Stability and immunogenicity properties of the gene-silencing polypurine reverse hoogsteen hairpins

Molecular Pharmaceutics

Volumn 11, Issue 1, 2014, Pages 254-264

  Villalobos, Xenia ^a   Rodríguez, Laura ^a   Prévot, Jeanne ^a   Oleaga, Carlota ^a   Ciudad, Carlos J ^a   Noé, Véronique ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

gene silencing; immunogenicity; inflammasome; nucleic acid; PPRH; stability; TLR

Indexed keywords

ALPHA INTERFERON; BETA INTERFERON; DIHYDROFOLATE REDUCTASE; GENE THERAPY AGENT; I KAPPA B; INFLAMMASOME; INTERFERON REGULATORY FACTOR 3; INTERLEUKIN 18; INTERLEUKIN 1BETA; INTERLEUKIN 1BETA CONVERTING ENZYME; INTERLEUKIN 6; OLIGODEOXYNUCLEOTIDE; POLYPURINE REVERSE HOOGSTEEN HAIRPIN; SMALL INTERFERING RNA; TOLL LIKE RECEPTOR; TUMOR NECROSIS FACTOR ALPHA; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CANCER CELL CULTURE; CELL SURVIVAL; CELL VIABILITY; CONTROLLED STUDY; DNA HAIRPIN; DRUG DEGRADATION; DRUG EFFICACY; DRUG HALF LIFE; DRUG STABILITY; DRUG STRUCTURE; ENZYME ACTIVATION; ENZYME ACTIVITY; GENE EXPRESSION; GENE SEQUENCE; GENE SILENCING; HUMAN; HUMAN CELL; IMMUNE RESPONSE; IMMUNOGENICITY; INNATE IMMUNITY; MTT ASSAY; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; WESTERN BLOTTING;

ANIMALS; BLOTTING, WESTERN; BREAST NEOPLASMS; CELL PROLIFERATION; CYTOKINES; ELECTROPHORETIC MOBILITY SHIFT ASSAY; FEMALE; GENE SILENCING; HALF-LIFE; HUMANS; INTERFERON REGULATORY FACTOR-3; MALE; MICE; NF-KAPPA B; PROSTATIC NEOPLASMS; PURINE NUCLEOTIDES; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; RNA, SMALL INTERFERING; TUMOR CELLS, CULTURED;

EID: 84891806774     PISSN: 15438384     EISSN: 15438392     Source Type: Journal    
DOI: 10.1021/mp400431f     Document Type: Article

References (35)

