CRISPR/Cas9-mediated genome engineering: An adeno-associated viral (AAV) vector toolbox

Biotechnology Journal

Volumn 9, Issue 11, 2014, Pages 1402-1412

  Senís, Elena ^a   Fatouros, Chronis ^a   Große, Stefanie ^a   Wiedtke, Ellen ^a   Niopek, Dominik ^b   Mueller, Ann Kristin ^a   Börner, Kathleen ^a,c   Grimm, Dirk ^a  

^a UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c German Centre for Infection Research (DZIF)   (Germany)

Author keywords

AAV; CRISPR; Gene editing; Genome engineering; Viral vectors

Indexed keywords

CLONE CELLS; MACHINERY; MAMMALS; RNA; VECTORS; VIRUSES;

ADENO-ASSOCIATED VIRUS; BROAD APPLICATION; CLINICAL TRANSLATION; CRISPR; EUKARYOTIC CELLS; GENOME ENGINEERING; INDUCED MUTATIONS; VIRAL VECTORS;

GENES;

CASPASE 9; DEOXYRIBONUCLEASE I; GUIDE RNA; MICRORNA 122; PARVOVIRUS VECTOR; MICRORNA; MIRN122 MICRORNA, HUMAN;

ADULT; ANIMAL EXPERIMENT; ARTICLE; CLONING; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; CRISPR CAS SYSTEM; EUKARYOTIC CELL; GENE MUTATION; GENE TARGETING; GENETIC ENGINEERING; GENETIC TRANSDUCTION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; JURKAT CELL LINE; LIVER CELL; MOUSE; NONHUMAN; NUCLEOTIDE BINDING SITE; PROMOTER REGION; PROTEIN EXPRESSION; SOUTHERN BLOTTING; T LYMPHOCYTE; VIRAL GENE DELIVERY SYSTEM; VIRUS CAPSID; ANIMAL; BINDING SITE; DEPENDOPARVOVIRUS; GENE VECTOR; GENETICS; HEK293 CELL LINE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES;

ANIMALS; BASE SEQUENCE; BINDING SITES; CRISPR-CAS SYSTEMS; DEPENDOVIRUS; GENETIC ENGINEERING; GENETIC VECTORS; HEK293 CELLS; HUMANS; MICE; MICRORNAS; MOLECULAR SEQUENCE DATA;

EID: 84908382195     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201400046     Document Type: Article

References (41)

