Skip to main content
NCBI home page
Protein & Cell logoLink to Protein & Cell
. 2011 Dec 15;2(12):950–956. doi: 10.1007/s13238-011-1132-0

Find and replace: editing human genome in pluripotent stem cells

Huize Pan 1, Weiqi Zhang 1, Weizhou Zhang 2,✉, Guang-Hui Liu 1,✉
PMCID: PMC4875250  PMID: 22173708

Abstract

Genetic manipulation of human pluripotent stem cells (hPSCs) provides a powerful tool for modeling diseases and developing future medicine. Recently a number of independent genome-editing techniques were developed, including plasmid, bacterial artificial chromosome, adeno-associated virus vector, zinc finger nuclease, transcription activator-like effecter nuclease, and helper-dependent adenoviral vector. Gene editing has been successfully employed in different aspects of stem cell research such as gene correction, mutation knock-in, and establishment of reporter cell lines (Raya et al., 2009; Howden et al., 2011; Li et al., 2011; Liu et al., 2011b; Papapetrou et al., 2011; Sebastiano et al., 2011; Soldner et al., 2011; Zou et al., 2011a). These techniques combined with the utility of hPSCs will significantly influence the area of regenerative medicine.

Keywords: gene targeting, gene editing, gene correction, pluripotent stem cell

Footnotes

These authors contributed equally to the work.

Contributor Information

Weizhou Zhang, Email: w4zhang@ucsd.edu.

Guang-Hui Liu, Email: ghliu@ibp.ac.cn.

