TY - JOUR T1 - iPSC culture expansion selects against putatively actionable mutations in the mitochondrial genome JF - bioRxiv DO - 10.1101/2020.11.05.369694 SP - 2020.11.05.369694 AU - Maike Kosanke AU - Colin Davenport AU - Monika Szepes AU - Lutz Wiehlmann AU - Tim Kohrn AU - Marie Dorda AU - Jonas Gruber AU - Kaja Menge AU - Maike Sievert AU - Anna Melchert AU - Ina Gruh AU - Ulrich Martin Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/11/05/2020.11.05.369694.abstract N2 - While human induced pluripotent stem cells (iPSCs) offer fascinating prospects for research and clinics, evaluating their genomic stability before applications is of utmost importance. During reprogramming, clonal hiPSC lines derived from the same parental cell population were observed to harbor different mitochondrial DNA (mtDNA) variants and variant heteroplasmy levels. It is unknown to date to which extent this unequal segregation of heteroplasmies between cells arises from mosaicism in the parental cell population, selection on mutated mtDNA molecules on the cellular or organelle level, genetic drift during reduction of mtDNA during reprogramming (genetic bottleneck), or de novo mutations. We analyzed mtDNA variants in 26 clonal iPSC lines by mtDNA sequencing. We did not observe a strong bottleneck or any selection for cells with specific mtDNA variants (clonal eliteness) during reprogramming. iPSC culture expansion, however, selects against putatively actionable mutations in the mitochondrial genome that may affect mitochondrial function and cell metabolism. In contrast, heteroplasmy levels of neutral variants remained stable or increased within clonal iPSC lines during culture expansion. Interestingly, the mtDNA copy number per cell got transiently reduced during targeted differentiation of iPSCs into cardiomyocytes, but mtDNA heteroplasmy levels were not affected. Altogether, our results point towards a scenario in which intra-cellular selection on mtDNA during culture expansion, but not during reprogramming or differentiation, pivotally shapes the mutational landscape of the mitochondrial genome in iPSCs. Other mechanisms such as inter-cellular selection, genetic bottleneck, and genetic drift exert minor impact.Competing Interest StatementThe authors have declared no competing interest. ER -