Chromosome X dosage modulates development of aneuploidy in genetically diverse mouse embryonic stem cells

The genetic integrity of pluripotent stem cells (PSC) is critical to their applications in research and therapy, but it is compromised by frequent development of structural chromosome variants associated with malignancy. Many PSC lines exhibit remarkable genetic stability, but little is known about the basis of the known variation in genomic integrity among different PSC isolates. Here, we identify aneuploidies using RNA-seq and proteomics data from a panel of mouse embryonic stem cell (mESC) lines derived from 170 Diversity Outbred mice. We found 62 lines with detectable aneuploid subpopulations and a subset of originally XX lines that lost one chromosome X (XO). Strikingly, a much lower proportion of XX lines were aneuploid, compared to XY or XO lines. Two single-cell RNA-seq datasets demonstrated that aneuploid XY DO mESC also show lower chromosome X gene expression, and a prospective study confirmed that XY mESC accumulate higher aneuploid proportions in culture than isogenic XX lines. We identify potential mechanisms for this protective effect of X chromosome dosage, including our findings that the lines with two active X chromosomes have a higher proportion of 2-cell-like cells and higher expression of X-linked tumor suppressor genes, both features associated with the maintenance of genomic integrity, and that they compete more robustly in co-culture with chromosomally abnormal cells than XY cells.