Site-specific integration and tailoring of cassette design for sustainable gene transfer

Nature Methods

Volumn 8, Issue 10, 2011, Pages 861-869

  Lombardo, Angelo ^a,b   Cesana, Daniela ^a,b   Genovese, Pietro ^a,b   Di Stefano, Bruno ^c,f   Provasi, Elena ^b,d   Colombo, Daniele F ^a,b   Neri, Margherita ^a,b   Magnani, Zulma ^d   Cantore, Alessio ^a,b   Lo Riso, Pietro ^a,b   Damo, Martina ^a,b   Pello, Oscar M ^a   Holmes, Michael C ^e   Gregory, Philip D ^e   Gritti, Angela ^a   Broccoli, Vania ^c   Bonini, Chiara ^d   Naldini, Luigi ^a,b  

^a SAN RAFFAELE SCIENTIFIC INSTITUTE   (Italy)

^b VITA SALUTE SAN RAFFAELE UNIVERSITY   (Italy)

^c San Raf faele Institute   (Italy)

^d SAN RAFFAELE HOSPITAL   (Italy)

^e SANGAMO BIOSCIENCES INC   (United States)

^f CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR CCR5; ZINC FINGER PROTEIN;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; EPIGENETICS; GENE CASSETTE; GENE LOCUS; GENE TRANSFER; GENETIC MANIPULATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; LYMPHOCYTE; MOUSE; NONHUMAN; PRIORITY JOURNAL; TRANSGENE;

DEPENDOVIRUS; GENE TRANSFER TECHNIQUES; HUMANS; MUTAGENESIS, INSERTIONAL; MUTAGENESIS, SITE-DIRECTED; RECEPTORS, CCR5; VIRUS INTEGRATION;

EID: 80053350622     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1674     Document Type: Article

References (45)

