Recent patents on therapeutic applications of the transcription factor decoy approach

Bibliography

• Martiniello-Wilks R, Tsatralis T, Russell P, Transcription-targeted gene therapy for androgen-independent prostate cancer. Cancer Gene Ther 2002;9(5):443-52
   Google Scholar
• Licht JD. Targeting aberrant transcriptional repression in leukemia: a therapeutic reality? J Clin Invest 2001;108(9):1277-8
   Google Scholar
• Chaires JB. Drug-DNA interactions. Curr Opin Struct Biol 1998;8:314-20
   PubMed Web of Science ®Google Scholar
• Boer DR, Canals A, Coll M. DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes. Dalton Trans 2009;3:399-414
   PubMed Web of Science ®Google Scholar
• Gambari R, Feriotto G, Rutigliano C, Biospecific interaction analysis (BIA) of low-molecular weight DNA-binding drugs. J Pharmacol Exp Ther 2000;294(1):370-7
   PubMed Web of Science ®Google Scholar
• Sleiman SF, Langley BC, Basso M, Mithramycin is a gene-selective Sp1 inhibitor that identifies a biological intersection between cancer and neurodegeneration. J Neurosci 2011;31(18):6858-70
   PubMed Web of Science ®Google Scholar
• Ciucci A, Feriotto G, Mischiati C, Distamycin analogues with improved sequence-specific DNA binding activities. Biochem Pharmacol 1994;48(8):1583-91
   Google Scholar
• Speight RE, Hart DJ, Blackburn JM. Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner. J Mol Recognit 2002;15(1):19-26
   Google Scholar
• Carbone GM, Napoli S, Valentini A, Triplex DNA-mediated downregulation of Ets2 expression results in growth inhibition and apoptosis in human prostate cancer cells. Nucleic Acids Res 2004;32(14):4358-67
   PubMed Web of Science ®Google Scholar
• Hildner KM, Schirmacher P, Atreya I, Targeting of the transcription factor STAT4 by antisense phosphorothioate oligonucleotides suppresses collagen-induced arthritis. J Immunol 2007;178(6):3427-36
   Google Scholar
• Na KY, Woo SK, Lee SD, Kwon HM. Silencing of TonEBP/NFAT5 transcriptional activator by RNA interference. J Am Soc Nephrol 2003;14(2):283-8
   Google Scholar
• Sankaran VG, Menne TF, Scepanovic D, MicroRNA-15a and -16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13. Proc Natl Acad Sci USA 2011;108(4):1519-24
   PubMed Web of Science ®Google Scholar
• Bontron S, Ucla C, Mach B, Steimle V. Efficient repression of endogenous major histocompatibility complex class II expression through dominant negative CIITA mutants isolated by a functional selection strategy. Mol Cell Biol 1997;17(8):4249-58
   PubMedGoogle Scholar
• Buitenhuis M, Baltus B, Lammers JW, Signal transducer and activator of transcription 5a (STAT5a) is required for eosinophil differentiation of human cord blood-derived CD34+ cells. Blood 2003;101(1):134-42
   Google Scholar
• Fry DW, Kraker AJ, McMichael A, A specific inhibitor of the epidermal growth factor receptor tyrosine kinase. Science 1994;265(5175):1093-5
   PubMed Web of Science ®Google Scholar
• Birkenkamp KU, Tuyt LM, Lummen C, The p38 MAP kinase inhibitor SB203580 enhances nuclear factor-kappa B transcriptional activity by a non-specific effect upon the ERK pathway. Br J Pharmacol 2000;131(1):99-107
   Google Scholar
• Yang X, Fennewald S, Luxon BA, Aptamers containing thymidine 3′-O-phosphorodithioates: synthesis and binding to nuclear factor-kappaB. Bioorg Med Chem Lett 1999;9(23):3357-62
   Google Scholar
• Cassiday LA, Maher LJ III. In vivo recognition of an RNA aptamer by its transcription factor target. Biochemistry 2001;40(8):2433-8
   Google Scholar
• King DJ, Bassett SE, Li X, Combinatorial selection and binding of phosphorothioate aptamers targeting human NF-kappa B RelA(p65) and p50. Biochemistry 2002;41(30):9696-706
   Google Scholar
• Dzau VJ. Transcriptional factor decoy. Circ Res 2002;90:1234-6
   PubMedGoogle Scholar
• Mann MJ, Dzau VJ. Therapeutic application of transcriptional factor decoy oligonucleotides. J Clin Invest 2000;106:1071-5
