Insulated Foamy Viral Vectors

Human Gene Therapy

Volumn 27, Issue 3, 2016, Pages 255-266

  Browning, Diana L ^a   Collins, Casey P ^b   Hocum, Jonah D ^b   Leap, David J ^b   Rae, Dustin T ^b   Trobridge, Grant D ^a,b  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CCAAT BINDING FACTOR; CCAAT BOX BINDING TRANSCRIPTION FACTOR NUCLEAR FACTOR I INSULATED VIRAL VECTOR; HYPERSENSITIVITY SITE 4 INSULATED VIRAL VECTOR; NUCLEAR FACTOR I; RETROVIRUS VECTOR; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR CTCF INSULATED VIRAL VECTOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; COPY NUMBER VARIATION; FIBROBLAST; GENOTOXICITY; HEMATOPOIETIC STEM CELL; HUMAN; HUMAN CELL; INSULATOR ELEMENT; LONG TERMINAL REPEAT; PLASMID; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION; SHUTTLE VECTOR; SPUMAVIRUS; UMBILICAL CORD BLOOD; VIRAL GENE DELIVERY SYSTEM; ADVERSE EFFECTS; CELL LINE; ENHANCER REGION; GENE ORDER; GENE TRANSFER; GENE VECTOR; GENETIC TRANSDUCTION; GENETICS; METABOLISM; REPORTER GENE; VIRUS DNA CELL DNA INTERACTION; VIRUS REPLICATION;

CELL LINE; ENHANCER ELEMENTS, GENETIC; GENE ORDER; GENE TRANSFER TECHNIQUES; GENES, REPORTER; GENETIC VECTORS; HEMATOPOIETIC STEM CELLS; HUMANS; INSULATOR ELEMENTS; PLASMIDS; SPUMAVIRUS; TRANSDUCTION, GENETIC; VIRUS INTEGRATION; VIRUS REPLICATION;

EID: 84962050350     PISSN: 10430342     EISSN: 15577422     Source Type: Journal    
DOI: 10.1089/hum.2015.110     Document Type: Article

References (68)

