Genome Instability drives oncogenic transformation in cancer, and the same phenomenon occurs in human pluripotent stem cells.

Human Pluripotent Stem Cells (hPSC) have limitless in-vitro proliferative capacity and can differentiate into any somatic cell type. These features make them ideal sources of cellular material for regenerative medicine applications. However, over prolonged in-vitro culture, hPSC are prone to acquiring recurrent genetic changes, ranging from SNPs to gross karyotypic abnormalities. Many of the changes observed in hPSC are common to cancers, raising significant concern over the safety of hPSC-derived products in therapy.

DNA damage, followed by unfaithful repair, precludes many of the genetic changes observed in hPSC. Pluripotent cells harbour higher constitutive levels of DNA damage than their differentiated counterparts, however, the causes of this damage remain poorly characterised.

We have used INDUCE-seq to map genome-wide endogenous DNA double-strand breaks in pluripotent and differentiated cells. From these data, we have discerned differences in the distribution of DNA breaks between isogenic pluripotent and differentiated cell types and have identified pluripotent-specific DNA damage hotspots, several of which fall within regions of recurrent genetic change in hPSC. By Integrating published sequencing datasets, and contextualising damage hotspots, we identify DNA replication stress as a putative cause of DNA damage and ultimately recurrent chromosomal translocations on chromosome 1q. We hope, ultimately, this work will inform modified culture conditions to minimise the occurrence of such variants in hPSC cultures.