooke S.T., Dean N.M., Baker B.F. Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem. 278:2003;7108-7118.
10. Roth C.M., Yarmush M.L. Nucleic acid biotechnology. Annu. Rev. Biomed. Eng. 1:1999;265-297.
11. Song L.Y., Ahkong Q.F., Rong Q., Wang Z., Ansell S., Hope M.J., Mui B. Characterization of the inhibitory effect of PEG-lipid conjugates on the intracellular delivery of plasmid and antisense DNA mediated by cationic lipid liposomes. Biochim. Biophys. Acta. 1558:2002;1-13.
12. Gonzalez Ferreiro M., Tillman L.G., Hardee G., Bodmeier R. Alginate/poly-L-lysine microparticles for the intestinal delivery of antisense oligonucleotides. Pharm. Res. 19:2002;755-764.
13. Cohen-Sacks H., Najajreh Y., Tchaikovski V., Gao G., Elazer V., Dahan R., Gati I., Kanaan M., Waltenberger J., Golomb G. Novel PDGFβR antisense encapsulated in polymeric nanospheres for the treatment of restenosis. Gene Ther. 9:2002;1607-1616.
14. Yoo H., Juliano R.L. Enhanced delivery of antisense oligonucleotides with fluorophore-conjugated PAMAM dendrimers. Nucleic Acids Res. 28:2000;4225-4231.
15. Manoharan M. Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery, and mechanism of action. Antisense Nucleic Acid Drug Dev. 12:2002;103-128.
16. Stein C.A. Keeping the biotechnology of antisense in context. Nat. Biotechnol. 17:1999;209.
17. Ho S.P., Bao Y., Lesher T., Malhotra R., Ma L.Y., Fluharty S.J., Sakai R.R. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat. Biotechnol. 16:1998;59-63.
18. Sohail M., Hochegger H., Klotzbucher A., Guellec R.L., Hunt T., Southern E.M. Antisense oligonucleotides selected by hybridisation to scanning arrays are effective reagents in vivo. Nucleic Acids Res. 29:2001;2041-2051.
19. Walton S.P., Stephanopoulos G.N., Yarmush M.L., Roth C.M. Prediction of antisense oligonucleotide binding affinity to a structured RNA target. Biotechnol. Bioeng. 65:1999;1-9.
20. Mathews D.H., Burkard M.E., Freier S.M., Wyatt J.R., Turner D.H. Predicting oligonucleotide affinity to nucleic acid targets. RNA. 5:1999;1458-1469.
21. Patzel V., Steidl U., Kronenwett R., Haas R., Sczakiel G. A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability. Nucleic Acids Res. 27:1999;4328-4334.
22. Walton S.P., Stephanopoulos G.N., Yarmush M.L., Roth C.M. Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA. Biophys. J. 82:2002;366-377 This study demonstrates a correlation between affinities computed from molecular thermodynamic modeling of antisense DNA interactions with target mRNA and those measured experimentally.
23. Patzel V., Sczakiel G. In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells. Nucleic Acids Res. 28:2000;2462-2466.
24. Ferrari J., Gunson J., Lofgren J., Krummen L., Warner T.G. Chinese hamster ovary cells with constitutively expressed sialidase antisense RNA produce recombinant DNase in batch culture with increased sialic acid. Biotechnol. Bioeng. 60:1998;589-595.
25. Dellambra E., Golisano O., Bondanza S., Siviero E., Lacal P., Molinari M., D'Atri S., De Luca M. Downregulation of 14-3-3σ prevents clonal evolution and leads to immortalization of primary human keratinocytes. J. Cell Biol. 149:2000;1117-1130.
26. αq gene knockout strategies Neuropharmacol. 42:2002;950-957.
27. Dargelos E., Moyen C., Dedieu S., Veschambre P., Poussard S., Vuillier-Devillers K., Brustis J.J., Cottin P. Development of an inducible system to assess p94 (CAPN3) function in cultured muscle cells. J. Biotechnol. 96:2002;271-279.
