Oligonucleotides as transcription factor decoys

Current Opinion in Molecular Therapeutics

Volumn 1, Issue 3, 1999, Pages 386-392

  Cho Chung, Yoon S ^a   Park, Yun Gyu ^a   Lee, Youl Nam ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; TRANSCRIPTION FACTOR;

ANTINEOPLASTIC ACTIVITY; ANTIVIRAL ACTIVITY; BINDING AFFINITY; DRUG EFFICACY; DRUG TARGETING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; REVIEW;

ANGIOPLASTY, TRANSLUMINAL, PERCUTANEOUS CORONARY; CELL ADHESION; CELL CYCLE PROTEINS; CELL NUCLEUS; CORONARY STENOSIS; CYCLIC AMP; DNA; DNA-BINDING PROTEINS; DRUG DESIGN; DRUG STABILITY; E2F TRANSCRIPTION FACTORS; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION; GENE PRODUCTS, TAT; GENES, REV; GENES, TAT; GLOMERULONEPHRITIS; HIV-1 REVERSE TRANSCRIPTASE; MYOCARDIAL INFARCTION; NF-KAPPA B; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; RECURRENCE; REGULATORY SEQUENCES, NUCLEIC ACID; REVERSE TRANSCRIPTASE INHIBITORS; SECOND MESSENGER SYSTEMS; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; TETRADECANOYLPHORBOL ACETATE; THIONUCLEOTIDES; TRANSCRIPTION FACTORS; TUNICA INTIMA;

EID: 2442756427     PISSN: 14648431     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (68)

