Retargeting Sleeping Beauty Transposon Insertions by Engineered Zinc Finger DNA-binding Domains

被引:51
作者
Voigt, Katrin [2 ]
Gogol-Doering, Andreas [2 ]
Miskey, Csaba [1 ,2 ]
Chen, Wei [2 ]
Cathomen, Toni [3 ,4 ]
Izsvak, Zsuzsanna [2 ]
Ivics, Zoltan [1 ,2 ]
机构
[1] Paul Ehrlich Inst, Div Med Biotechnol, D-63225 Langen, Germany
[2] Max Delbruck Ctr Mol Med, Berlin, Germany
[3] Hannover Med Sch, Inst Expt Hematol, D-3000 Hannover, Germany
[4] Univ Med Ctr Freiburg, Dept Transfus Med, Freiburg, Germany
关键词
TARGET SITE SELECTION; HUMAN-CELLS; GENE-THERAPY; DIRECTED INTEGRATION; FUSION PROTEINS; HUMAN GENOME; VIRAL-DNA; IN-VITRO; NUCLEASES; RETROTRANSPOSON;
D O I
10.1038/mt.2012.126
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
The Sleeping Beauty (SB) transposon is a nonviral, integrating vector system with proven efficacy in preclinical animal models, and thus holds promise for future clinical applications. However, SB has a close-to-random insertion profile that could lead to genotoxic effects, thereby presenting a potential safety issue. We evaluated zinc finger (ZF) DNA-binding domains (DBDs) for their abilities to introduce a bias into SB's insertion profile. E2C, that binds a unique site in the erbB-2 gene, mediated locus-specific transposon insertions at low frequencies. A novel ZF targeting LINE1 repeats, ZF-B, showed specific binding to an 18-bp site represented by similar to 12,000 copies in the human genome. We mapped SB insertions using linear-amplification (LAM)-PCR and Illumina sequencing. Targeted insertions with ZF-B peaked at approximately fourfold enrichment of transposition around ZF-B binding sites yielding similar to 45% overall frequency of insertion into LINE1. A decrease in the ZF-B dataset with respect to transposon insertions in genes was found, suggesting that LINE1 repeats act as a sponge that "soak up" a fraction of SB insertions and thereby redirect them away from genes. Improvements in ZF technology and a careful choice of targeted genomic regions may improve the safety profile of SB for future clinical applications.
引用
收藏
页码:1852 / 1862
页数:11
相关论文
共 49 条
[1]   A DNA transposon-based approach to functional screening in neural stem cells [J].
Albieri, Ilaria ;
Onorati, Marco ;
Calabrese, Giovanna ;
Moiana, Alessia ;
Biasci, Daniele ;
Badaloni, Aurora ;
Camnasio, Stefano ;
Spiliotopoulos, Dimitrios ;
Ivics, Zoltan ;
Cattaneo, Elena ;
Consalez, G. Giacomo .
JOURNAL OF BIOTECHNOLOGY, 2010, 150 (01) :11-21
[2]   Custom zinc-finger nucleases for use in human cells [J].
Alwin, S ;
Gere, MB ;
Guhl, E ;
Effertz, K ;
Barbas, CF III ;
Sega, DJ ;
Weitzman, MD ;
Cathomen, T .
MOLECULAR THERAPY, 2005, 12 (04) :610-617
[3]   Chance or necessity? Insertional mutagenesis in gene therapy and its consequences [J].
Baum, C ;
von Kalle, C ;
Staal, FJT ;
Li, ZX ;
Fehse, B ;
Schmidt, M ;
Weerkamp, F ;
Karlsson, S ;
Wagemaker, G ;
Williams, DA .
MOLECULAR THERAPY, 2004, 9 (01) :5-13
[4]   Toward controlling gene expression at will:: Specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks [J].
Beerli, RR ;
Segal, DJ ;
Dreier, B ;
Barbas, CF .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (25) :14628-14633
[5]   L1 (LINE-1) retrotransposon evolution and amplification in recent human history [J].
Boissinot, S ;
Chevret, P ;
Furano, AV .
MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (06) :915-928
[6]   TETHERING HUMAN-IMMUNODEFICIENCY-VIRUS-1 INTEGRASE TO A DNA SITE DIRECTS INTEGRATION TO NEARBY SEQUENCES [J].
BUSHMAN, FD .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (20) :9233-9237
[7]   Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites [J].
Bushman, FD ;
Miller, MD .
JOURNAL OF VIROLOGY, 1997, 71 (01) :458-464
[8]   A chimeric protein containing the N terminus of the adeno-associated virus rep protein recognizes its target site in an in vivo assay [J].
Cathomen, T ;
Collete, D ;
Weitzman, MD .
JOURNAL OF VIROLOGY, 2000, 74 (05) :2372-2382
[9]   Modulating target site selection during human immunodeficiency virus DNA integration in vitro with an engineered tethering factor [J].
Ciuffi, Angela ;
Diamond, Tracy L. ;
Hwang, Young ;
Marshall, Heather M. ;
Bushman, Frederic D. .
HUMAN GENE THERAPY, 2006, 17 (09) :960-967
[10]   Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains [J].
Cuddapah, Suresh ;
Jothi, Raja ;
Schones, Dustin E. ;
Roh, Tae-Young ;
Cui, Kairong ;
Zhao, Keji .
GENOME RESEARCH, 2009, 19 (01) :24-32