   PubMed Web of Science ®Google Scholar
• Morishita R, Sugimoto T, Aoki M, In vivo transfection of cis element “decoy” against nuclear factor-kB binding site prevents myocardial infarction. Nat Med 1997;3:894-9
   PubMed Web of Science ®Google Scholar
• Tomita T, Takano H, Tomita N, Transcription factor decoy for NF-kB inhibits cytokine and adhesion molecule expressions in synovial cells derived from rheumatoid arthritis. Rheumatology 2000;39:749-57
   PubMed Web of Science ®Google Scholar
• Borgatti M, Lampronti I, Romanelli A, Transcription factor decoy molecules based on a peptide nucleic acid (PNA)-DNA chimera mimicking Sp1 binding sites. J Biol Chem 2003;278:7500-9
   PubMed Web of Science ®Google Scholar
• Karin M, Lin A. NF-kB at the crossroads of life and death. Nat Immunol 2002;3:221-7
   PubMed Web of Science ®Google Scholar
• Yamamoto Y, Gaynor RB. Role of the NF-kB pathway in the pathogenesis of human disease states. Curr Mol Med 2001;1:287-96
   PubMedGoogle Scholar
• Yang X, Karsenty G. Transcription factors in bone: developmental and pathological aspects. Trends Mol Med 2002;8:340-5
   PubMed Web of Science ®Google Scholar
• Nebert DW. Transcription factors and cancer: an overview. Toxicology 2002;181-182:131-41
   PubMed Web of Science ®Google Scholar
• Redell MS, Tweardy DJ. Targeting transcription factors for cancer therapy. Curr Pharm Des 2005;11:2873-87
   PubMed Web of Science ®Google Scholar
• Borgatti M, Bezzerri V, Mancini I, Induction of IL-6 gene expression in a CF bronchial epithelial cell line by Pseudomonas aeruginosa is dependent on transcription factors belonging to the Sp1 superfamily. Biochem Biophys Res Commun 2007;357:977-83
   PubMed Web of Science ®Google Scholar
• Bezzerri V, Borgatti M, Nicolis E, Transcription Factor Oligodeoxynucleotides to NF-{kappa}B Inhibit Transcription of IL-8 in Bronchial Cells. Am J Respir Cell Mol Biol 2008;39:86-96
   PubMed Web of Science ®Google Scholar
• Piva R, Penolazzi L, Lambertini E, Induction of apoptosis of human primary osteoclasts treated with a transcription factor decoy mimicking a promoter region of estrogen receptor alpha. Apoptosis 2005;66:1079-94
   Google Scholar
• Morishita R, Tomita N, Kaneda Y, Ogihara T. Molecular therapy to inhibit NFkappaB activation by transcription factor decoy oligonucleotides. Curr Opin Pharmacol 2004;4:139-46
   PubMed Web of Science ®Google Scholar
• Isomura I, Morita A. Regulation of NF-kB signaling by decoy oligodeoxynucleotides. Microbiol Immunol 2006;50:559-63
   PubMed Web of Science ®Google Scholar
• Mcevoy LM, Parham C, Zhang J, Ehrhardt R. NF-kB oligonucleotide decoy molecules. US20070078102; 2007
   Google Scholar
• Morishita R, Aoki M, Ogihara T, Kawasaki T. Decoy-containing pharmaceutical compositions and method of using the same. US20070142314; 2007
   Google Scholar
• Sawa Y. Agents for protection from neointimal formation in grafts comprising an nfkappab decoy. US20060233815; 2006
   Google Scholar
• Nakajima T, Temma A, Suzuki N. Novel Oligonucleotide and NF-kB Decoy Comprising the Same. US20100167390; 2010
   Google Scholar
• Strober W, Fuss I, Kitani A, Fichtner-feighl S. Compositions and Methods for the Treatment of Inflammatory Bowel Disease Utilizing NF-KappaB Decoy Polynucleotides. US2009214630; 2009
   Google Scholar
• Morishita R, Aoki M, Ogihara T, Medical composition containing nf-kb decoy for treating and preventing respiratory diseases and method of using the same. US20070183983; 2007
   Google Scholar
• Morishita R, Ogihara T, Aoki M, Miyake T. Chimeric (Double) Decoy. US20070259826; 2007
   Google Scholar
• Penolazzi L, Lambertini E, Borgatti M, Decoy oligodeoxynucleotides targeting NF-kB transcription factors: induction of apoptosis in human primary osteoclasts. Biochem Pharmacol 2003;66:1189-98
   Google Scholar
• Borgatti M, Breda L, Cortesi R, Cationic liposomes as delivery systems for double-stranded PNA-DNA chimeras exhibiting decoy activity against NF-kB transcription factors. Biochem Pharmacol 2002;64:609-16
