Induced pluripotent stem cells (iPSCs) are a type of pluripotent stem cell that can be generated directly from adult cells via introduction of four specific genes encoding transcription factors. The iPSC technology was set up by Shinya Yamanaka at 2006 and held great promise in the field of regenerative medicine.

Four transcription factors mediated reprogramming could potentially induce or enlarge mutations in the iPSCs, and the impacts of the mutations on the developmental potential of the iPSCs need further evaluation. Based on the sequential reprogramming system combining with whole genome sequencing, Prof. CAI Jun's group at Beijing Institute of Genomics of Chinese Academy of Sciences, collaborated with Prof. GAO shaorong at the School of Life Sciences and Technology of Tongji University and Prof. TIAN Jianhui at College of Animal Sciences and Technology of China Agricultural University, revealed accumulated single-nucleotide variations (SNVs) throughout the sequential reprogramming process, which accounted for the gradual decrease in viability of the all-iPSC mice.

In this sequential reprogramming system, the viabilities of later-generation all-iPSCs were greatly reduced. Combined MeDIP-seq and RNA-seq results indicated that the decreased viability was unrelated with epigenetic effects. Further investigation revealed that SNVs accumulated throughout the sequential process. Functional annotation of these SNVs demonstrated that these mutations would cause developmental failures in mice, and corresponding abnormal phenotypes were supported by histopathological examination. The origins of these accumulated SNVs were evaluated via droplet digital PCR (ddPCR), and the results showed that about two-thirds of the SNVs pre-existed in the all-iPSC mouse tissues which generated during development, rather than merely in iPSC induction.