1. Ellis, J. Silencing and variegation of gammaretrovirus and lentivirus vectors. Hum. Gene Ther. 16, 1241-1246 (2005). (Pubitemid 41611651)
2. Naldini, L. Ex vivo gene transfer and correction for cellbased therapies. Nat. Rev. Genet. 12, 301-315 (2011).
3. Lombardo, A. et al. Gene editing in human stem cells using zinc finger nucleases and integrasedefective lentiviral vector delivery. Nat. Biotechnol. 25, 1298-1306 (2007). (Pubitemid 350076515)
4. Zou, J. et al. Gene targeting of a diseaserelated gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell 5, 97-110 (2009).
5. Maeder, M.L. et al. Rapid "opensource" engineering of customized zincfinger nucleases for highly efficient gene modification. Mol. Cell 31, 294-301 (2008). (Pubitemid 352001401)
6. Porteus, M.H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in human cells. Science 300, 763 (2003). (Pubitemid 36532103)
7. Carroll, D. Progress and prospects: zincfinger nucleases as gene therapy agents. Gene Ther. 15, 1463-1468 (2008).
8. Urnov, F.D., Rebar, E.J., Holmes, M.C., Zhang, H.S. & Gregory, P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 11, 636-646 (2010).
9. Gondo, Y., Fukumura, R., Murata, T. & Makino, S. Nextgeneration gene targeting in the mouse for functional genomics. BMB Rep. 42, 315-323 (2009).
10. Frazer, K.A., Murray, S.S., Schork, N.J. & Topol, E.J. Human genetic variation and its contribution to complex traits. Nat. Rev. Genet. 10, 241-251 (2009).
11. de Boer, B.A., Ruijter, J.M., Voorbraak, F.P. & Moorman, A.F. More than a decade of developmental gene expression atlases: where are we now? Nucleic Acids Res. 37, 7349-7359 (2009).
12. Cartier, N. et al. Hematopoietic stem cell gene therapy with a lentiviral vector in Xlinked adrenoleukodystrophy. Science 326, 818-823 (2009).
13. Aiuti, A. et al. Gene therapy for immunodeficiency due to adenosine deaminase deficiency. N. Engl. J. Med. 360, 447-458 (2009).
14. Samulski, R.J. et al. Targeted integration of adenoassociated virus (AAV) into human chromosome 19. EMBO J. 10, 3941-3950 (1991). (Pubitemid 21905423)
15. Liu, R. et al. Homozygous defect in HIV1 coreceptor accounts for resistance of some multiplyexposed individuals to HIV1 infection. Cell 86, 367-377 (1996). (Pubitemid 26272077)
16. Smith, J.R. et al. Robust, persistent transgene expression in human embryonic stem cells is achieved with AAVS1targeted integration. Stem Cells 26, 496-504 (2008). (Pubitemid 351413610)
17. Henckaerts, E. et al. Sitespecific integration of adenoassociated virus involves partial duplication of the target locus. Proc. Natl. Acad. Sci. USA 106, 7571-7576 (2009).
18. Hockemeyer, D. et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zincfinger nucleases. Nat. Biotechnol. 27, 851-857 (2009).
19. Zou, J. et al. Oxidase deficient neutrophils from Xlinked chronic granulomatous disease iPS cells: functional correction by zinc finger nuclease mediated safe harbor targeting. Blood 117, 5561-5572 (2011).
20. Matrai, J. et al. Hepatocytetargeted expression by integrasedefective lentiviral vectors induces antigenspecific tolerance in mice with low genotoxic risk. Hepatology 53, 1696-1707 (2011).
21. Hafenrichter, D.G. et al. Quantitative evaluation of liverspecific promoters from retroviral vectors after in vivo transduction of hepatocytes. Blood 84, 3394-3404 (1994). (Pubitemid 24352902)
22. Okuyama, T. et al. Liver-directed gene therapy: a retroviral vector with a complete LTR and the ApoE enhanceralpha 1antitrypsin promoter dramatically increases expression of human alpha 1antitrypsin in vivo. Hum. Gene Ther. 7, 637-645 (1996).
23. Miao, C.H. et al. Inclusion of the hepatic locus control region, an intron, and untranslated region increases and stabilizes hepatic factor IX gene expression in vivo but not in vitro. Mol. Ther. 1, 522-532 (2000).
24. Ogata, T., Kozuka, T. & Kanda, T. Identification of an insulator in AAVS1, a preferred region for integration of adenoassociated virus DNA. J. Virol. 77, 9000-9007 (2003). (Pubitemid 36936108)
25. Li, C. et al. A small regulatory element from chromosome 19 enhances liver-specific gene expression. Gene Ther. 16, 43-51 (2009).
26. Zhou, V.W., Goren, A. & Bernstein, B.E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12, 7-18 (2011).
27. CavazzanaCalvo, M. et al. Transfusion independence and HMGA2 activation after gene therapy of human betathalassaemia. Nature 467, 318-322 (2010).
28. Papapetrou, E.P. et al. Genomic safe harbors permit high beta-globin transgene expression in thalassemia induced pluripotent stem cells. Nat. Biotechnol. 29, 73-78 (2011).
29. Jacquier, A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 10, 833-844 (2009).
30. Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872 (2007). (Pubitemid 350138099)
31. Miller, J.C. et al. An improved zincfinger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778-785 (2007). (Pubitemid 47052191)
32. Bondanza, A. et al. Suicide gene therapy of graftversushost disease induced by central memory human T lymphocytes. Blood 107, 1828-1836 (2006). (Pubitemid 43289360)
33. Kaneko, S. et al. IL7 and IL15 allow the generation of suicide genemodified alloreactive selfrenewing central memory human T lymphocytes. Blood 113, 1006-1015 (2009).
34. Riddell, S.R. & Greenberg, P.D. The use of antiCD3 and antiCD28 monoclonal antibodies to clone and expand human antigenspecific T cells. J. Immunol. Methods 128, 189-201 (1990). (Pubitemid 20120262)
35. Vescovi, A.L. et al. Isolation and cloning of multipotential stem cells from the embryonic human CNS and establishment of transplantable human neural stem cell lines by epigenetic stimulation. Exp. Neurol. 156, 71-83 (1999). (Pubitemid 29152984)
36. Vescovi, A.L. & Snyder, E.Y. Establishment and properties of neural stem cell clones: plasticity in vitro and in vivo. Brain Pathol. 9, 569-598 (1999). (Pubitemid 29316294)
37. Neri, M. et al. Efficient in vitro labeling of human neural precursor cells with superparamagnetic iron oxide particles: relevance for in vivo cell tracking. Stem Cells 26, 505-516 (2008). (Pubitemid 351413611)
38. Watanabe, K. et al. A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat. Biotechnol. 25, 681-686 (2007). (Pubitemid 46897207)
39. Roy, N.S. et al. Functional engraftment of human ES cellderived dopaminergic neurons enriched by coculture with telomeraseimmortalized midbrain astrocytes. Nat. Med. 12, 1259-1268 (2006). (Pubitemid 44706928)
40. Pfaffl, M.W. A new mathematical model for relative quantification in realtime RTPCR. Nucleic Acids Res. 29, e45 (2001).
41. Zhao, S. & Fernald, R.D. Comprehensive algorithm for quantitative real-time polymerase chain reaction. J. Comput. Biol. 12, 1047-1064 (2005). (Pubitemid 41580022)
42. Hellemans, J., Mortier, G., De Paepe, A., Speleman, F. & Vandesompele, J. qBase relative quantification framework and software for management and automated analysis of realtime quantitative PCR data. Genome Biol. 8, R19 (2007).
43. Lee, T.I., Johnstone, S.E. & Young, R.A. Chromatin immunoprecipitation and microarraybased analysis of protein location. Nat. Protoc. 1, 729-748 (2006).
44. Wuarin, J. & Schibler, U. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol. Cell Biol. 14, 7219-7225 (1994). (Pubitemid 24326386)
45. Masternak, K., Peyraud, N., Krawczyk, M., Barras, E. & Reith, W. Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nat. Immunol. 4, 132-137 (2003). (Pubitemid 36193014)