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Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells

Nature volume 478, pages 391–394 (2011)Cite this article

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Abstract

Human induced pluripotent stem cells (iPSCs) represent a unique opportunity for regenerative medicine because they offer the prospect of generating unlimited quantities of cells for autologous transplantation, with potential application in treatments for a broad range of disorders1,2,3,4. However, the use of human iPSCs in the context of genetically inherited human disease will require the correction of disease-causing mutations in a manner that is fully compatible with clinical applications3,5. The methods currently available, such as homologous recombination, lack the necessary efficiency and also leave residual sequences in the targeted genome6. Therefore, the development of new approaches to edit the mammalian genome is a prerequisite to delivering the clinical promise of human iPSCs. Here we show that a combination of zinc finger nucleases (ZFNs)7 and piggyBac8,9 technology in human iPSCs can achieve biallelic correction of a point mutation (Glu342Lys) in the α1-antitrypsin (A1AT, also known as SERPINA1) gene that is responsible for α1-antitrypsin deficiency. Genetic correction of human iPSCs restored the structure and function of A1AT in subsequently derived liver cells in vitro and in vivo. This approach is significantly more efficient than any other gene-targeting technology that is currently available and crucially prevents contamination of the host genome with residual non-human sequences. Our results provide the first proof of principle, to our knowledge, for the potential of combining human iPSCs with genetic correction to generate clinically relevant cells for autologous cell-based therapies.

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Figure 1: Correction of the G290T mutation in the Tyr gene in mouse iPSCs.
Figure 2: Correction of the Z mutation in human A1ATD-iPSCs.
Figure 3: Functional analysis of restored A1AT in corrected iPSC-derived hepatocyte-like cells.

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ArrayExpress

Gene Expression Omnibus

Data deposits

Exome sequence data have been deposited at the European Genome-Phenome Archive (http://www.ebi.ac.uk/ega/) hosted by the European Bioinformatics Institute under accession EGAS00001000055. CGH and SNP array data have been deposited with EBI ArrayExpress (http://www.ebi.ac.uk/arrayexpress/) under accession number E-MEXP-3316 and with Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE31035, respectively.

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Acknowledgements

We thank A. Klug and M. Minczuk for their advice, M. A. Li for comments on the manuscript, P. Ellis, N. Hammond and C. McGee for CGH analysis, the Sanger Institute sequencing facility for exome sequencing, N. Conte and S. Rice for assistance with bioinformatic analysis, M. Alexander for her help with cell culture reagents. We also thank L. Zhang, S. Hinkley and the production group for ZFN assembly and validation, K. Tong and X. Meng for technical assistance, J. C. Miller and E. Leung for ZFN off-target site analysis and S. Abrahamson and P. D. Gregory for careful reading of the manuscript. This work was supported by the Wellcome Trust (WT077187; A.B.), the MRC Senior non-clinical fellowship and the Cambridge Hospitals National Institute for Health Research Biomedical Research Center (L.V.), the Medical Research Council and Papworth NHS Trust (D.A.L.), the Bill and Melinda Gates Foundation, Inserm and Institut Pasteur (H.S.-M.) and Japan Science and Technology Agency (N.F.). K.Y. is supported by a postdoctoral fellowship of Japan Society for the Promotion of Science. S.T.R. and F.J.R. are Wellcome Trust Clinical Training Fellows. I.V. is supported by a fellowship from the International Human Frontiers Science Program Organization.

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Author notes

  1. Kosuke Yusa, S. Tamir Rashid, David A. Lomas, Allan Bradley and Ludovic Vallier: These authors contributed equally to this work.

Authors and Affiliations

  1. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

    Kosuke Yusa, Foad J. Rouhani & Allan Bradley

  2. Department of Surgery, Anne McLaren Laboratory for Regenerative Medicine, West Forvie Building, Robinson Way, University of Cambridge, Cambridge CB2 0SZ, UK

    S. Tamir Rashid, Nicholas R. F. Hannan, Foad J. Rouhani & Ludovic Vallier

  3. Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB0 2XY, UK

    S. Tamir Rashid, Elena Miranda, Adriana Ordóñez, Stefan J. Marciniak & David A. Lomas

  4. Innate Immunity Unit, Institut Pasteur, 75724 Paris, France

    Helene Strick-Marchand, Sylvie Darche & James P. Di Santo

  5. INSERM, U668, 75724 Paris, France

    Helene Strick-Marchand, Sylvie Darche & James P. Di Santo

  6. Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-UC-SODERCAN Avda. Cardenal Herrera Oria s/n 39011 Santander, Spain

    Ignacio Varela

  7. Sangamo BioSciences Inc., Richmond, 94804, California, USA

    Pei-Qi Liu, David E. Paschon & Michael C. Holmes

  8. Dept. Biologia e Biotecnologie ‘Charles Darwin’, Università di Roma “La Sapienza”, p.le Aldo Moro 5, 00185 Rome, Italy

    Elena Miranda

  9. Division of Gastroenterology and Hepatology, Department of Medicine, Cambridge University Hospitals NHS Trust, Cambridge CB2 2QQ, UK

    Graeme Alexander

  10. DNAVEC Corporation, Tsukuba, Ibaraki 300-2611, Japan

    Noemi Fusaki & Mamoru Hasegawa

  11. PRESTO, JST, Saitama 332-0012, Japan

    Noemi Fusaki

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Contributions

K.Y. and S.T.R. are joint first authors. D.A.L., A.B. and L.V. contributed equally to this work. K.Y., S.T.R., D.A.L., A.B. and L.V. conceived the research and wrote the manuscript with comments from all authors. K.Y. performed gene correction in mouse and human iPSCs and conducted all experiments using piggyBac in Cambridge, UK. S.T.R., E.M., A.O., N.R.F.H., F.J.R., G.A. and S.J.M. performed in vitro phenotypic analysis of corrected human iPSCs. S.T.R., H.S.-M., S.D. and J.P.D.S. performed in vivo work. I.V. performed data analysis of exome sequencing. P.Q.-L., D.E.P. and M.C.H. generated and validated ZFNs. N.F. and M.H. generated Sendai virus vectors.

Corresponding authors

Correspondence to Allan Bradley or Ludovic Vallier.

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Competing interests

[Competing financial interests: P.-Q.L., D.E.P. and M.C.H. are employees of Sangamo BioSciences. N.F. and M.H. are employees of DNAVEC. All other authors declare no competing financial interests.]

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Yusa, K., Rashid, S., Strick-Marchand, H. et al. Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells. Nature 478, 391–394 (2011). https://doi.org/10.1038/nature10424

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