Identification and validation of marker genes for the detection of residual iPSCs in iPSC-derived Cardiomyocytes

Human induced pluripotent stem cell (iPSC) based cell therapies represent a promising approach for regenerative medicine. However, iPSC-derived cell therapy products may contain residual undifferentiated iPSCs that could, due to their teratogenic properties and genetic instability, lead to tumor formation after implantation into patients. Hence, highly sensitive and specific methods to detect residual undifferentiated iPSCs are indispensable for safety evaluation of cell therapy products. Here, we used RNA-seq data to identify potential marker genes for iPSC impurities in iPSC-derived tissues. We demonstrated that identifying such marker genes in a tissue-specific way provides a larger and more specific set of potential marker genes than considering all tissue types in the analysis. By spiking different amount of iPSCs in iPSCs derived cardiomyocytes (iCMs), we evaluated selected candidate genes regarding their specificity as well as sensitivity in iCMs, and compared their performance to the previously suggested markers LIN28A, Nanog and TDGF1. The genes CAMKV, EPHA1, ESRG, IDO1, LECT1, LINC00678, LIN28A, LCK, L1TD1, VRTN and ZCAN10 specifically detected contaminant iPSC amongst iCMs with an LOD of 0.001-0.1%. In conclusion, we provide an approach on how to identify a set of highly specific and sensitive markers that can be used for safety assessment of iPSC-derived tissues