1. Bordignon C, Notarangelo LD, Nobili N, et al. Gene therapy in peripheral blood lymphocytes and bone marrow for ADA-immunodeficient patients. Science 1995;270:470-475.
2. Hacein-Bey-Abina S, Le Deist F, Carlier F, et al. Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy. N Engl J Med 2002;346:1185-1193.
3. Wang GP, Berry CC, Malani N, et al. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood 2010;115:4356-4366.
4. Cavazzana-Calvo M, Payen E, Negre O, et al. Transfusion independence and HMGA2 activation after gene therapy of human b-thalassaemia. Nature 2010;467:318-322.
5. Santilli G, Almarza E, Brendel C, et al. Biochemical correction of X-CGD by a novel chimeric promoter regulating high levels of transgene expression in myeloid cells. Mol Ther 2011;19:122-132.
6. Aiuti A, Biasco L, Scaramuzza S, et al. Lentiviral hematopoietic stem cell gene therapy in patients with Wiskott-Aldrich syndrome. Science 2013;341: 1233151.
7. Hacein-Bey-Abina S, von Kalle C, Schmidt M, et al. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. N Engl J Med 2003;348:255-256.
8. Hacein-Bey-Abina S, Garrigue A, Wang GP, et al. Insertional oncogenesis in 4 patients after retrovirusmediated gene therapy of SCID-X1. J Clin Invest 2008;118:3132-3142.
9. Li Z, Dullmann J, Schiedlmeier B, et al. Murine leukemia induced by retroviral gene marking. Science 2002;296:497.
10. Braun CJ, Boztug K, Paruzynski A, et al. Gene therapy for Wiskott-Aldrich syndrome - long-term efficacy and genotoxicity. Sci Transl Med 2014;6: 227-233.
11. Howe SJ, Mansour MR, Schwarzwaelder K, et al. Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis after gene therapy of SCID-X1 patients. J Clin Invest 2008;118:3143-3150.
12. Ott MG, Schmidt M, Schwarzwaelder K, et al. Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1. Nat Med 2006;12:401-409.
13. Zychlinski D, Schambach A, Modlich U, et al. Physiological promoters reduce the genotoxic risk of integrating gene vectors. Mol Ther 2008;16: 718-725.
14. Bokhoven M, Stephen SL, Knight S, et al. Insertional gene activation by lentiviral and gammaretroviral vectors. J Virol 2009;83:283-294.
15. Bosticardo M, Ghosh A, Du Y, et al. Selfinactivating retroviral vector-mediated gene transfer induces oncogene activation and immortalization of primary murine bone marrow cells. Mol Ther 2009;17:1910-1918.
16. Trobridge GD. Genotoxicity of retroviral hematopoietic stem cell gene therapy. Exp Opin Biol Ther 2011;11:581-593.
17. Trobridge G. Improved foamy virus vectors with minimal viral sequences. Mol Ther 2002;6:321-328.
18. Li CL, Xiong D, Stamatoyannopoulos G, et al. Genomic and functional assays demonstrate reduced gammaretroviral vector genotoxicity associated with use of the cHS4 chromatin insulator. Mol Ther 2009;17:716-724.
19. Coci EG, Maetzig T, Zychlinski D, et al. Novel selfinactivating vectors for reconstitution of Wiskott-Aldrich syndrome. Curr Gene Ther 2015;15:245-254.
20. Trobridge GD, Miller DG, Jacobs MA, et al. Foamy virus vector integration sites in normal human cells. Proc Natl Acad Sci U S A 2006;103:1498-1503.
21. Nowrouzi A, Dittrich M, Klanke C, et al. Genomewide mapping of foamy virus vector integrations into a human cell line. J Gen Virol 2006;87:1339-1347.
22. Deyle DR, Khan IF, Ren G, et al. Lack of genotoxicity due to foamy virus vector integration in human iPSCs. Gene Ther 2013;20:868-873.
23. Josephson NC, Vassilopoulos G, Trobridge GD, et al. Transduction of human NOD/SCID-repopulating cells with both lymphoid and myeloid potential by foamy virus vectors. Proc Natl Acad Sci U S A 2002;99: 8295-8300.
24. Nasimuzzaman M, Kim YS, Wang YD, et al. Hightiter foamy virus vector transduction and integration sites of human CD34+ cell-derived SCIDrepopulating cells. Mol Ther Methods Clin Dev 2014;1:14020.
25. Hendrie PC, Huo Y, Stolitenko RB, et al. A rapid and quantitative assay for measuring neighboring gene activation by vector proviruses. Mol Ther 2008;16:534-540.
26. Trobridge G, and Russell DW. Cell cycle requirements for transduction by foamy virus vectors compared with those of oncovirus and lentivirus vectors. J Virol 2004;78:2327-2335.
27. Emery DW. The use of chromatin insulators to improve the expression and safety of integrating gene transfer vectors. Hum Gene Ther 2011;22: 761-774.
28. Arumugam PI, Higashimoto T, Urbinati F, et al. Genotoxic potential of lineage-specific lentivirus vectors carrying the b-globin locus control region. Mol Ther 2009;17:1929-1937.
29. Neff T, Shotkoski F, and Stamatoyannopoulos G. Stem cell gene therapy, position effects and chromatin insulators. Stem Cells 1997;15(Suppl 1):265-271.
30. West AG, Gaszner M, and Felsenfeld G. Insulators: many functions, many mechanisms. Genes Dev 2002;16:271-288.
31. Burgess-Beusse B, Farrell C, Gaszner M, et al. The insulation of genes from external enhancers and silencing chromatin. Proc Natl Acad Sci U S A 2002;99:16433-16437.
32. Wallace JA, and Felsenfeld G. We gather together: insulators and genome organization. Curr Opin Genet Dev 2007;17:400-407.
33. Arumugam PI, Urbinati F, Velu CS, et al. The 3-region of the chicken hypersensitive site-4 insulator has properties similar to its core and is required for full insulator activity. PLoS One 2009;4:e6995.
34. Gaussin A, Modlich U, Bauche C, et al. CTF/NF1 transcription factors act as potent genetic insulators for integrating gene transfer vectors. Gene Ther 2012;19:15-24.
35. Chung JH, Whiteley M, and Felsenfeld G. A 5-element of the chicken b-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell 1993;74:505-514.
