Chromosome X Dosage Modulates Development of Aneuploidy in Genetically Diverse Mouse Embryonic Stem Cells [D0_scRNA-seq]. Chromosome X Dosage Modulates Development of Aneuploidy in Genetically Diverse Mouse Embryonic Stem Cells [D0_scRNA-seq]

The genetic integrity of pluripotent stem cells (PSC) is integral to their applications in research and therapy, but it is compromised by frequent development of copy number variations. Little is known about the basis of the variable genomic integrity among different PSC lines. 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 identified 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 data sets demonstrated that aneuploid XY DO mESC also show lower Chromosome X gene expression and that XY mESC accumulate higher aneuploid proportions in culture than isogenic XX lines. Possible mechanisms for this protective effect of X chromosome dosage include our discovery that the lines with two active X Chromosomes have a higher expression of 2-cell-like state genes, and differential expression of X-linked tumor suppressor genes associated with DNA damage response. Overall design: The sample submitted contains embryonic stem cells (ESCs) derived from diversity outbred (DO) mice. The cell lines were derived indepdently and pooled in equal proportion for sequencing. The pooled sample was then divided and sequenced across 4 lanes.

多能干细胞（pluripotent stem cell, PSC）的遗传完整性对其科研与临床应用不可或缺，但频繁发生的拷贝数变异会损害其遗传完整性。目前学界对不同PSC系间基因组完整性差异的分子基础仍知之甚少。本研究利用来自170只多样性远交（Diversity Outbred, DO）小鼠的小鼠胚胎干细胞（mouse embryonic stem cell, mESC）系的RNA-seq及蛋白质组学数据，开展非整倍体鉴定。本研究共鉴定出62个携带可检测到的非整倍体细胞亚群的细胞系，以及部分原本为XX核型的细胞系丢失一条X染色体（XO）的样本。值得注意的是，与XY或XO核型细胞系相比，XX核型细胞系的非整倍体比例显著更低。两项单细胞RNA-seq数据集证实，非整倍体XY DO mESC同样表现出X染色体基因表达水平下调，且体外培养过程中，XY mESC的非整倍体细胞比例较同核型的XX细胞系更高。这种X染色体剂量带来的保护效应可能的机制包括：本研究发现携带两条活性X染色体的细胞系其2细胞样状态基因的表达水平更高，且与DNA损伤应答相关的X连锁肿瘤抑制基因存在差异表达。实验设计概况：本次提交的样本为源自多样性远交小鼠的胚胎干细胞（ESCs）。所有细胞系均独立构建，并按等比例混合后进行测序；混合后的样本被分为4个测序泳道分别完成测序。