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Generation and characterization of transgene-free human induced pluripotent stem cells and conversion to putative clinical-grade status

Jason P Awe1, Patrick C Lee1, Cyril Ramathal2, Agustin Vega-Crespo1, Jens Durruthy-Durruthy2, Aaron Cooper3, Saravanan Karumbayaram4, William E Lowry4, Amander T Clark4, Jerome A Zack4, Vittorio Sebastiano2, Donald B Kohn4, April D Pyle4, Martin G Martin5, Gerald S Lipshutz6, Patricia E Phelps7, Renee A Reijo Pera2 and James A Byrne14*

Author Affiliations

1 Department of Molecular and Medical Pharmacology, 23–120 Center for Health Sciences, University of California, Los Angeles (UCLA), 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA

2 Department of Obstetrics and Gynecology, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford University, 265 Campus Drive, Stanford, Stanford, CA 94305, USA

3 Department of Microbiology, Immunology and Molecular Genetics, 609 Charles E. Young Drive East, UCLA, Los Angeles, CA 90095, USA

4 Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, 615 Charles E Young Drive South, UCLA, Los Angeles, CA 90095, USA

5 Department of Pediatrics, Division of Gastroenterology and Nutrition, 10833 Le Conte Ave, UCLA, Los Angeles, CA 90095, USA

6 Department of Surgery, 200 UCLA Medical Plaza, UCLA, Los Angeles, CA 90095, USA

7 Department of Integrative Biology and Physiology, 612 Charles E. Young Drive East, UCLA, Los Angeles, CA 90095, USA

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Stem Cell Research & Therapy 2013, 4:87  doi:10.1186/scrt246

Published: 26 July 2013



The reprogramming of a patient’s somatic cells back into induced pluripotent stem cells (iPSCs) holds significant promise for future autologous cellular therapeutics. The continued presence of potentially oncogenic transgenic elements following reprogramming, however, represents a safety concern that should be addressed prior to clinical applications. The polycistronic stem cell cassette (STEMCCA), an excisable lentiviral reprogramming vector, provides, in our hands, the most consistent reprogramming approach that addresses this safety concern. Nevertheless, most viral integrations occur in genes, and exactly how the integration, epigenetic reprogramming, and excision of the STEMCCA reprogramming vector influences those genes and whether these cells still have clinical potential are not yet known.


In this study, we used both microarray and sensitive real-time PCR to investigate gene expression changes following both intron-based reprogramming and excision of the STEMCCA cassette during the generation of human iPSCs from adult human dermal fibroblasts. Integration site analysis was conducted using nonrestrictive linear amplification PCR. Transgene-free iPSCs were fully characterized via immunocytochemistry, karyotyping and teratoma formation, and current protocols were implemented for guided differentiation. We also utilized current good manufacturing practice guidelines and manufacturing facilities for conversion of our iPSCs into putative clinical grade conditions.


We found that a STEMCCA-derived iPSC line that contains a single integration, found to be located in an intronic location in an actively transcribed gene, PRPF39, displays significantly increased expression when compared with post-excised stem cells. STEMCCA excision via Cre recombinase returned basal expression levels of PRPF39. These cells were also shown to have proper splicing patterns and PRPF39 gene sequences. We also fully characterized the post-excision iPSCs, differentiated them into multiple clinically relevant cell types (including oligodendrocytes, hepatocytes, and cardiomyocytes), and converted them to putative clinical-grade conditions using the same approach previously approved by the US Food and Drug Administration for the conversion of human embryonic stem cells from research-grade to clinical-grade status.


For the first time, these studies provide a proof-of-principle for the generation of fully characterized transgene-free human iPSCs and, in light of the limited availability of current good manufacturing practice cellular manufacturing facilities, highlight an attractive potential mechanism for converting research-grade cell lines into putatively clinical-grade biologics for personalized cellular therapeutics.