Zinc-finger nucleases as a novel therapeutic strategy for targeting hepatitis B virus DNAs

Molecular Therapy

Volumn 18, Issue 5, 2010, Pages 947-954

  Cradick, Thomas J ^a   Keck, Kathy ^a   Bradshaw, Shannon ^b   Jamieson, Andrew C ^c   McCaffrey, Anton P ^a  

^a UNIVERSITY OF IOWA   (United States)

^b DREW UNIVERSITY   (United States)

^c Llenroc Research   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CORE PROTEIN; NUCLEASE; UNCLASSIFIED DRUG; VIRUS DNA; VIRUS RNA; ZINC FINGER NUCLEASE;

ARTICLE; CONTROLLED STUDY; DNA CLEAVAGE; DNA REPAIR; FRAMESHIFT MUTATION; GENE TARGETING; HEPATITIS B VIRUS; HEPATITIS C VIRUS; HUMAN; HUMAN CELL; NONHUMAN; RESTRICTION SITE;

BLOTTING, NORTHERN; CELL LINE; CELL LINE, TUMOR; DNA, VIRAL; ENDONUCLEASES; HEPATITIS B; HEPATITIS B VIRUS; HUMANS; POLYMERASE CHAIN REACTION; ZINC FINGERS;

HEPATITIS B VIRUS; HEPATITIS C VIRUS;

EID: 77952011493     PISSN: 15250016     EISSN: 15250024     Source Type: Journal    
DOI: 10.1038/mt.2010.20     Document Type: Article

References (44)