1. Kim, H., Kim, J. S., A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 2014, 15, 321-334.
2. Kakarougkas, A., Jeggo, P. A., DNA DSB repair pathway choice: An orchestrated handover mechanism. Br. J. Radiol. 2014, 87, 20130685.
3. Mali, P., Yang, L., Esvelt, K. M., Aach, J. et al., RNA-guided human genome engineering via Cas9. Science 2013, 339, 823-826.
4. Cong, L., Ran, F. A., Cox, D., Lin, S. et al., Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339, 819-823.
5. Sander, J. D., Joung, J. K., CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 2014, 32, 347-355.
6. Wiedenheft, B., Sternberg, S. H., Doudna, J. A., RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012, 482, 331-338.
7. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M. et al., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337, 816-821.
8. Chylinski, K., Le Rhun, A., Charpentier, E., The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol. 2013, 10, 726-737.
9. Mali, P., Esvelt, K. M., Church, G. M., Cas9 as a versatile tool for engineering biology. Nat. Methods 2013, 10, 957-963.
10. Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A. et al., Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152, 1173-1183.
11. Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L. et al., Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 2013, 31, 227-229.
12. DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X. et al., Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013, 41, 4336-4343.
13. Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M. et al., One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 2013, 153, 910-918.
14. Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X. et al., Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 2013, 343, 84-87.
15. Wang, T., Wei, J. J., Sabatini, D. M., Lander, E. S., Genetic screens in human cells using the CRISPR/Cas9 system. Science 2013, 343, 80-84.
16. Grimm, D., Kay, M. A., From virus evolution to vector revolution: Use of naturally occurring serotypes of adeno-associated virus (AAV) as novel vectors for human gene therapy. Curr. Gene Ther. 2003, 3, 281-304.
17. Muller, O. J., Kaul, F., Weitzman, M. D., Pasqualini, R. et al., Random peptide libraries displayed on adeno-associated virus to select for targeted gene therapy vectors. Nat. Biotechnol. 2003, 21, 1040-1046.
18. Li, M., Jayandharan, G. R., Li, B., Ling, C. et al., High-efficiency transduction of fibroblasts and mesenchymal stem cells by tyrosine-mutant AAV2 vectors for their potential use in cellular therapy. Hum. Gene Ther. 2010, 21, 1527-1543.
19. Grimm, D., Lee, J. S., Wang, L., Desai, T. et al., In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno-associated viruses. J. Virol. 2008, 82, 5887-5911.
20. Filipowicz, W., Grosshans, H., The liver-specific microRNA miR-122: Biology and therapeutic potential. Prog. Drug Res. 2011, 67, 221-238.
21. Sander, J. D., Maeder, M. L., Reyon, D., Voytas, D. F. et al., ZiFiT (zinc finger targeter): An updated zinc finger engineering tool. Nucleic Acids Res. 2010, 38, W462-W468.
22. Maeder, M. L., Thibodeau-Beganny, S., Sander, J. D., Voytas, D. F., Joung, J. K., Oligomerized pool engineering (OPEN): An "open-source" protocol for making customized zinc-finger arrays. Nat. Protocols 2009, 4, 1471-1501.
23. Sander, J. D., Cade, L., Khayter, C., Reyon, D. et al., Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat. Biotechnol. 2011, 29, 697-698.
24. Börner, K., Niopek, D., Cotugno, G., Kaldenbach, M. et al., Robust RNAi enhancement via human Argonaute-2 overexpression from plasmids, viral vectors and cell lines. Nucleic Acids Res. 2013, 41, e199.
25. Grimm, D., Production methods for gene transfer vectors based on adeno-associated virus serotypes. Methods 2002, 28, 146-157.
26. Grimm, D., Kern, A., Rittner, K., Kleinschmidt, J. A., Novel tools for production and purification of recombinant adenoassociated virus vectors. Hum. Gene Ther. 1998, 9, 2745-2760.
27. Schwank, G., Koo, B.-K., Sasselli, V., Dekkers, J. F. et al., Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell 2013, 13, 653-658.
28. Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y. et al., Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 2004, 15, 185-197.
29. Grimm, D., Wang, L., Lee, J. S., Schurmann, N. et al., Argonaute proteins are key determinants of RNAi efficacy, toxicity, and persistence in the adult mouse liver. J. Clin. Invest. 2010, 120, 3106-3119.
30. Grimm, D., Streetz, K. L., Jopling, C. L., Storm, T. A. et al., Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006, 441, 537-541.
31. Grimm, D., Zhou, S., Nakai, H., Thomas, C. E. et al., Preclinical in vivo evaluation of pseudotyped adeno-associated virus vectors for liver gene therapy. Blood 2003, 102, 2412-2419.
32. Cho, S. W., Kim, S., Kim, Y., Kweon, J. et al., Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014, 24, 132-141.
33. Kuscu, C., Arslan, S., Singh, R., Thorpe, J., Adli, M., Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 2014, 32, 677-683.
34. Veres, A., Gosis, B. S., Ding, Q., Collins, R. et al., Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 2014, 15, 27-30.
35. Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C. et al., Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 2014, 32, 670-676.
36. Nathwani, A. C., Tuddenham, E. G., Rangarajan, S., Rosales, C. et al., Adenovirus-associated virus vector-mediated gene transfer in hemophilia B. N. Engl. J. Med. 2011, 365, 2357-2365.
37. Chen, B., Gilbert, L. A., Cimini, B. A., Schnitzbauer, J. et al., Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 2013, 155, 1479-1491.
38. High, K. H., Nathwani, A., Spencer, T., Lillicrap, D. et al., Current status of haemophilia gene therapy. Haemophilia 2014, 20, 43-49.
39. Dalkara, D., Sahel, J. A., Gene therapy for inherited retinal degenerations. C. R. Biol. 2014, 337, 185-192.
40. Colella, P., Trapani, I., Cesi, G., Sommella, A. et al., Efficient gene delivery to the cone-enriched pig retina by dual AAV vectors. Gene Ther. 2014, 21, 450-456.
41. Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., Joung, J. K., Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 2014, 32, 279-284.