1. Hu MCT, Davidson N: The inducible lac operator-repressor system is functional in mammalian cells. Cell (1987) 48:555-566.
2. Brown M, Figge J, Hansen U, Wright C, Jeang K-T, Khoury G, Uvingston DM, Roberts TM: lac repressor can regulate expression from a hybrid SV40 early promoter containing a lac operator in animal cells. Cell (1987) 49:603-612.
3. Friedman AD, Triezenberg SJ, McKnight SL: Expression of a truncated viral trans-activator selectively Impedes lytic infection by its cognate virus. Nature (1988) 335:452-454.
4. Wang XF, Calame K: SV40 enhancer-binding factors are required at the establishment but not the maintenance step of enhancer-dependent transcriptional activation. Cell (1986) 47:241-247.
5. Maher LJ, Wold B, Dervan PB: Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. Science (1989) 245:725-730.
6. Zon G: Oligonucleotide analogues as potential chemotherapeutic agents. Pharm Res (1988) 5:539-549.
7. Agrawal S, Jiang Z, Zhao Q, Shaw D, Cai Q, Roskey A, Channavajjala L, Saxinger C, Zhang R: Mixed-backbone oligonucleotides as second generation antisense oligonucleotides: In vitro and In vivo studies. Proc Natl Acad Sci USA (1997) 94:2620-2625.
8. Crooke ST: Therapeutic applications of oligonucleotides. Annu Rev Pharmacol Toxicol (1992) 32:329-376. Thorough overview on oligonucleotide therapeutics in the context of modern drug discovery and development.
9. Agrawal S, Zhao Q: Antisense therapeutics. Curr Opin Chem Biol (1998) 2:519-528. Excellent review on antisense therapeutics: antisense versus non-antisense mechanism of action, pharmacokinetics, toxicology and second generation oligonucleotides.
10. Bielinska A, Shivdasani RA, Zhang LQ, Nabel GJ: Regulation of gene expression with double-stranded phosphorothioate oligonucleotides. Science (1990) 250:997-1000. The first demonstration showing that DNA binding proteins recognize specific bases outside the helix, independent of the phosphodiester linkages.
11. Clowes AW, Clowes MM, Fingerle J, Reidy MA: Regulation of smooth muscle cell growth in injured artery. J Cardiovasc Pharmacol (1989) 14:S12-S15.
12. Gibbons GH, Dzau VJ: The emerging concept of vascular remodeling. N Engl J Med (1994) 330:1431-1438.
13. Weintraub SJ, Prater CA, Dean DC: Retinoblastoma protein switches the E2F site from positive to negative element. Nature (1992) 358:259-261.
14. Pagano M, Draetta G, Jansen Durr J: Association of cdk2 kinase with the transcription factor E2F during S phase. Science (1992) 255:1144-1147.
15. Morishita R, Gibbons GH, Horiuchi M, Ellison KE, Nakajima M, Zhang L, Kaneda Y, Ogihara T, Dzau VJ: A novel molecular strategy using cis element 'decoy' of E2F binding site inhibits smooth muscle proliferation in vivo. Proc Natl Acad Sci USA (1995) 92:5855-5859. The first report on therapeutic strategy to prevent neointimal hyperplasia by the use of transcription factor decoy.
16. Morishita R, Higaki J, Tomita N, Ogihara T: Application of transcription factor 'decoy' strategy as means of gene therapy and study of gene expression in cardiovascular disease. Department of Geriatric Medicine, Osaka University Medical School, Suita, Japan (1998). Excellent mini-review on application of transcription factor decoy on cardiovascular disease therapeutics.
17. Maeshima Y, Kashihara N, Yasuda T, Sugiyama H, Sekikawa T, Okamoto K, Kanao K, Watanabe Y, Kanwar YS, Makino H: Inhibition of mesanglal cell proliferation by E2F decoy oligodeoxynucleotide in vitro and in vivo. J Clin Invest (1998) 101:2589-2597.
18. Morishita R, Sugimoto T, Aoki M, Kida I, Tomita N, Moriguchi A, Maeda K, Sawa Y, Kaneda Y, Higaki J, Ogihara T: In vivo transfection of cis element 'decoy' against NFκB binding site prevented myocardial Infarction as gene therapy. Nat Med (1997) 3:894-899. First demonstration of decoy oligonucleotide strategy against NFKB as a new therapeutic modality of gene therapy for myocardial infarction.
19. Cullen BR, Greene WC: Regulatory pathways governing HIV-1 replication. Cell (1989) 58:423-426.
20. Rosen CA, Pavlakis GN: Tat and rev: positive regulators of HIV gene expression. AIDS (1990) 4:499-509.
21. Graham G, Maio J: RNA transcripts of the human immunodeficiency virus transactivation response element can inhibit action of the viral transactivator. Proc Natl Acad Sci USA (1990) 87:5817-5821.
22. Lisziewicz J, Rappaport J, Dhar R: Tat-regulated production of multimerized TAR RNA inhibits HIV-1 gene expression. New Biol (1991) 3:82-89.
23. Sullenger BA, Gallardo HF, Ungers GE, Gilboa E: Over-expression of TAR sequences renders cells resistant to human immunodeficiency virus replication. Cell (1990) 63:601-608.
24. Sullenger BA, Lee TC, Smith CA, Ungers GE, Gilboa E: Expression of chimeric tRNA-driven antisense transcripts renders NIH 3T3 cells highly resistant to Moloney murine leukemia virus replication. Mol Cell Biol (1990) 10:6512-6523.
