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Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System

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Abstract

Genome engineering and human iPS cells are two powerful technologies, which can be combined to highlight phenotypic differences and identify pathological mechanisms of complex diseases by providing isogenic cellular material. However, very few data are available regarding precise gene correction in human iPS cells. Here, we describe an optimized stepwise protocol to deliver CRISPR/Cas9 plasmids in human iPS cells. We highlight technical issues especially those associated to human stem cell culture and to the correction of a point mutation to obtain isogenic iPS cell line, without inserting any resistance cassette. Based on a two-steps clonal isolation protocol (mechanical picking followed by enzymatic dissociation), we succeed to select and expand corrected human iPS cell line with a great efficiency (more than 2 % of the sequenced colonies). This protocol can also be used to obtain knock-out cell line from healthy iPS cell line by the NHEJ pathway (with about 15 % efficiency) and reproduce disease phenotype. In addition, we also provide protocols for functional validation tests after every critical step.

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References

  1. Sebat, J., Levy, D. L., & McCarthy, S. E. (2009). Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders. Trends in Genetics, 25, 528–535.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. Dipple, K. M., & McCabe, E. R. (2000). Phenotypes of patients with “simple” Mendelian disorders are complex traits: thresholds, modifiers, and systems dynamics. American Journal of Human Genetics, 66, 1729–1735.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Musunuru, K. (2013). Genome editing of human pluripotent stem cells to generate human cellular disease models. Disease Models & Mechanisms, 6, 896–904.

    Article  CAS  Google Scholar 

  4. Kim, H., Jang, M. J., Kang, M. J., & Han, Y. M. (2011). Epigenetic signatures and temporal expression of lineage-specific genes in hESCs during differentiation to hepatocytes in vitro. Human Molecular Genetics, 20, 401–412.

    Article  CAS  PubMed  Google Scholar 

  5. Lister, R., Pelizzola, M., Kida, Y. S., et al. (2011). Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature, 471, 68–73.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Ruiz, S., Diep, D., Gore, A., et al. (2012). Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proceedings of the National Academy of Sciences of the United States of America, 109, 16196–16201.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Zwaka, T. P., & Thomson, J. A. (2003). Homologous recombination in human embryonic stem cells. Nature Biotechnology, 21, 319–321.

    Article  CAS  PubMed  Google Scholar 

  8. Placantonakis, D. G., Tomishima, M. J., Lafaille, F., et al. (2009). BAC transgenesis in human embryonic stem cells as a novel tool to define the human neural lineage. Stem Cells, 27, 521–532.

    Article  CAS  PubMed  Google Scholar 

  9. Song, H., Chung, S. K., & Xu, Y. (2010). Modeling disease in human ESCs using an efficient BAC-based homologous recombination system. Cell Stem Cell, 6, 80–89.

    Article  CAS  PubMed  Google Scholar 

  10. Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., & Doudna, J. (2013). RNA-programmed genome editing in human cells. eLife, 2, e00471.

    Article  PubMed Central  PubMed  Google Scholar 

  11. Cong, L., Ran, F. A., Cox, D., et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science (New York, NY), 339, 819–823.

    Article  CAS  Google Scholar 

  12. Mali, P., Yang, L., Esvelt, K. M., et al. (2013). RNA-guided human genome engineering via Cas9. Science (New York, NY), 339, 823–826.

    Article  CAS  Google Scholar 

  13. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (New York, NY), 337, 816–821.

    Article  CAS  Google Scholar 

  14. Lin, S., Staahl, B. T., Alla, R. K., & Doudna, J. A. (2014). Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife, 3, e04766.

    PubMed  Google Scholar 

  15. Chen, F., Pruett-Miller, S. M., Huang, Y., et al. (2011). High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nature Methods, 8, 753–755.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Doench, J. G., Hartenian, E., Graham, D. B., et al. (2014). Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nature Biotechnology, 32, 1262–1267.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Huang, X., Wang, Y., Yan, W., et al. (2015). Production of gene-corrected adult beta globin protein in human erythrocytes differentiated from patient iPSCs after genome editing of the sickle point mutation. Stem Cells, 33, 1470–1479.

    Article  CAS  PubMed  Google Scholar 

  18. Li, H. L., Fujimoto, N., Sasakawa, N., et al. (2015). Precise correction of the dystrophin gene in duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9. Stem Cell Reports, 4, 143–154.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Miyaoka, Y., Chan, A. H., Judge, L. M., et al. (2014). Isolation of single-base genome-edited human iPS cells without antibiotic selection. Nature Methods, 11, 291–293.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Reinhardt, P., Schmid, B., Burbulla, L. F., et al. (2013). Genetic correction of a LRRK2 mutation in human iPSCs links parkinsonian neurodegeneration to ERK-dependent changes in gene expression. Cell Stem Cell, 12, 354–367.

    Article  CAS  PubMed  Google Scholar 

  21. Soldner, F., Laganiere, J., Cheng, A. W., et al. (2011). Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell, 146, 318–331.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Ye, L., Wang, J., Beyer, A. I., et al. (2014). Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Delta32 mutation confers resistance to HIV infection. Proceedings of the National Academy of Sciences of the United States of America, 111, 9591–9596.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Yusa, K. (2013). Seamless genome editing in human pluripotent stem cells using custom endonuclease-based gene targeting and the piggyBac transposon. Nature Protocols, 8, 2061–2078.

    Article  CAS  PubMed  Google Scholar 

  24. Wen, Z., Nguyen, H. N., Guo, Z., et al. (2014). Synaptic dysregulation in a human iPS cell model of mental disorders. Nature, 515, 414–418.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Guschin, D. Y., Waite, A. J., Katibah, G. E., Miller, J. C., Holmes, M. C., & Rebar, E. J. (2010). A rapid and general assay for monitoring endogenous gene modification. Methods in Molecular Biology, 649, 247–256.

    Article  CAS  PubMed  Google Scholar 

  26. Froger, A., Hall, J. E. (2007). Transformation of plasmid DNA into E. coli using the heat shock method. Journal of Visualized Experiments: JoVE, 253.

  27. Vouillot, L., Thelie, A., & Pollet, N. (2015). Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3, 5, 407–415.

    Article  PubMed Central  PubMed  Google Scholar 

  28. Smithies, O., Gregg, R. G., Boggs, S. S., Koralewski, M. A., & Kucherlapati, R. S. (1985). Insertion of DNA sequences into the human chromosomal beta-globin locus by homologous recombination. Nature, 317, 230–234.

    Article  CAS  PubMed  Google Scholar 

  29. Hasty, P., Rivera-Perez, J., & Bradley, A. (1991). The length of homology required for gene targeting in embryonic stem cells. Molecular and Cellular Biology, 11, 5586–5591.

    PubMed Central  CAS  PubMed  Google Scholar 

  30. Lin, Y., Cradick, T. J., Brown, M. T., et al. (2014). CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Research, 42, 7473–7485.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Takahashi, K., Tanabe, K., Ohnuki, M., et al. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 131, 861–872.

    Article  CAS  PubMed  Google Scholar 

  32. Gasiunas, G., Barrangou, R., Horvath, P., & Siksnys, V. (2012). Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 109, E2579–E2586.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Ran, F. A., Hsu, P. D., Lin, C. Y., et al. (2013). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154, 1380–1389.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Correspondence to Brigitte Malgrange.

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Grobarczyk, B., Franco, B., Hanon, K. et al. Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System. Stem Cell Rev and Rep 11, 774–787 (2015). https://doi.org/10.1007/s12015-015-9600-1

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  • DOI: https://doi.org/10.1007/s12015-015-9600-1

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