References

  1. Asuri, P., Bartel, M.A., Vazin, T., Jang, J.H., Wong, T.B., and Schaffer, D.V. Directed evolution of adeno-associated virus for enhanced gene delivery and gene targeting in human pluripotent stem cells. Mol Ther. 2011 Nov 22. DOI: 10.1038/mt.2011.255. [Epub ahead of print] [DOI] [PMC free article] [PubMed]
  2. Braam S.R., Denning C., van den Brink S., Kats P., Hochstenbach R., Passier R., Mummery C.L. Improved genetic manipulation of human embryonic stem cells. Nat Methods. 2008;5:389–392. doi: 10.1038/nmeth.1200. [DOI] [PubMed] [Google Scholar]
  3. Bu L., Gao X., Jiang X., Chien K.R., Wang Z. Targeted conditional gene knockout in human embryonic stem cells. Cell Res. 2010;20:379–382. doi: 10.1038/cr.2010.23. [DOI] [PubMed] [Google Scholar]
  4. Bu L., Jiang X., Martin-Puig S., Caron L., Zhu S., Shao Y., Roberts D.J., Huang P.L., Domian I.J., Chien K.R. Human ISL1 heart progenitors generate diverse multipotent cardiovascular cell lineages. Nature. 2009;460:113–117. doi: 10.1038/nature08191. [DOI] [PubMed] [Google Scholar]
  5. Buecker C., Chen H.H., Polo J.M., Daheron L., Bu L., Barakat T. S., Okwieka P., Porter A., Gribnau J., Hochedlinger K., et al. A murine ESC-like state facilitates transgenesis and homologous recombination in human pluripotent stem cells. Cell Stem Cell. 2010;6:535–546. doi: 10.1016/j.stem.2010.05.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cathomen T., Joung J.K. Zinc-finger nucleases: the next generation emerges. Mol Ther. 2008;16:1200–1207. doi: 10.1038/mt.2008.114. [DOI] [PubMed] [Google Scholar]
  7. Cermak T., Doyle E.L., Christian M., Wang L., Zhang Y., Schmidt C., Baller J.A., Somia N.V., Bogdanove A.J., Voytas D.F. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011;39:e82. doi: 10.1093/nar/gkr218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Costa M., Dottori M., Sourris K., Jamshidi P., Hatzistavrou T., Davis R., Azzola L., Jackson S., Lim S.M., Pera M., et al. A method for genetic modification of human embryonic stem cells using electroporation. Nat Protoc. 2007;2:792–796. doi: 10.1038/nprot.2007.105. [DOI] [PubMed] [Google Scholar]
  9. Davis R.P., Ng E.S., Costa M., Mossman A.K., Sourris K., Elefanty A.G., Stanley E.G. Targeting a GFP reporter gene to the MIXL1 locus of human embryonic stem cells identifies human primitive streak-like cells and enables isolation of primitive hematopoietic precursors. Blood. 2008;111:1876–1884. doi: 10.1182/blood-2007-06-093609. [DOI] [PubMed] [Google Scholar]
  10. DeKelver R.C., Choi V.M., Moehle E.A., Paschon D.E., Hockemeyer D., Meijsing S.H., Sancak Y., Cui X., Steine E.J., Miller J.C., et al. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res. 2010;20:1133–1142. doi: 10.1101/gr.106773.110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Deyle D.R., Khan I.F., Ren G., Wang P.-R., Kho J., Schwarze U., Russell D.W. Normal collagen and bone production by gene-targeted human osteogenesis imperfecta iPSCs. Mol Ther. 2011;25:209. doi: 10.1038/mt.2011.209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Di Domenico A.I., Christodoulou I., Pells S.C., McWhir J., Thomson A.J. Sequential genetic modification of the hprt locus in human ESCs combining gene targeting and recombinase-mediated cassette exchange. Cloning Stem Cells. 2008;10:217–230. doi: 10.1089/clo.2008.0016. [DOI] [PubMed] [Google Scholar]
  13. Elliott, D.A., Braam, S.R., Koutsis, K., Ng, E.S., Jenny, R., Lagerqvist, E.L., Biben, C., Hatzistavrou, T., Hirst, C.E., Yu, Q.C., et al. NKX2-5 (eGFP/w) hESCs for isolation of human cardiac progenitors and cardiomyocytes. Nat Methods. DOI: 10.1038/nmeth.1740. [Epub ahead of print]. [DOI] [PubMed]
  14. Fischer Y., Ganic E., Ameri J., Xian X., Johannesson M., Semb H. NANOG reporter cell lines generated by gene targeting in human embryonic stem cells. PLoS One. 2010;5:5. doi: 10.1371/journal.pone.0012533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gabriel R., Lombardo A., Arens A., Miller J.C., Genovese P., Kaeppel C., Nowrouzi A., Bartholomae C.C., Wang J., Friedman G., et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol. 2011;29:816–823. doi: 10.1038/nbt.1948. [DOI] [PubMed] [Google Scholar]
  16. Goulburn A.L., Alden D., Davis R.P., Micallef S.J., Ng E.S., Yu Q. C., Lim S.M., Soh C.L., Elliott D.A., Hatzistavrou T., et al. A Targeted NKX2.1 Hesc reporter line enables identification of human basal forebrain derivatives. Stem Cells. 2011;29:462–473. doi: 10.1002/stem.587. [DOI] [PubMed] [Google Scholar]