25. Lee S-W, Gallardo HF, Gaspar O, Smith C, Gilboa E: Inhibition of HIV-1 in CEM cells by a potent TAR decoy. Gene Ther (1995) 2:377-384. Describes short RNA oligonucleotides corresponding to the HIV TAR sequence, which inhibit HIV expression and replication by blocking the binding of the HIV regulatory protein Tat to the authentic TAR region. Using improved expression systems, the viral gene expression was almost completely blocked.
26. Lee S-W, Gallardo HF, Gilboa E, Smith C: Inhibition of human immunodeficiency virus type 1 in human T cells by a potent Rev response element decoy consisting of the 13-nucleotide minimal Rev-binding domain. J Virol (1994) 68:8254-8264.
27. Nabel G, Baltimore D: An inducible transcription factor activates expression of human immunodeficiency virus In T cells. Nature (1987) 326:711-713.
28. Lenardo M, Pierce JW, Baltimore D: Protein-binding sites in Ig gene enhancers determine transcriptional activity and Inducibility. Science (1987) 236:1573-1577.
29. Baeuerle PA, Baltimore D: The physiology of the NF-κB transcription factor. Mol Aspects Cell Regul (1991) 6:409-432.
30. Nolan GP, Ghosh S, Liou HC, Tempst P, Baltimore D: DNA binding and IKB inhibition of the cloned p65 subunit of NF-κB, a rel-related polypeptide. Cell (1991) 64:961-969.
31. Ruben SM, Dillon PJ, Schreck R, Henkel T, Chen CH, Maher M, Baeuerle PA, Rosen CA: Isolation of a rel-related human cDNA that potentially encodes the 65-kD subunit of NF-κB. Science (1991) 251:1490-1493.
32. Bours V, DeJardin E, Goujon-Letawe F, Merville MP, Castronovo V:The NF-κB transcription factor and cancer: High expression of NFκB-and IκB-related proteins in tumor cell lines. Biochem Pharmacol (1994) 47:145-149.
33. Kunsch C, Ruben SM, Rosen CA: Selection of optimal κB/Rel DNA-blnding motifs: Interaction of both subunits of NF-κB with DNA is required for transcriptional activation. Mol Cell Biol (1992) 12:4412-4421.
34. Parry GC, Mackman N: A set of inducible genes expressed by activated human monocytic and endothelial cells contain κB-like sites that specifically bind c-Rel-p65 heterodimers. J Biol Chem (1994) 269:20823-20825.
35. Himes SR, Coles LS, Katsikeros R, Lang RK, Shannon MF: HTLV-1 tax activation of the GM-CSF and G-CSF promoters requires the interaction of NF-κB with other transcription factor families. Oncogene (1993) 8:3189-3197.
36. Dunn SM, Coles LS, Lang RK, Gerondakis S, Vadas MA, Shannon MF: Requirement for nuclear factor (NF)-κB p65 and NF-interleukin-6 binding elements in the tumor necrosis factor response region of the granulocyte colony-stimulating factor promoter. Blood (1994) 83:2469-2479.
37. Sharma HW, Perez JR, Higgins-Sochaski KA, Hsaio R, Narayanan R: Transcription factor decoy approach to decipher the role of NF-κB In oncogenesis. Anticancer Res (1996) 16:61-69. Demonstration of the role of RelA subunit of NFκB in tumor cell growth. Uses transcription factor decoy strategy to distinctively regulate RelA to inhibit tumor cell growth.
38. Sharma HW, Narayanan R: The NF-κB transcription factor In oncogenesis. Anticancer Res (1996) 16:589-596.
39. Higgins KA, Perez JR, Coleman TA, Dorshkind K, McComas WA, Sarmiento UM, Rosen CA, Narayanan R: Antisense inhibition of the p65 subunit of NF-κB blocks tumorigenicity and causes tumor regression. Proc Natl Acad Sci USA (1993) 90:9901-9905.
40. McIntyre KW, Lombard-Gillooly K, Perez JR, Kunsch C, Sarmiento UM, Larigan JD, Landreth KT, Narayanan R: A sense phosphorothioate oligonucleotide directed to the initiation codon of transcription factor NF-κB p65 causes sequence-specific immune stimulation. Antisense Res Dev (1993) 3:309-322.
41. Sarmiento UM, Perez JR, Becker JM, Narayanan R: In vivo toxicological effects of rel A antisense phosphorothioates In CD-1 mice. Antisense Res Dev (1994) 4:99-107.
42. Sha WC, Liou HC, Tuomanen El, Baltimore D: Targeted disruption of the p50 subunit of NF-κB leads to multifocal defects in immune responses. Cell (1995) 80:321-330.
43. Weih F, Carrasco D, Durham SK, Barton DS, Rizzo CA, Ryseck RP, Lira SA, Bravo R: Multiorgan inflammation and hematopoietic abnormalities in mice with a targeted disruption of RelB, a member of the NF-κB/Rel family. Cell (1995) 80:331-340.
44. Beg AA, Sha WC, Bronson RT, Ghosh S, Baltimore D: Embryonic lethality and liver degeneration in mice lacking the RelA component of NF-kappa B. Nature (1995) 376:167-170.
45. Eck SL, Perkins ND, Carr DP, Nabel GJ: Inhibition of phorbol ester-induced cellular adhesion by competitive binding of NF-κB In vivo. Mol Cell Biol (1993) 13:6530-6536. Demonstration that NFκB-specific double-stranded oligonucleotides can inhibit PMA-induced changes in two distinct cell types. This finding suggests that NFκB performs a fundamental role in mediating a wide range of cellular processes and is required for the expression of molecules which mediate adhesion.