   PubMedGoogle Scholar
• Penolazzi L, Borgatti M, Lambertini E, Peptide nucleic acid-DNA decoy chimeras targeting NF-kB transcription factors: Induction of apoptosis in human primary osteoclasts. Int J Mol Med 2004;14:145-52
   PubMedGoogle Scholar
• Cabrini G, Bezzerri V, Mancini I, Targeting transcription factor activity as a strategy to inhibit pro-inflammatory genes involved in cystic fibrosis: decoy oligonucleotides and low-molecular weight compounds. Curr Med Chem 2010;17(35):4392-404
   Google Scholar
• Bodas M, Vij N. The NF-kB signaling in cystic fibrosis lung disease: pathophysiology and therapeutic potential. Discov Med 2010;9:346-56
   PubMed Web of Science ®Google Scholar
• Kieninger E, Regamey N. Targeting inflammation in cystic fibrosis. Respiration 2010;79:189-90
   Google Scholar
• Cooper JA Jr, Parks JM, Carcelen R, Attenuation of interleukin-8 production by inhibiting nuclear factor-kappaB translocation using decoy oligonucleotides. Biochem Pharmacol 2000;59:605-13
   Google Scholar
• Gambari R, Borgatti M, Bezzerri V, Decoy oligodeoxyribonucleotides and peptide nucleic acids-DNA chimeras targeting nuclear factor kappa-B: inhibition of IL-8 gene expression in cystic fibrosis cells infected with Pseudomonas aeruginosa. Biochem Pharmacol 2010;80(12):1887-94
   Google Scholar
• Yoshizumi T, Ikeda Y, Kaneda Y, Sueishi K. Ex vivo transfer of nuclear factor-kappaB decoy ameliorates hepatic cold ischemia/reperfusion injury. Transplant Proc 2009;41:1504-7
   Google Scholar
• Takahashi T, Togo S, Kumamoto T, Transfection of NF-kB decoy oligodeoxynucleotides into macrophages reduces murine fatal liver failure after excessive hepatectomy. J Surg Res 2009;154:179-86
   Google Scholar
• Suzuki M, Inoue G, Gemba T, Nuclear factor-kappa B decoy suppresses nerve injury and improves mechanical allodynia and thermal hyperalgesia in a rat lumbar disc herniation model. Eur Spine J 2009;18:1001-7
   Google Scholar
• Shimizu H, Nakagami H, Morita S, New treatment of periodontal diseases by using NF-kB decoy oligodeoxynucleotides via prevention of bone resorption and promotion of wound healing. Antioxid Redox Signal 2009;11:2065-75
   Google Scholar
• Penolazzi L, Magri E, Lambertini E, “In vivo” local transfection of a cis element decoy mimicking an estrogen receptor alpha gene promoter region induces apoptosis of osteoclasts following application of orthodontic forces to rat teeth. Apoptosis 2006;11:1653-6
   Google Scholar
• Kim KH, Lee ES, Cha SH, Transcriptional regulation of NF-kB by ring type decoy oligodeoxynucleotide in an animal model of nephropathy. Exp Mol Pathol 2009;86:114-20
   Web of Science ®Google Scholar
• Kimura S, Egashira K, Chen L, Nanoparticle-mediated delivery of nuclear factor kappaB decoy into lungs ameliorates monocrotaline-induced pulmonary arterial hypertension. Hypertension 2009;53:877-83
   PubMed Web of Science ®Google Scholar
• De Stefano D, De Rosa G, Maiuri MC, Oligonucleotide decoy to NF-kB slowly released from PLGA microspheres reduces chronic inflammation in rat. Pharmacol Res 2009;60:33-40
   PubMed Web of Science ®Google Scholar
• Li YT, He B, Wang YZ, Wang J. Effects of intratracheal administration of nuclear factor-kappaB decoy oligodeoxynucleotides on long-term cigarette smoke-induced lung inflammation and pathology in mice. Respir Res 2009;10:79
   Google Scholar
• Park GY, Christman JW. Nuclear factor kappa B is a promising therapeutic target in inflammatory lung disease. Curr Drug Targets 2006;7:661-8
   PubMed Web of Science ®Google Scholar
• Fichtner-Feigl S, Young CA, Kitani A, IL-13 signaling via IL-13R alpha2 induces major downstream fibrogenic factors mediating fibrosis in chronic TNBS colitis. Gastroenterology 2008;135(6):2003-13
   PubMed Web of Science ®Google Scholar