1. Bruix, J and Llovet, JM (2003). Hepatitis B virus and hepatocellular carcinoma. J Hepatol 39 Suppl 1: S59-S63.
2. Perrillo, RP (1993). Interferon in the management of chronic hepatitis B. Dig Dis Sci 38:577-593.
3. Muzyczka, N and Berns, KI (2001). Fields Virology, vol. 2. Lippincott Williams and Wilkins: Philadelphia, PA. pp. 2327-2359.
4. Wu, TT, Coates, L, Aldrich, CE, Summers, J and Mason, WS (1990). In hepatocytes infected with duck hepatitis B virus, the template for viral RNA synthesis is amplified by an intracellular pathway. Virology 175:255-261.
5. Dienstag, JL, Schiff, ER, Wright, TL, Perrillo, RP, Hann, HW, Goodman, Z et al. (1999). Lamivudine as initial treatment for chronic hepatitis B in the United States. N Engl J Med 341:1256-1263.
6. Kim, YG, Cha, J and Chandrasegaran, S (1996). Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 93:1156-1160.
7. Cathomen, T and Joung, JK (2008). Zinc-finger nucleases: the next generation emerges. Mol Ther 16:1200-1207.
8. Carroll, D (2008). Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Ther 15:1463-1468.
9. Bibikova, M, Carroll, D, Segal, DJ, Trautman, JK, Smith, J, Kim, YG et al. (2001). Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21:289-297.
10. Porteus, MH and Baltimore, D (2003). Chimeric nucleases stimulate gene targeting in human cells. Science 300:763.
11. Smith, J, Bibikova, M, Whitby, FG, Reddy, AR, Chandrasegaran, S and Carroll, D (2000). Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 28:3361-3369.
12. Händel, EM, Alwin, S and Cathomen, T (2009). Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity. Mol Ther 17:104-111.
13. Pavletich, NP and Pabo, CO (1991). Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252:809-817.
14. Elrod-Erickson, M, Rould, MA, Nekludova, L and Pabo, CO (1996). Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure 4:1171-1180.
15. Choo, Y and Klug, A (1994). Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc Natl Acad Sci USA 91:11163-11167. (Pubitemid 24349646)
16. Segal, DJ, Dreier, B, Beerli, RR and Barbas, CF 3rd (1999). Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences. Proc Natl Acad Sci USA 96:2758-2763.
17. Dreier, B, Beerli, RR, Segal, DJ, Flippin, JD and Barbas, CF 3rd (2001). Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 276:29466-29478.
18. Liu, Q, Xia, Z, Zhong, X and Case, CC (2002). Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J Biol Chem 277:3850-3856.
19. Dreier, B, Fuller, RP, Segal, DJ, Lund, CV, Blancafort, P, Huber, A et al. (2005). Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem 280:35588-35597.
20. Choo, Y and Klug, A (1994). Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci USA 91:11168-11172.
21. Maeder, ML, Thibodeau-Beganny, S, Osiak, A, Wright, DA, Anthony, RM, Eichtinger, M et al. (2008). Rapid 'open-source' engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31:294-301.
22. Ramirez, CL, Foley, JE, Wright, DA, Müller-Lerch, F, Rahman, SH, Cornu, TI et al. (2008). Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods 5:374-375.
23. Papworth, M, Moore, M, Isalan, M, Minczuk, M, Choo, Y and Klug, A (2003). Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors. Proc Natl Acad Sci USA 100:1621-1626.
24. Zimmerman, KA, Fischer, KP, Joyce, MA and Tyrrell, DL (2008). Zinc finger proteins designed to specifically target duck hepatitis B virus covalently closed circular DNA inhibit viral transcription in tissue culture. J Virol 82:8013-8021.
25. Cornu, TI, Thibodeau-Beganny, S, Guhl, E, Alwin, S, Eichtinger, M, Joung, JK et al. (2008). DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol Ther 16:352-358.
26. Pruett-Miller, SM, Connelly, JP, Maeder, ML, Joung, JK and Porteus, MH (2008). Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol Ther 16:707-717.
27. Marion, PL, Salazar, FH, Liittschwager, K, Bordier, BB, Seeger, C, Winters, MA et al. (2003). A transgenic mouse lineage useful for testing antivirals targeting hepatitis B virus. In: Schinazi, RF, Rice, C and Sommadossi, JP (eds). Frontiers in Viral Hepatitis. Elsevier Science: Amsterdam. pp 197-209.
28. Hirt, B (1967). Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol 26:365-369.
29. Keck, K, Volper, EM, Spengler, RM, Long, DD, Chan, CY, Ding, Y et al. (2009). Rational design leads to more potent RNA interference against hepatitis B virus: factors effecting silencing efficiency. Mol Ther 17:538-547.
30. Porteus, MH (2006). Mammalian gene targeting with designed zinc finger nucleases. Mol Ther 13:438-446.
31. Brunet, E, Simsek, D, Tomishima, M, DeKelver, R, Choi, VM, Gregory, P et al. (2009). Chromosomal translocations induced at specified loci in human stem cells. Proc Natl Acad Sci USA 106:10620-10625.
32. Santiago, Y, Chan, E, Liu, PQ, Orlando, S, Zhang, L, Urnov, FD et al. (2008). Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci USA 105:5809-5814. (Pubitemid 351758454)
33. Perez, EE, Wang, J, Miller, JC, Jouvenot, Y, Kim, KA, Liu, O et al. (2008). Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 26:808-816.
34. Urnov, FD, Miller, JC, Lee, YL, Beausejour, CM, Rock, JM, Augustus, S et al. (2005). Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435:646-651.
35. Szczepek, M, Brondani, V, Büchel, J, Serrano, L, Segal, DJ and Cathomen, T (2007). Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol 25:786-793.
36. Miller, JC, Holmes, MC, Wang, J, Guschin, DY, Lee, YL, Rupniewski, I et al. (2007). An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25:778-785.
37. Hurt, JA, Thibodeau, SA, Hirsh, AS, Pabo, CO and Joung, JK (2003). Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 100:12271-12276.
38. Joung, JK, Ramm, EI and Pabo, CO (2000). A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci USA 97:7382-7387.
39. Galibert, F, Mandart, E, Fitoussi, F, Tiollais, P and Charnay, P (1979). Nucleotide sequence of the hepatitis B virus genome (subtype ayw) cloned in E. coli. Nature 281:646-650.
40. Isalan, M, Klug, A and Choo, Y (1998). Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers. Biochemistry 37:12026-12033.
41. Moore, M, Klug, A and Choo, Y (2001). Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units. Proc Natl Acad Sci USA 98:1437-1441.
42. Fu, F, Sander, JD, Maeder, M, Thibodeau-Beganny, S, Joung, JK, Dobbs, D et al. (2009). Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res 37 (Database issue): D279-D283.
43. Zhang, L, Spratt, SK, Liu, Q, Johnstone, B, Qi, H, Raschke, EE et al. (2000). Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene. J Biol Chem 275:33850-33860.
44. Smith, J, Berg, JM and Chandrasegaran, S (1999). A detailed study of the substrate specificity of a chimeric restriction enzyme. Nucleic Acids Res 27:674-681.