Correction: Stem cell-derived clade F AAVs mediate high-efficiency homologous recombination-based genome editing (Proceedings of the National Academy of Sciences of the United States of America (2018) 115 (E7379-E7388) DOI: 10.1073/pnas.1802343115);Stem cell-derived clade F AAVs mediate high-efficiency homologous recombination-based genome editing

Proceedings of the National Academy of Sciences of the United States of America

Volumn 115, Issue 31, 2018, Pages E7379-E7388

  Smith, Laura J ^a   Wright, Jason ^b   Clark, Gabriella ^a   Ul Hasan, Taihra ^a   Jin, Xiangyang ^a   Fong, Abigail ^a   Chandra, Manasa ^a   St Martin, Thia ^b   Rubin, Hillard ^b   Knowlton, David ^b   Ellsworth, Jeff L ^b   Fong, Yuman ^a   Wong, Kamehameha K ^a   Chatterjee, Saswati ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^b Homology Medicines Inc   (United States)

Author keywords

Adeno associated virus; Genome editing; Hematopoietic stem cells; Homologous recombination; In vivo genome editing

Indexed keywords

BRCA2 PROTEIN; BRCA2 PROTEIN, HUMAN; IL2RG PROTEIN, HUMAN; INTERLEUKIN 2 RECEPTOR GAMMA;

ADENO ASSOCIATED VIRUS; ANIMAL EXPERIMENT; ARTICLE; CLADISTICS; COMPLEMENTARY HOMOLOGY; CONTROLLED STUDY; ENDOTHELIUM CELL; EVOLUTIONARY HOMOLOGY; GENE; GENE EDITING; GENE LOCUS; HEMATOPOIETIC STEM CELL; HEMATOPOIETIC STEM CELL DERIVED ADENO ASSOCIATED VIRUS VECTOR; HOMOLOGOUS RECOMBINATION; HUMAN; HUMAN CELL; HUMAN GENOME; IL2RG GENE; IN VIVO STUDY; INDEL MUTATION; INVERTED TERMINAL REPEAT; LIVER CELL; MOUSE; MUSCLE CELL; NONHUMAN; PRIORITY JOURNAL; VIRUS INCLUSION; DEPENDOPARVOVIRUS; GENE VECTOR; GENETICS; K-562 CELL LINE; METABOLISM; PHYSIOLOGY;

BRCA2 PROTEIN; DEPENDOVIRUS; GENE EDITING; GENETIC VECTORS; HEMATOPOIETIC STEM CELLS; HOMOLOGOUS RECOMBINATION; HUMANS; INTERLEUKIN RECEPTOR COMMON GAMMA SUBUNIT; K562 CELLS;

EID: 85051815326     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1819306115     Document Type: Erratum

References (77)

