Elevated Coding Mutation Rate During the Reprogramming of Human Somatic Cells into Induced Pluripotent Stem Cells

TLDR

Mutations in human induced pluripotent stem cells (iPSCs) pose a risk for clinical use due to preferential reprogramming of mutated founder cells and selection of mutations during iPSC culture. The study aims to determine whether mutations in iPSCs arise from stress associated with oncogene expression during reprogramming. The authors performed whole‑exome sequencing of human foreskin fibroblasts and derived iPSCs at two passages and used simulation to show that mutation intensity during reprogramming is ninefold higher than the background culture rate. In vitro passaging contributed 7% of the iPSC coding mutation load, 19% of mutations preexisted as rare variants in parental fibroblasts, and the remaining 74% were acquired during reprogramming, indicating that reprogramming stress significantly contributes to the mutation burden.

Abstract

Mutations in human induced pluripotent stem cells (iPSCs) pose a risk for their clinical use due to preferential reprogramming of mutated founder cell and selection of mutations during maintenance of iPSCs in cell culture. It is unknown, however, if mutations in iPSCs are due to stress associated with oncogene expression during reprogramming. We performed whole exome sequencing of human foreskin fibroblasts and their derived iPSCs at two different passages. We found that in vitro passaging contributed 7% to the iPSC coding point mutation load, and ultradeep amplicon sequencing revealed that 19% of the mutations preexist as rare mutations in the parental fibroblasts suggesting that the remaining 74% of the mutations were acquired during cellular reprogramming. Simulation suggests that the mutation intensity during reprogramming is ninefold higher than the background mutation rate in culture. Thus the factor induced reprogramming stress contributes to a significant proportion of the mutation load of iPSCs.