28. Prati E.G., Matasci M., Suter T.B., Dinter A., Sburlati A.R., Bailey J.E. Engineering of coordinated up- and down-regulation of two glycosyltransferases of the O-glycosylation pathway in Chinese hamster ovary (CHO) cells. Biotechnol. Bioeng. 79:2002;580-585 An enticing metabolic engineering strategy that uses antisense RNA as part of a tricistronic expression vector for coordinated upregulation and downregulation of opposing enzymatic pathways.
29. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 409:2001;363-366.
30. 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. 411:2001;494-498.
31. Hammond S.M., Bernstein E., Beach D., Hannon G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature. 404:2000;293-296.
32. Scherr M., Morgan M.A., Eder M. Gene silencing mediated by small interfering RNAs in mammalian cells. Curr. Med. Chem. 10:2003;245-256.
33. Shi Y. Mammalian RNAi for the masses. Trends Genet. 19:2003;9-12 This paper provides a comprehensive description of plasmid vectors for siRNA delivery to mammalian cells and includes several examples of potential medical applications.
34. Paddison P.J., Caudy A.A., Bernstein E., Hannon G.J., Conklin D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16:2002;948-958 This study, by some of the leaders in the field of RNAi research, shows that endogenously encoded inducers of the RNAi machinery (let-7 and lin-4) can drive the transcription of short RNA hairpins for the downregulation of specific genes in a variety of normal and cancer cell lines.
35. McCaffrey A.P., Meuse L., Pham T.T., Conklin D.S., Hannon G.J., Kay M.A. RNA interference in adult mice. Nature. 418:2002;38-39 Naked siRNAs and shRNAs transcribed in vivo from DNA templates were delivered to the liver of adult mice and inhibited transgene (hepatitis C virus gene) expression.
36. Gitlin L., Karelsky S., Andino R. Short interfering RNA confers intracellular antiviral immunity in human cells. Nature. 418:2002;430-434.
37. Donzé O., Picard D. RNA interference in mammalian cells using siRNAs synthesized with T7 RNA polymerase. Nucleic Acids Res. 30:2002;e46.
38. Myers J.W., Jones J.T., Meyer T., Ferrell J.E. Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat. Biotechnol. 21:2003;324-328.
39. Yu J.Y., DeRuiter S.L., Turner D.L. RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad Sci. USA. 99:2002;6047-6052.
40. Brummelkamp T.R., Bernards R., Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science. 296:2002;550-553.
41. Devroe E., Silver P.A. Retrovirus-delivered siRNA. BMC Biotechnol. 2:2002;15.
42. Shen C., Buck A.K., Liu X., Winkler M., Reske S.N. Gene silencing by adenovirus-delivered siRNA. FEBS Lett. 539:2003;111-114.
43. Rubinson D.A., Dillon C.P., Kwiatkowski A.V., Sievers C., Yang L., Kopinja J., Zhang M., McManus M.T., Gertler F.B., Scott M.L.et al. A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat. Genet. 33:2003;401-406.
44. Bohula E.A., Salisbury A.J., Sohail M., Playford M.P., Riedemann J., Southern E.M., Macaulay V.M. The efficacy of small interfering RNAs targeted to the type 1 IGF receptor is influenced by secondary structure in the IGF1R transcript. J. Biol. Chem. 278:2003;15991-15997 This study demonstrates the use of oligonucleotide scanning arrays to screen the type 1 insulin-like growth factor receptor (IGF1R) mRNA transcript to identify sites accessible to targeting by antisense oligonucleotides or siRNAs. Additionally, maximum siRNA-mediated inhibition of IGF1R expression corresponded with increasing accessibility of the target sequence within the transcript, thus indicating that secondary structure in the target transcript has a major effect on siRNA efficacy.
45. 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. 391:1998;806-811.
46. Bertrand J.R., Pottier M., Vekris A., Opolon P., Maksimenko A., Malvy C. Comparison of antisense oligonucleotides and siRNAs in cell culture and in vivo. Biochem. Biophys. Res. Commun. 296:2002;1000-1004.