1. Jasin M (1996) Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet 12:224–228.
2. Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW (1983) The double-strand-break repair model for recombination. Cell 33:25–35.
3. Pâques F, Haber JE (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 63:349–404.
4. Bibikova M, Golic M, Golic KG, Carroll D (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161:1169–1175.
5. Zhang F, et al. (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 29:149–153.
6. Miller JC, et al. (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–148.
7. Mali P, et al. (2013) RNA-guided human genome engineering via Cas9. Science 339: 823–826.
8. Cong L, et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823.
9. Jinek M, et al. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821.
10. Zetsche B, et al. (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771.
11. Lieber MR (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79:181–211.
12. Jeggo PA (1998) DNA breakage and repair. Adv Genet 38:185–218.
13. Daya S, Cortez N, Berns KI (2009) Adeno-associated virus site-specific integration is mediated by proteins of the nonhomologous end-joining pathway. J Virol 83:11655–11664.
14. Rudin N, Haber JE (1988) Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences. Mol Cell Biol 8:3918–3928.
15. Capecchi MR (1989) Altering the genome by homologous recombination. Science 244: 1288–1292.
16. Rouet P, Smih F, Jasin M (1994) Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc Natl Acad Sci USA 91:6064–6068.
17. Hustedt N, Durocher D (2016) The control of DNA repair by the cell cycle. Nat Cell Biol 19:1–9.
18. Cox DB, Platt RJ, Zhang F (2015) Therapeutic genome editing: Prospects and challenges. Nat Med 21:121–131.
19. Fu Y, et al. (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31:822–826.
20. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M (2014) Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 32: 677–683.
21. Tsai SQ, et al. (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33:187–197.
22. Ran FA, et al. (2015) In vivo genome editing using Staphylococcus aureus Cas9. Nature 520:186–191.
23. Komor AC, Badran AH, Liu DR (2017) CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell 169:559,
24. erratum (2017) 168:20–36.
25. Russell DW, Hirata RK (1998) Human gene targeting by viral vectors. Nat Genet 18: 325–330.
26. Porteus MH, Cathomen T, Weitzman MD, Baltimore D (2003) Efficient gene targeting mediated by adeno-associated virus and DNA double-strand breaks. Mol Cell Biol 23: 3558–3565.
27. Vasileva A, Linden RM, Jessberger R (2006) Homologous recombination is required for AAV-mediated gene targeting. Nucleic Acids Res 34:3345–3360.
28. Barzel A, et al. (2015) Promoterless gene targeting without nucleases ameliorates haemophilia B in mice. Nature 517:360–364.
29. Miller DG, et al. (2006) Gene targeting in vivo by adeno-associated virus vectors. Nat Biotechnol 24:1022–1026.
30. Khan IF, Hirata RK, Russell DW (2011) AAV-mediated gene targeting methods for human cells. Nat Protoc 6:482–501.
31. Smith LJ, et al. (2014) Gene transfer properties and structural modeling of human stem cell-derived AAV. Mol Ther 22:1625–1634.
32. Podsakoff G, Wong KK, Jr, Chatterjee S (1994) Efficient gene transfer into nondividing cells by adeno-associated virus-based vectors. J Virol 68:5656–5666.
33. Santat L, et al. (2005) Recombinant AAV2 transduction of primitive human hematopoietic stem cells capable of serial engraftment in immune-deficient mice. Proc Natl Acad Sci USA 102:11053–11058.
34. Zincarelli C, Soltys S, Rengo G, Rabinowitz JE (2008) Analysis of AAV serotypes 1-9 mediated gene expression and tropism in mice after systemic injection. Mol Ther 16: 1073–1080.
35. Chatterjee S, Johnson PR, Wong KK, Jr (1992) Dual-target inhibition of HIV-1 in vitro by means of an adeno-associated virus antisense vector. Science 258:1485–1488.
36. Fisher-Adams G, Wong KK, Jr, Podsakoff G, Forman SJ, Chatterjee S (1996) Integration of adeno-associated virus vectors in CD34+ human hematopoietic progenitor cells after transduction. Blood 88:492–504.
37. Paz H, et al. (2007) Quiescent subpopulations of human CD34-positive hematopoietic stem cells are preferred targets for stable recombinant adeno-associated virus type 2 transduction. Hum Gene Ther 18:614–626.
38. Kotin RM, et al. (1990) Site-specific integration by adeno-associated virus. Proc Natl Acad Sci USA 87:2211–2215.
39. Zhong L, et al. (2004) Impaired nuclear transport and uncoating limit recombinant adeno-associated virus 2 vector-mediated transduction of primary murine hematopoietic cells. Hum Gene Ther 15:1207–1218.
40. Ponnazhagan S, et al. (1997) Adeno-associated virus type 2-mediated transduction in primary human bone marrow-derived CD34+ hematopoietic progenitor cells: Donor variation and correlation of transgene expression with cellular differentiation. J Virol 71:8262–8267.
41. Mroske C, Rivera H, Ul-Hasan T, Chatterjee S, Wong KK (2012) A capillary electrophoresis sequencing method for the identification of mutations in the inverted terminal repeats of adeno-associated virus. Hum Gene Ther Methods 23:128–136.