• Han W, Liu GN. EGR-1 decoy ODNs inhibit vascular smooth muscle cell proliferation and neointimal hyperplasia of balloon-injured arteries in rat. Life Sci 2010;86(7-8):234-43
   Google Scholar
• Morishita R, Gibbons GH, Horiuchi M, A gene therapy strategy using a transcription factor decoy of the E2F binding site inhibits smooth muscle proliferation in vivo. Proc Natl Acad Sci USA 1995;92(13):5855-9
   PubMed Web of Science ®Google Scholar
• Gambari R, Penolazzi L, Piva R. Double-Stranded Synthetic Oligonucleotides Useful For Inducing Apoptosis of Osteoclasts For the Treatment of Osteopenic Pathologies. US20080171717; 2008
   Google Scholar
• Huang K, Lin J. Transcription Factor Decoys And Use Thereof. US20110054010; 2011
   Google Scholar
• Hunt AC, Lim C, Garovoy MR. Polynucleotide decoys that inhibit MHC-II expression and uses thereof. US5859226; 1999
   Google Scholar
• Parham C, Mcevoy L, Zhang J, Rao X. E2F oligonucleotide decoy molecules. US20050164240; 2005
   Google Scholar
• Mcevoy L, Powell L, Zhang J, Morris K. HIF oligonucleotide decoy molecules. US20050215503; 2005
   Google Scholar
• Grandis J, Johnson DE, Leong P. STAT3 decoy oligonucleotides and uses thereof. US20060293264; 2006
   Google Scholar
• Klem R. Methods and composition for treating a cell-proliferative disorder using CRE decoy oligomers, BCL-2 antisense oligomers, and hybrid oligomers thereof. US7060690; 2006
   Google Scholar
• Mauviel A. Blocking Sp1 transcription factor broadly inhibits extracellular matrix gene expression in vitro and in vivo: implications for the treatment of tissue fibrosis. US20020137715; 2002
   Google Scholar
• Walsh K. GATA-6 transcription factor: compositions and methods. US5990092; 1999
   Google Scholar
• Arai K, Miyatake S, Takemoto N. Decoy for treating and/or preventing th2 cytokine-associated allergic disease, gata3 mutant protein and medicinal compositions containing the same. US20050222062; 2005
   Google Scholar
• Hecker M, Wagner A. Modulation of expression of STAT-1 dependent genes. US7320964; 2008
   Google Scholar
• Jones WK. Oligonucleotide decoys and methods of use. US20090099108; 2009
   Google Scholar
• Fillmore H, Martin Rege JI. Chimeric transcription factor decoy oligonucleotides. US20080233644; 2008
   Google Scholar
• Wang Z. Transcription factor decoy oligodeoxynucleotides having multiple cis elements. US20090227661; 2009
   Google Scholar
• Klem RE. Methods and composition for treating a cell-proliferative disorder using CRE decoy oligomers, BCL-2 antisense oligomers and hybrid oligomers thereof. US7060690; 2006
   Google Scholar
• Lee I, Morishita R. Circular dumbell oligodeoxynucleotides (CDODN) containing DNA binding sites of transcription. US20070014840; 2007
   Google Scholar
• Bou-Gharios G, Garrett LA, Rossert J, A potent far-upstream enhancer in the mouse pro alpha 2(I) collagen gene regulates expression of reporter genes in transgenic mice. J Cell Biol 1996;134(5):1333-44
   Google Scholar
• Shinohara K, Hamamoto H, Kobayashi K, Composition for external application comprising transcription factor decoy as active ingredients. US2011092438; 2011
   Google Scholar
• Lee I, Morishita R. Cyclic dumbell decoy oligodeoxynucleotide (CDODN) containing transcribed DNA-bound site. JP2009142295; 2009
   Google Scholar
• Morishita R, Aoki M, Ogihara T, Kawasaki T. Decoy-containing pharmaceutical compositions and method of using the same. JP2009102428; 2009
   Google Scholar
• Gemba T, Ueno N. Transcription factor decoy. US2009143319; 2009
   Google Scholar
• Naparstek Y, Hershko A. Regulatory sequences derived from IL-10 promoter and uses thereof in modulation of immune response. WO2009024986; 2009
   Google Scholar
• Mcevoy L, Powell L, Zhang J, Morris K. HIF oligonucleotide decoy molecule. JP2008109935; 2008
   Google Scholar
• Hecker M, Rauto M, Wagner A. Regulation of transcription of gene within varscular cell. JP2007135603; 2007
   Google Scholar