47. Jarad G., Wang B., Khan S., DeVore J., Miao H., Wu K., Nishimura S.L., Wible B.A., Konieczkowski M., Sedor J.R.et al. Fas activation induces renal tubular epithelial cell β8 integrin expression and function in the absence of apoptosis. J. Biol. Chem. 277:2002;47826-47833.
48. Stein P., Svoboda P., Schultz R.M. Transgenic RNAi in mouse oocytes: a simple and fast approach to study gene function. Dev. Biol. 256:2003;188-194.
49. Pan D.A., Hardie D.G. A homologue of AMP-activated protein kinase in Drosophila melanogaster is sensitive to AMP and is activated by ATP depletion. Biochem. J. 367:2002;179-186.
50. Makimura H., Mizuno T.M., Mastaitis J.W., Agami R., Mobbs C.V. Reducing hypothalamic AGRP by RNA interference increases metabolic rate and decreases body weight without influencing food intake. BMC Neurosci. 3:2002;18 A demonstration of RNAi-mediated downregulation of an endogeous gene in vivo. Reduction of the Agouti-related protein in mice by siRNAs and siRNA-expressing plasmid vectors led to an increase in metabolic activity and decrease in body weight without influencing food intake.
51. Tummala S.B., Welker N.E., Papoutsakis E.T. Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J. Bacteriol. 185:2003;1923-1934 An analysis of design features of antisense RNA and demonstration of its use for altering the selectivity of acetone formation in C. acetobutylicum.
52. 32 as a transient metabolic controller in Escherichia coli: effects on yield of active organophosphorus hydrolase. Appl. Env. Microbiol. 66:2000;4366-4371.
53. Moser S., Rimann M., Fux C., Schlatter S., Bailey J.E., Fussenegger M. Dual-regulated expression technology: a new era in the adjustment of heterologous gene expression in mammalian cells. J. Gene Med. 3:2001;529-549.
54. Kip1 sense and antisense enables positive and negative growth control of Chinese hamster ovary cells. Nucleic Acids Res. 29:2001;e19.
55. Hidaka C., Ibarra C., Hannafin J.A., Torzilli P.A., Quitoriano M., Jen S.S., Warren R.F., Crystal R.G. Formation of vascularized meniscal tissue by combining gene therapy with tissue engineering. Tissue Eng. 8:2002;93-105.
56. Shea L.D., Smiley E., Bonadio J., Mooney D.J. DNA delivery from polymer matrices for tissue engineering. Nat. Biotechnol. 17:1999;551-554.
57. Cordeiro M.F., Mead A., Ali R.R., Alexander R.A., Murray S., Chen C., York-Defalco C., Dean N.M., Schultz G.S., Khaw P.T. Novel antisense oligonucleotides targeting TGF-β inhibit in vivo scarring and improve surgical outcome. Gene Ther. 10:2003;59-71 Demonstrates the use of 2′-O-methoxyethyl-modified phosphorothioate antisense oligonucleotides against TGF-β to inhibit post-operative ocular scarring activity in vitro and in vivo.
58. Shay J.W., Wright W.E. The use of telomerized cells for tissue engineering. Nat. Biotechnol. 18:2000;22-23.
59. Teng L., Specht M.C., Barden C.B., Fahey T.J. III Antisense hTERT inhibits thyroid cancer cell growth. J. Clin. Endocrinol. Metab. 88:2003;1362-1366.
60. Cho Y.S., Kim M.K., Cheadle C., Neary C., Becker K.G., Cho-Chung Y.S. Antisense DNAs as multisite genomic modulators identified by DNA microarray. Proc. Natl. Acad Sci. USA. 98:2001;9819-9823.
61. Chi J.T., Chang H.Y., Wang N.N., Chang D.S., Dunphy N., Brown P.O. Genomewide view of gene silencing by small interfering RNAs. Proc. Natl. Acad Sci. USA. 100:2003;6343-6346.
62. Semizarov D., Frost L., Sarthy A., Kroeger P., Halbert D.N., Fesik S.W. Specificity of short interfering RNA determined through gene expression signatures. Proc. Natl. Acad Sci. USA. 100:2003;6347-6352.