  17. Hockemeyer D., Soldner F., Beard C., Gao Q., Mitalipova M., DeKelver R.C., Katibah G.E., Amora R., Boydston E.A., Zeitler B., et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol. 2009;27:851–857. doi: 10.1038/nbt.1562. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hockemeyer D., Wang H., Kiani S., Lai C.S., Gao Q., Cassady J. P., Cost G.J., Zhang L., Santiago Y., Miller J.C., et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol. 2011;29:731–734. doi: 10.1038/nbt.1927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Howden S.E., Gore A., Li Z., Fung H.L., Nisler B.S., Nie J., Chen G., McIntosh B.E., Gulbranson D.R., Diol N.R., et al. Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy. Proc Natl Acad Sci U S A. 2011;108:6537–6542. doi: 10.1073/pnas.1103388108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Irion S., Luche H., Gadue P., Fehling H.J., Kennedy M., Keller G. Identification and targeting of the ROSA26 locus in human embryonic stem cells. Nat Biotechnol. 2007;25:1477–1482. doi: 10.1038/nbt1362. [DOI] [PubMed] [Google Scholar]
  21. Jopling C., Boue S., Izpisua Belmonte J.C. Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration. Nat Rev Mol Cell Biol. 2011;12:79–89. doi: 10.1038/nrm3043. [DOI] [PubMed] [Google Scholar]
  22. Kamei K., Guo S., Yu Z.T., Takahashi H., Gschweng E., Suh C., Wang X., Tang J., McLaughlin J., Witte O.N., et al. An integrated microfluidic culture device for quantitative analysis of human embryonic stem cells. Lab Chip. 2009;9:555–563. doi: 10.1039/B809105F. [DOI] [PubMed] [Google Scholar]
  23. Khan I.F., Hirata R.K., Wang P.R., Li Y., Kho J., Nelson A., Huo Y., Zavaljevski M., Ware C., Russell D.W. Engineering of human pluripotent stem cells by AAV-mediated gene targeting. Mol Ther. 2010;18:1192–1199. doi: 10.1038/mt.2010.55. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Kiefer J.C. Primer and interviews: Advances in targeted gene modification. Dev Dyn. 2011;240:2688–2696. doi: 10.1002/dvdy.22780. [DOI] [PubMed] [Google Scholar]
  25. Kim H.W., Svendsen C.N. Gene editing in stem cells hits the target. Cell Stem Cell. 2011;9:93–94. doi: 10.1016/j.stem.2011.07.011. [DOI] [PubMed] [Google Scholar]
  26. Li M., Suzuki K., Qu J., Saini P., Dubova I., Yi F., Lee J., Sancho-Martinez I., Liu G.H., Belmonte J.C. Efficient correction of hemoglobinopathy-causing mutations by homologous recombination in integration-free patient iPSCs. Cell Res. 2011;34:1350–1351. doi: 10.1038/cr.2011.186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Liu G.H., Barkho B.Z., Ruiz S., Diep D., Qu J., Yang S.L., Panopoulos A.D., Suzuki K., Kurian L., Walsh C., et al. Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature. 2011;472:221–225. doi: 10.1038/nature09879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Liu G.H., Suzuki K., Qu J., Sancho-Martinez I., Yi F., Li M., Kumar S., Nivet E., Kim J., Soligalla R.D., et al. Targeted gene correction of laminopathy-associated LMNA mutations in patientspecific iPSCs. Cell Stem Cell. 2011;8:688–694. doi: 10.1016/j.stem.2011.04.019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lombardo A., Cesana D., Genovese P., Di Stefano B., Provasi E., Colombo D.F., Neri M., Magnani Z., Cantore A., Lo Riso P., et al. Site-specific integration and tailoring of cassette design for sustainable gene transfer. Nat Methods. 2011;8:861–869. doi: 10.1038/nmeth.1674. [DOI] [PubMed] [Google Scholar]
  30. Lombardo A., Genovese P., Beausejour C.M., Colleoni S., Lee Y. L., Kim K.A., Ando D., Urnov F.D., Galli C., Gregory P.D., et al. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol. 2007;25:1298–1306. doi: 10.1038/nbt1353. [DOI] [PubMed] [Google Scholar]
  31. Miller J.C., Tan S., Qiao G., Barlow K.A., Wang J., Xia D.F., Meng X., Paschon D.E., Leung E., Hinkley S.J., et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol. 2011;29:143–148. doi: 10.1038/nbt.1755. [DOI] [PubMed] [Google Scholar]
  32. Mitsui K., Suzuki K., Aizawa E., Kawase E., Suemori H., Nakatsuji N., Mitani K. Gene targeting in human pluripotent stem cells with adeno-associated virus vectors. Biochem Biophys Res Commun. 2009;388:711–717. doi: 10.1016/j.bbrc.2009.08.075. [DOI] [PubMed] [Google Scholar]
