UC San Diego

The ability to induce pluripotency in human adult somatic cells by defined transcription factor expression is a revolutionary prospect in regenerative medicine. This discovery has the potential to both open new research avenues for diseases in tissue types that are difficult to obtain and to revolutionize medicine through the use of patient-derived replacement tissue. However, questions remain about the safety and efficacy of these induced pluripotent stem cells (iPSCs). Because iPSC generation protocols tend to be low efficiency, require derivation from adult tissue, often utilize viral transfection, force the expression of known oncogenes, and involve a large number of rapid cell divisions during reprogramming, it was thought that the iPSC genome itself might contain some genetic mutation. Additionally, the progenitor cell type used for iPSC derivation seemed to cause some differentiation pathways to be more highly favored, indicating that iPSCs might possess some sort of "epigenetic memory" of their progenitor state. Thanks to modern advances in high throughput sequencing, we were able to assess the genomic and epigenomic state of induced pluripotent stem cells, and thus determine if iPSCs could be used in either a clinical or a research context. We demonstrate that induced pluripotent stem cells contain a large number of point mutations across their genome regardless of donor age, time in culture, progenitor cell type, or reprogramming method. While a majority of these mutations arise due to rare progenitor mutations becoming fixed through clonal selection during reprogramming, approximately 43% arise either during the reprogramming step or during iPSC expansion. We additionally show that, in addition to epigenetic memory of the progenitor cell state and aberrant DNA methylation, nearly all iPSC lines carry a unique reprogramming-specific epigenetic signature that remains even after further differentiation and impacts gene expression in iPSC-derived cells. Taken together, these results demonstrate that iPSCs must still overcome major hurdles prior to their widespread clinical use. Rigorous work towards establishing clinical safety standards for genetic and epigenetic integrity in pluripotent-derived therapies will be essential before the promise of induced pluripotency can be fully realized