1. Whitehead, K. A.; Langer, R.; Anderson, D. G. Knocking down barriers: advances in siRNA delivery Nat. Rev. Drug Discovery 2009, 8 (2) 129-138
2. Kole, R.; Krainer, A. R.; Altman, S. RNA therapeutics: beyond RNA interference and antisense oligonucleotides Nat. Rev. Drug Discovery 2012, 11 (2) 125-140
3. Whitehead, K. A.; Dahlman, J. E.; Langer, R. S.; Anderson, D. G. Silencing or stimulation? siRNA delivery and the immune system Annu. Rev. Chem. Biomol. Eng. 2011, 2, 77-96
4. Brown, J.; Wang, H.; Hajishengallis, G. N.; Martin, M. TLR-signaling networks: an integration of adaptor molecules, kinases, and cross-talk J. Dent. Res. 2011, 90 (4) 417-427
5. Roberts, T. L.; Idris, A.; Dunn, J. A.; Kelly, G. M.; Burnton, C. M.; Hodgson, S.; Hardy, L. L.; Garceau, V.; Sweet, M. J.; Ross, I. L.; Hume, D. A.; Stacey, K. J. HIN-200 proteins regulate caspase activation in response to foreign cytoplasmic DNA Science 2009, 323 (5917) 1057-1060
6. de Almagro, M. C.; Coma, S.; Noe, V.; Ciudad, C. J. Polypurine hairpins directed against the template strand of DNA knock down the expression of mammalian genes J. Biol. Chem. 2009, 284 (17) 11579-11589
7. de Almagro, M. C.; Mencia, N.; Noe, V.; Ciudad, C. J. Coding polypurine hairpins cause target-induced cell death in breast cancer cells Hum. Gene Ther. 2011, 22 (4) 451-463
8. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic local alignment search tool J. Mol. Biol. 1990, 215 (3) 403-410
9. Bartok, E.; Bauernfeind, F.; Khaminets, M. G.; Jakobs, C.; Monks, B.; Fitzgerald, K. A.; Latz, E.; Hornung, V. iGLuc: a luciferase-based inflammasome and protease activity reporter Nat. Methods 2013, 10 (2) 147-154
10. Oleaga, C.; Welten, S.; Belloc, A.; Sole, A.; Rodriguez, L.; Mencia, N.; Selga, E.; Tapias, A.; Noe, V.; Ciudad, C. J. Identification of novel Sp1 targets involved in proliferation and cancer by functional genomics Biochem. Pharmacol. 2012, 84 (12) 1581-1591
11. Judge, A.; MacLachlan, I. Overcoming the innate immune response to small interfering RNA Hum. Gene Ther. 2008, 19 (2) 111-124
12. Schlee, M.; Hornung, V.; Hartmann, G. siRNA and isRNA: two edges of one sword Mol. Ther. 2006, 14 (4) 463-470
13. Atianand, M. K.; Fitzgerald, K. A. Molecular basis of DNA recognition in the immune system J. Immunol. 2013, 190 (5) 1911-1918
14. Omidi, Y.; Hollins, A. J.; Benboubetra, M.; Drayton, R.; Benter, I. F.; Akhtar, S. Toxicogenomics of non-viral vectors for gene therapy: a microarray study of lipofectin- and oligofectamine-induced gene expression changes in human epithelial cells J. Drug Target. 2003, 11 (6) 311-323
15. Pan, C. Q.; Ulmer, J. S.; Herzka, A.; Lazarus, R. A. Mutational analysis of human DNase I at the DNA binding interface: implications for DNA recognition, catalysis, and metal ion dependence Protein Sci. 1998, 7 (3) 628-636
16. Haupenthal, J.; Baehr, C.; Kiermayer, S.; Zeuzem, S.; Piiper, A. Inhibition of RNAse A family enzymes prevents degradation and loss of silencing activity of siRNAs in serum Biochem. Pharmacol. 2006, 71 (5) 702-710
17. Bartlett, D. W.; Davis, M. E. Effect of siRNA nuclease stability on the in vitro and in vivo kinetics of siRNA-mediated gene silencing Biotechnol. Bioeng. 2007, 97 (4) 909-921
18. Layzer, J. M.; McCaffrey, A. P.; Tanner, A. K.; Huang, Z.; Kay, M. A.; Sullenger, B. A. In vivo activity of nuclease-resistant siRNAs RNA 2004, 10 (5) 766-71
19. Dykxhoorn, D. M.; Palliser, D.; Lieberman, J. The silent treatment: siRNAs as small molecule drugs Gene Ther. 2006, 13 (6) 541-552
20. Turner, J. J.; Jones, S. W.; Moschos, S. A.; Lindsay, M. A.; Gait, M. J. MALDI-TOF mass spectral analysis of siRNA degradation in serum confirms an RNAse A-like activity Mol. Biosyst. 2007, 3 (1) 43-50
21. Jones, S. J.; Worrall, A. F.; Connolly, B. A. Site-directed mutagenesis of the catalytic residues of bovine pancreatic deoxyribonuclease I J. Mol. Biol. 1996, 264 (5) 1154-1163
22. Fujihara, J.; Yasuda, T.; Ueki, M.; Iida, R.; Takeshita, H. Comparative biochemical properties of vertebrate deoxyribonuclease I Comp. Biochem. Physiol. B Biochem. Mol. Biol. 2012, 163 (3-4) 263-73
23. Bishop, J. S.; Guy-Caffey, J. K.; Ojwang, J. O.; Smith, S. R.; Hogan, M. E.; Cossum, P. A.; Rando, R. F.; Chaudhary, N. Intramolecular G-quartet motifs confer nuclease resistance to a potent anti-HIV oligonucleotide J. Biol. Chem. 1996, 271 (10) 5698-5703
24. Bates, P. J.; Choi, E. W.; Nayak, L. V. G-rich oligonucleotides for cancer treatment Methods Mol. Biol. 2009, 542, 379-392
25. Blume, S. W.; Lebowitz, J.; Zacharias, W.; Guarcello, V.; Mayfield, C. A.; Ebbinghaus, S. W.; Bates, P.; Jones, D. E., Jr.; Trent, J.; Vigneswaran, N.; Miller, D. M. The integral divalent cation within the intermolecular purine*purine. pyrimidine structure: a variable determinant of the potential for and characteristics of the triple helical association Nucleic Acids Res. 1999, 27 (2) 695-702
26. 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 (4) 457-462
27. Sioud, M. Induction of inflammatory cytokines and interferon responses by double-stranded and single-stranded siRNAs is sequence-dependent and requires endosomal localization J. Mol. Biol. 2005, 348 (5) 1079-1090
28. Hornung, V.; Guenthner-Biller, M.; Bourquin, C.; Ablasser, A.; Schlee, M.; Uematsu, S.; Noronha, A.; Manoharan, M.; Akira, S.; de Fougerolles, A.; Endres, S.; Hartmann, G. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7 Nat. Med. 2005, 11 (3) 263-270
29. Hanagata, N. Structure-dependent immunostimulatory effect of CpG oligodeoxynucleotides and their delivery system Int. J. Nanomed. 2012, 7, 2181-2195
30. Davis, B. K.; Wen, H.; Ting, J. P. The inflammasome NLRs in immunity, inflammation, and associated diseases Annu. Rev. Immunol. 2001, 29, 707-735
31. Kool, E. T. Recognition of DNA, RNA, and Proteins by Circular Oligonucleotides Acc. Chem. Res. 1998, 31 (8) 502-510
32. Rubin, E.; Rumney, S. t.; Wang, S.; Kool, E. T. Convergent DNA synthesis: a non-enzymatic dimerization approach to circular oligodeoxynucleotides Nucleic Acids Res. 1995, 23 (17) 3547-3553
33. Chu, B. C.; Orgel, L. E. The stability of different forms of double-stranded decoy DNA in serum and nuclear extracts Nucleic Acids Res. 1992, 20 (21) 5857-5858
34. Mencia, N.; Selga, E.; Noe, V.; Ciudad, C. J. Underexpression of miR-224 in methotrexate resistant human colon cancer cells Biochem. Pharmacol. 2011, 82 (11) 1572-1582
35. Barros, S.; Mencia, N.; Rodriguez, L.; Oleaga, C.; Santos, C.; Noe, V.; Ciudad, C. J. The redox state of cytochrome c modulates resistance to methotrexate in human MCF7 breast cancer cells PLoS One 2013, 8 (5) e63276