• Nakajima T, Tsuchimochi K, Yagishita N, Decoy Nucleic Acid to Synoviolin Gene Promoter. US2009029929; 2009
   Google Scholar
• Nakajima T, Yamasaki S, Yagishita N, Nerve Cell Differentiation Inducer. US2007219150; 2007
   Google Scholar
• Parham C, Mcevoy L, Zhang J, Rao X. E2F oligonucleotide decoy molecules. WO2005035547; 2005
   Google Scholar
• Hoel AW, Conte MS. Edifoligide: a transcription factor decoy to modulate smooth muscle cell proliferation in vein bypass. Cardiovasc Drug Rev 2007;25(3):221-34
   Google Scholar
• Mann MJ, Whittemore AD, Donaldson MC, Ex-vivo gene therapy of human vascular bypass grafts with E2F decoy: the PREVENT single-centre, randomised, controlled trial. Lancet 1999;354(9189):1493-8
   PubMed Web of Science ®Google Scholar
• Kaneda Y, Morishita R, Dzau VJ. Prevention of restenosis by gene therapy. Ann N Y Acad Sci 1997;811:299-308
   PubMed Web of Science ®Google Scholar
• Egashira K, Suzuki J, Ito H, Long-term follow up of initial clinical cases with NF-kappaB decoy oligodeoxynucleotide transfection at the site of coronary stenting. J Gene Med 2008;10(7):805-9
   Google Scholar
• Jun-Ichi S, Hiroshi I, Ryo G, Initial clinical cases of the use of a NF-kappaB decoy at the site of coronary stenting for the prevention of restenosis. Circ J 2004;68(3):270-1
   Google Scholar
• Conte MS, Bandyk DF, Clowes AW, Results of PREVENT III: a multicenter, randomized trial of edifoligide for the prevention of vein graft failure in lower extremity bypass surgery. J Vasc Surg 2006;43(4):742-51
   PubMed Web of Science ®Google Scholar
• Alexander JH, Hafley G, Harrington RA, Efficacy and safety of edifoligide, an E2F transcription factor decoy, for prevention of vein graft failure following coronary artery bypass graft surgery: PREVENT IV: a randomized controlled trial. JAMA 2005;294(19):2446-54
   PubMed Web of Science ®Google Scholar
• Alexander JH, Ferguson TB Jr, Joseph DM; PREVENT IV Investigators. The PRoject of Ex-vivo Vein graft ENgineering via Transfection IV (PREVENT IV) trial: study rationale, design, and baseline patient characteristics. Am Heart J 2005;150(4):643-9
   Google Scholar
• Cai X, Freedman NJ. New therapeutic possibilities for vein graft disease in the post-edifoligide era. Future Cardiol 2006;2(4):493-501
   Google Scholar
• Nielsen PE, Egholm M, Berg RH, Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991;254:1497-500
   PubMed Web of Science ®Google Scholar
• Uhlmann E. Peptide nucleic acids (PNA) and PNA-DNA chimeras: from high binding affinity towards biological function. Biol Chem 1998;379:1045-52
   PubMed Web of Science ®Google Scholar
• Romanelli A, Pedone C, Saviano M, Molecular interactions with nuclear factor kappaB (NF-kB) transcription factors of a PNA-DNA chimera mimicking NF-kB binding sites. Eur J Biochem 2001;268:6066-75
   PubMedGoogle Scholar
• Yuan X, Ma Z, Zhou W, Lipid-mediated delivery of peptide nucleic acids to pulmonary endothelium. Biochem Biophys Res Commun 2003;302(1):6-11
   PubMed Web of Science ®Google Scholar
• Ganguly S, Chaubey B, Tripathi S, Pharmacokinetic analysis of polyamide nucleic-acid-cell penetrating peptide conjugates targeted against HIV-1 transactivation response element. Oligonucleotides 2008;18(3):277-86
   Google Scholar
• Upadhyay A, Ponzio NM, Pandey VN. Immunological Response to Peptide Nucleic Acid and its Peptide Conjugate Targeted to Transactivation Response (TAR) Region of HIV-1 RNA Genome. Oligonucleotides 2008;18:329-36
   PubMed Web of Science ®Google Scholar
• MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ. Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet 2011;27(4):141-8
   Google Scholar
• Ladunga I. An overview of the computational analyses and discovery of transcription factor binding sites. Methods Mol Biol 2010;674:1-22
   Google Scholar
• Collas P. The current state of chromatin immunoprecipitation. Mol Biotechnol 2010;45(1):87-100
   PubMed Web of Science ®Google Scholar