42. Sargent RG, Brenneman MA, Wilson JH (1997) Repair of site-specific double-strand breaks in a mammalian chromosome by homologous and illegitimate recombination. Mol Cell Biol 17:267–277.
43. Pipiras E, Coquelle A, Bieth A, Debatisse M (1998) Interstitial deletions and intra-chromosomal amplification initiated from a double-strand break targeted to a mammalian chromosome. EMBO J 17:325–333.
44. Sherry ST, et al. (2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 29:308–311.
45. Genovese P, et al. (2014) Targeted genome editing in human repopulating haema-topoietic stem cells. Nature 510:235–240.
46. Miyaoka Y, et al. (2016) Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Sci Rep 6:23549.
47. Hirata RK, Russell DW (2000) Design and packaging of adeno-associated virus gene targeting vectors. J Virol 74:4612–4620.
48. Powell SN, Kachnic LA (2003) Roles of BRCA1 and BRCA2 in homologous recombination, DNA replication fidelity and the cellular response to ionizing radiation. Oncogene 22:5784–5791.
49. Oettinger MA, Schatz DG, Gorka C, Baltimore D (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248:1517–1523.
50. Liu P, et al. (1993) Regional mapping of human DNA excision repair gene ERCC4 to chromosome 16p13.13-p13.2. Mutagenesis 8:199–205.
51. Meyn MS (1995) Ataxia-telangiectasia and cellular responses to DNA damage. Cancer Res 55:5991–6001.
52. Tauchi H, et al. (2002) Nbs1 is essential for DNA repair by homologous recombination in higher vertebrate cells. Nature 420:93–98.
53. Ellis NA, et al. (1995) The Bloom’s syndrome gene product is homologous to RecQ helicases. Cell 83:655–666.
54. Joenje H, et al. (1997) Evidence for at least eight Fanconi anemia genes. Am J Hum Genet 61:940–944.
55. Joenje H, et al. (2000) Complementation analysis in Fanconi anemia: Assignment of the reference FA-H patient to group A. Am J Hum Genet 67:759–762.
56. Meetei AR, et al. (2004) X-linked inheritance of Fanconi anemia complementation group B. Nat Genet 36:1219–1224.
57. Ikeda H, et al. (2003) Genetic reversion in an acute myelogenous leukemia cell line from a Fanconi anemia patient with biallelic mutations in BRCA2. Cancer Res 63: 2688–2694.
58. Takata M, et al. (2006) The Fanconi anemia pathway promotes homologous recombination repair in DT40 cell line. Subcell Biochem 40:295–311.
59. Michl J, Zimmer J, Tarsounas M (2016) Interplay between Fanconi anemia and homologous recombination pathways in genome integrity. EMBO J 35:909–923.
60. Strathdee CA, Gavish H, Shannon WR, Buchwald M (1992) Cloning of cDNAs for Fanconi’s anaemia by functional complementation. Nature 356:763–767.
61. Moynahan ME, Pierce AJ, Jasin M (2001) BRCA2 is required for homology-directed repair of chromosomal breaks. Mol Cell 7:263–272.
62. Davies AA, et al. (2001) Role of BRCA2 in control of the RAD51 recombination and DNA repair protein. Mol Cell 7:273–282.
63. Feng Z, et al. (2011) Rad52 inactivation is synthetically lethal with BRCA2 deficiency. Proc Natl Acad Sci USA 108:686–691.
64. Friedrich G, Soriano P (1991) Promoter traps in embryonic stem cells: A genetic screen to identify and mutate developmental genes in mice. Genes Dev 5:1513–1523.
65. Kisseberth WC, Brettingen NT, Lohse JK, Sandgren EP (1999) Ubiquitous expression of marker transgenes in mice and rats. Dev Biol 214:128–138.
66. Wang L, et al. (2015) Comparative study of liver gene transfer with AAV vectors based on natural and engineered AAV capsids. Mol Ther 23:1877–1887.
67. Smith L, et al. (2011) Functional mapping of tissue tropism of naturally occurring adeno-associated virus isolates from human hematopoietic stem cells. Mol Ther 19(Suppl 1):S127–S128.
68. Paulk NK, et al. (2010) Adeno-associated virus gene repair corrects a mouse model of hereditary tyrosinemia in vivo. Hepatology 51:1200–1208.
69. Borel F, et al. (2017) Survival advantage of both human hepatocyte xenografts and genome-edited hepatocytes for treatment of alpha-1 antitrypsin deficiency. Mol Ther 25:2477–2489.
70. Giel-Moloney M, Krause DS, Chen G, Van Etten RA, Leiter AB (2007) Ubiquitous and uniform in vivo fluorescence in ROSA26-EGFP BAC transgenic mice. Genesis 45:83–89.
71. Cataldi MP, McCarty DM (2010) Differential effects of DNA double-strand break repair pathways on single-strand and self-complementary adeno-associated virus vector genomes. J Virol 84:8673–8682.
72. Brown T (1993) Southern blotting. Curr Protoc Mol Biol 21:2.9.1–2.9.20.
73. Sather BD, et al. (2015) Efficient modification of CCR5 in primary human hematopoietic cells using a megaTAL nuclease and AAV donor template. Sci Transl Med 7: 307ra156.
74. Wang J, et al. (2015) Homology-driven genome editing in hematopoietic stem and progenitor cells using ZFN mRNA and AAV6 donors. Nat Biotechnol 33:1256–1263.
75. Wang J, et al. (2016) Highly efficient homology-driven genome editing in human T cells by combining zinc-finger nuclease mRNA and AAV6 donor delivery. Nucleic Acids Res 44:e30.
76. De Ravin SS, et al. (2016) Targeted gene addition in human CD34(+) hematopoietic cells for correction of X-linked chronic granulomatous disease. Nat Biotechnol 34: 424–429.
77. Ling C, et al. (2016) High-efficiency transduction of primary human hematopoietic stem/progenitor cells by AAV6 vectors: Strategies for overcoming donor-variation and implications in genome editing. Sci Rep 6:35495.