Jumping genes in pluripotent stem cells may affect safety of cell therapies

Written by Alexandra Thompson

Research led by the Paul-Ehrlich-Institut (Germany) in an international effort has demonstrated that reprogramming human cells into iPSCs activates normally repressed, endogenous mobile DNA resuling in genetic and epigenetic changes that can effect cell function and potentially have a tumorigenic effect, raising concerns about the biosafety of cell therapies derived from iPSCs.

Human iPSCs can be differentiated into many cells types and therefore hold potential for disease modeling, drug testing and development of cell therapies. However, an international team led by Dr Gerald Schumann from the Paul-Ehrlich-Institut (Germany) has found that the reprogramming process activates endogenous mobile DNA — also known as retrotransposons or jumping genes — and therefore may have a significant biosafety issues. These genes can insert into locations in the genome, making unwanted genetic or epigenetic changes, affecting the function of differentiated cells, or could even have a tumorigenic effect.

Genetic and epigenetic abnormalities had previously been reported, but the Paul-Ehrlich-Institut team in collaboration with the research groups of Drs Geoffrey Faulkner (University of Queensland, Australia) and Jose Garcia-Perez (Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology, Spain) aimed to investigate the incidence and impact of these retrotranspositions in human iPSCs. By applying a new high-throughput sequencing approach known as ‘Retrotransposon Capture Sequencing’ (RC-Seq), the researchers compared the genomes of eight human iPSC lines with those of their differentiated parental cells from which the hiPSC lines were derived from.

The scientists uncovered that mobilization of jumping genes occurred at a frequency of approximately one retrotransposition event per human iPSC, and four out of eight lines acquired mobilization and as a result new insertions of endogenous jumping genes occurred in the genomes. Furthermore, mobilization of preexisting endogenous L1 (one of the mobile genetic elements) generated new functional L1 copies capable of jumping themselves, and an intronic L1 insertion in the CADPS2 gene was found to be acquired during human iPSC cultivation and to disrupt CADPS2 expression, demonstrating a negative effect on the resulting cells.

“Genomic integrity of pluripotent stem cells can be impaired by the mobilization of endogenous transposable elements which is mediated by endogenous L1 activity. This raises the question to what extent the safety of cellular therapies is affected if differentiated cells derived from such hiPSCs are applied,” Dr Schumann explained. Further work will include testing the safety of human iPSC-derived cell therapies.

Sources: www.pei.de/EN/information/journalists-press/press-releases/2016/01-mobilization-jumping-genes-pluripotent-stem-cells-may-affect-safety-stem-cell-based-therapies.html; Klawitter S, Fuchs NV, Upton KR et al. Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nat. Commun. doi:10.1038/ncomms10286 (2016) (Epub ahead of print).