36. Chung JH, Bell AC, and Felsenfeld G. Characterization of the chicken b-globin insulator. Proc Natl Acad Sci U S A 1997;94:575-580.
37. Pankiewicz R, Karlen Y, Imhof MO, et al. Reversal of the silencing of tetracycline-controlled genes requires the coordinate action of distinctly acting transcription factors. J Gene Med 2005;7:117-132.
38. Ferrari S, Simmen KC, Dusserre Y, et al. Chromatin domain boundaries delimited by a histone-binding protein in yeast. J Biol Chem 2004;279:55520-55530.
39. Cesana D, Ranzani M, Volpin M, et al. Uncovering and dissecting the genotoxicity of self-inactivating lentiviral vectors in vivo. Mol Ther 2014;22:774-785.
40. Trobridge GD, Beard BC, Wu RA, et al. Stem cell selection in vivo using foamy vectors cures canine pyruvate kinase deficiency. PLoS One 2012;7:e45173.
41. Olszko ME, Adair JE, Linde I, et al. Foamy viral vector integration sites in SCID-repopulating cells after MGMTP140K-mediated in vivo selection. Gene Ther 2015;22:591-595.
42. Trobridge GD, Wu RA, Hansen M, et al. Cocalpseudotyped lentiviral vectors resist inactivation by human serum and efficiently transduce primate hematopoietic repopulating cells. Mol Ther 2010; 18:725-733.
43. Kiem HP, Wu RA, Sun G, et al. Foamy combinatorial anti-HIV vectors with MGMTP140K potently inhibit HIV-1 and SHIV replication and mediate selection in vivo. Gene Ther 2010;17:37-49.
44. Zhao C, Teng EM, Summers RG Jr, et al. Distinct morphological stages of dentate granule neuron maturation in the adult mouse hippocampus. J Neurosci 2006;26:3-11.
45. Beard BC, Adair JE, Trobridge GD, et al. Highthroughput genomic mapping of vector integration sites in gene therapy studies. Methods Mol Biol 2014;1185:321-344.
46. Rae DT, Collins CP, Hocum JD, et al. Modified genomic sequencing PCR using the MiSeq platform to identify retroviral integration sites. Hum Gene Ther Methods 2015:26:221-227.
47. Zhang J, Kobert K, Flouri T, et al. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 2014;30:614-620.
48. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
49. Hocum JD, Battrell LR, Maynard R, et al. VISA - Vector integration site analysis server: a webbased server to rapidly identify retroviral integration sites from next-generation sequencing. BMC Bioinformatics 2015;16:212.
50. Urbinati F, Arumugam P, Higashimoto T, et al. Mechanism of reduction in titers from lentivirus vectors carrying large inserts in the 3-LTR. Mol Ther 2009;17:1527-1536.
51. Ramezani A, Hawley TS, and Hawley RG. Combinatorial incorporation of enhancer-blocking components of the chicken b-globin 5-HS4 and human T-cell receptor a/d BEAD-1 insulators in selfinactivating retroviral vectors reduces their genotoxic potential. Stem Cells 2008;26:3257-3266.
52. Kim TH, Abdullaev ZK, Smith AD, et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007;128:1231-1245.
53. Hanawa H, Yamamoto M, Zhao H, et al. Optimized lentiviral vector design improves titer and transgene expression of vectors containing the chicken b-globin locus HS4 insulator element. Mol Ther 2009;17:667-674.
54. Emery DW, Yannaki E, Tubb J, et al. A chromatin insulator protects retrovirus vectors from chromosomal position effects. Proc Natl Acad Sci U S A 2000;97:9150-9155.
55. An W, and Telesnitsky A. Frequency of direct repeat deletion in a human immunodeficiency virus type 1 vector during reverse transcription in human cells. Virology 2001;286:475-482.
56. Nielsen TT, Jakobsson J, Rosenqvist N, et al. Incorporating double copies of a chromatin insulator into lentiviral vectors results in less viral integrants. BMC Biotechnology 2009;9:13.
57. Breda L, Casu C, Gardenghi S, et al. Therapeutic hemoglobin levels after gene transfer in bthalassemia mice and in hematopoietic cells of bthalassemia and sickle cells disease patients. PLoS One 2012;7:e32345.
58. FitzGerald TJ, Henault S, Sakakeeny M, et al. Expression of transfected recombinant oncogenes increases radiation resistance of clonal hematopoietic and fibroblast cell lines selectively at clinical low dose rate. Radiation Res 1990;122:44-52.
59. Modlich U, Navarro S, Zychlinski D, et al. Insertional transformation of hematopoietic cells by self-inactivating lentiviral and gammaretroviral vectors. Mol Ther 2009;17:1919-1928.
60. Cattoglio C, Facchini G, Sartori D, et al. Hot spots of retroviral integration in human CD34+ hematopoietic cells. Blood 2007;110:1770-1778.
61. Suzuki T, Shen H, Akagi K, et al. New genes involved in cancer identified by retroviral tagging. Nat Genet 2002;32:166-174.
62. Liu M, Maurano MT, Wang H, et al. Genomic discovery of potent chromatin insulators for human gene therapy. Nat Biotechnol 2015;33:198-203.
63. Nakahashi H, Kwon KR, Resch W, et al. A genomewide map of CTCF multivalency redefines the CTCF code. Cell Rep 2013;3:1678-1689.
64. Rhee HS, and Pugh BF. Comprehensive genomewide protein-DNA interactions detected at singlenucleotide resolution. Cell 2011;147:1408-1419.
65. Chen H, Tian Y, Shu W, et al. Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PLoS One 2012;7:e41374.
66. Kiem HP, Allen J, Trobridge G, et al. Foamy-virusmediated gene transfer to canine repopulating cells. Blood 2007;109:65-70.
67. Malik P, and Arumugam PI. Gene therapy for bthalassemia. Hematology Am Soc Hematol Educ Program 2005:45-50.
68. Hunter MJ, Zhao H, Tuschong LM, et al. Gene therapy for canine leukocyte adhesion deficiency with lentiviral vectors using the murine stem cell virus and human phosphoglycerate kinase promoters. Hum Gene Ther 2011;22:689-696.