46. Roesler WJ, Vandenbark GR, Hanson RW: Cyclic AMP and the induction of eukaryotic gene transcription. J Biol Chem (1986) 263:9063-9066. Excellent and comprehensive mini review on the basal and cAMP-induced gene transcription by CRE (cAMP response element).
47. Park YG, Nesterova M, Agrawal S, Cho-Chung YS: Dual blockade of cyclic AMP response element-(CRE) and AP-1-directed transcription by CRE-transcription factor decoy oligonucleotide. J Biol Chem (1999) 274:1573-1580. The first demonstration of synthetic single-stranded oligonucleotide of perfect palindrome structure that self-hybridizes to form hairpin/duplex as transcription factor decoy for the CRE-enhancer. The decoy-inhibition of basal CRE-enhancer activity led to inhibition of tumor growth in vivo without harming normal cell growth.
48. Nowak I, Seipel K, Schwarz M, Jans DA, Hemmings BA: Isolation of a cDNA and characterization of the 5′ flanking region of the gene encoding the type 1 regulatory subunit of the cAMP-dependent protein kinase. Eur J Biochem (1987) 167:27-33.
49. Chrivia JC, Uhler MD, McKnight GS: Characterization of genomic clones coding for the C alpha and C beta subunits of mouse cAMP-dependent protein kinase. J Biol Chem (1988) 263:5739-5744.
50. Fried M, Crothers DM: Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acid Res (1981) 9:6505-6525.
51. Kwok RPS, Lundblad JR, Chrivia JC, Richards JP, Bächinger HP, Brennan RG, Roberts SGE, Green MR, Goodman RH: Nuclear protein CBP is a coactivator for the transcription factor CREB. Nature (1994) 370:223-226.
52. Arias J, Alberts AS, Brindle P, Claret FX, Smeal T, Karin M, Feramisco J, Montminy M: Activation of cAMP and mitogen responsive genes relies on a common nuclear factor. Nature (1994) 370:226-229.
53. Gu W, Shi XL, Roeder RG: Synergistic activation of transcription by CBP and p53. Nature (1997) 387:819-823.
54. Agadir A, Shealy YF, Hill DL, Zhang X: Retinyl methyl ether down-regulates activator protein 1 transcriptional activation in breast cancer cells. Cancer Res (1997) 57:3444-3450.
55. Nilsson M, Ford J, Bohm S, Toftgárd R: Characterization of a nuclear factor that binds juxtaposed with ATF3/Jun on a composite response element specifically mediating induced transcription in response to an epidermal growth factor/Ras/Raf signaling pathway. Cell Growth Differ (1997) 8:913-920.
56. Williams JS, Andrisani OM: The hepatitis B virus X protein targets the basic region-leucine zipper domain of CREB. Proc Natl Acad Sci USA (1995) 92:3819-3823.
57. Lundblad JR, Kwok RPS, Laurance ME, Huang MS, Richards JP, Brennan RG, Goodman RH: The human T-cell leukemia virus-1 transcriptional activator tax enhances cAMP-responsive element-binding protein (CREB) binding activity through interactions with the DNA minor groove. J Biol Chem (1998) 273:19251-19259.
58. Chu BC, Orgel LE: Binding of hairpin and dumbbell DNA to transcription factors. Nucleic Acids Res (1991) 19:6958.
59. Chu BCF, Orgel LE: The stability of different forms of double-stranded decoy DNA in serum and nuclear extracts. Nucleic Acids Res (1992) 20:5857-5858.
60. McMurray CT, Wilson WD, Douglass JO: Hairpin formation within the enhancer region of the human enkephalin gene. Proc Natl Acad Sci USA (1991) 88:666-670. Demonstration of a 23-bp oligonucleotide of enkephalin gene enhancer which undergoes a reversible conformational change from a duplex to a cruciform structure of two hairpins suggesting the formation of a cruciform might regulate transcription.
61. Gacy AM, McMurray CT: Hairpin formation within the human enkephalin enhancer region. Kinetic Analysis. Biochemistry (1994) 33:11951-11959.
62. Comb M, Mermod N, Hyman SE, Pearlberg J, Ross ME, Goodman HM: Proteins bound at adjacent DNA elements act synergistically to regulate human proenkephalln cAMP inducible transcription. EMBO J (1988) 7:3793-3805.
63. Bazett-Jones DP, Brown ML: Electron microscopy reveals that transcription factor TFIIIA bends 5S DNA. Mol Cell Biol (1989) 9:336-341.
64. Kerppola TK, Curran T: DNA bending by Fos and Jun: the flexible hinge model. Science (1991) 254:1210-1214.
65. Perez-Martin J, Espinoza M: Protein-induced bending as a transcriptional switch. Science (1993) 260:805-807.
66. Horwitz MSZ, Loeb LA: Ix-induced cruciform extrusion. An E coli promoter that regulates transcription by DNA superhel. Science (1988) 241:703-705.
67. Bianchi ME, Beltrame M, Paonessa G: Specific recognition of cruciform DNA by nuclear protein HMG1. Science (1989) 243:1056-1059.
68. Glucksmann MA, Markiewicz P, Malone C, Rothman-Denes LB; Specific sequences and a hairpin structure In the template strand are required for N4 virion RNA polymerase promoter recognition. Cell (1992) 70:491-500.