  33. Mussolino C., Morbitzer R., Lütge F., Dannemann N., Lahaye T., Cathomen T. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res. 2011;39:9283–9293. doi: 10.1093/nar/gkr597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Papapetrou E.P., Lee G., Malani N., Setty M., Riviere I., Tirunagari L.M., Kadota K., Roth S.L., Giardina P., Viale A., et al. Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. Nat Biotechnol. 2011;29:73–78. doi: 10.1038/nbt.1717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Pattanayak V., Ramirez C.L., Joung J.K., Liu D.R. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods. 2011;8:765–770. doi: 10.1038/nmeth.1670. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Ramachandra C.J., Shahbazi M., Kwang T.W., Choudhury Y., Bak X.Y., Yang J., Wang S. Efficient recombinasemediated cassette exchange at the AAVS1 locus in human embryonic stem cells using baculoviral vectors. Nucleic Acids Res. 2011;39:e107. doi: 10.1093/nar/gkr409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Raya A., Rodríguez-Pizà I., Guenechea G., Vassena R., Navarro S., Barrero M.J., Consiglio A., Castellà M., Río P., Sleep E., et al. Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cells. Nature. 2009;460:53–59. doi: 10.1038/nature08129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Ruby K.M., Zheng B. Gene targeting in a HUES line of human embryonic stem cells via electroporation. Stem Cells. 2009;27:1496–1506. doi: 10.1002/stem.73. [DOI] [PubMed] [Google Scholar]
  39. Sakurai K., Shimoji M., Tahimic C.G.T., Aiba K., Kawase E., Hasegawa K., Amagai Y., Suemori H., Nakatsuji N. Efficient integration of transgenes into a defined locus in human embryonic stem cells. Nucleic Acids Res. 2010;38:e96. doi: 10.1093/nar/gkp1234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sancho-Martinez I., Li M., Izpisua Belmonte J.C. Disease correction the iPSC way: advances in iPSC-based therapy. Clin Pharmacol Ther. 2011;89:746–749. doi: 10.1038/clpt.2010.341. [DOI] [PubMed] [Google Scholar]
  41. Sebastiano V., Maeder M.L., Angstman J.F., Haddad B., Khayter C., Yeo D.T., Goodwin M.J., Hawkins J.S., Ramirez C.L., Batista L.F., et al. In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases. Stem Cells. 2011;29:1717–1726. doi: 10.1002/stem.718. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Soldner F., Laganière J., Cheng A.W., Hockemeyer D., Gao Q., Alagappan R., Khurana V., Golbe L.I., Myers R.H., Lindquist S., et al. Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell. 2011;146:318–331. doi: 10.1016/j.cell.2011.06.019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Song H., Chung S.K., Xu Y. Modeling disease in human ESCs using an efficient BAC-based homologous recombination system. Cell Stem Cell. 2010;6:80–89. doi: 10.1016/j.stem.2009.11.016. [DOI] [PubMed] [Google Scholar]
  44. Suzuki K., Mitsui K., Aizawa E., Hasegawa K., Kawase E., Yamagishi T., Shimizu Y., Suemori H., Nakatsuji N., Mitani K. Highly efficient transient gene expression and gene targeting in primate embryonic stem cells with helperdependent adenoviral vectors. Proc Natl Acad Sci U S A. 2008;105:13781–13786. doi: 10.1073/pnas.0806976105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Urbach A., Schuldiner M., Benvenisty N. Modeling for Lesch-Nyhan disease by gene targeting in human embryonic stem cells. Stem Cells. 2004;22:635–641. doi: 10.1634/stemcells.22-4-635. [DOI] [PubMed] [Google Scholar]
  46. Xue H., Wu S., Papadeas S.T., Spusta S., Swistowska A.M., MacArthur C.C., Mattson M.P., Maragakis N.J., Capecchi M.R., Rao M.S., et al. A targeted neuroglial reporter line generated by homologous recombination in human embryonic stem cells. Stem Cells. 2009;27:1836–1846. doi: 10.1002/stem.129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Yusa K., Rashid S.T., Strick-Marchand H., Varela I., Liu P.-Q., Paschon D.E., Miranda E., Ordóñez A., Hannan N.R.F., Rouhani F.J., et al. Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells. Nature. 2011;478:391–394. doi: 10.1038/nature10424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Zhang F., Cong L., Lodato S., Kosuri S., Church G.M., Arlotta P. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol. 2011;29:149–153. doi: 10.1038/nbt.1775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Zou J., Maeder M.L., Mali P., Pruett-Miller S.M., Thibodeau-Beganny S., Chou B.K., Chen G., Ye Z., Park I.H., Daley G.Q., et al. Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell. 2009;5:97–110. doi: 10.1016/j.stem.2009.05.023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Zou J., Mali P., Huang X., Dowey S.N., Cheng L. Sitespecific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease. Blood. 2011;118:4599–4608. doi: 10.1182/blood-2011-02-335554. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Zou J., Sweeney C.L., Chou B.K., Choi U., Pan J., Wang H., Dowey S.N., Cheng L., Malech H.L. Oxidasedeficient neutrophils from X-linked chronic granulomatous disease iPS cells: functional correction by zinc finger nuclease-mediated safe harbor targeting. Blood. 2011;117:5561–5572. doi: 10.1182/blood-2010-12-328161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Zwaka T.P., Thomson J.A. Homologous recombination in human embryonic stem cells. Nat Biotechnol. 2003;21:319–321. doi: 10.1038/nbt788. [DOI] [PubMed] [Google Scholar]

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES