Lu Junjie, Li Hu, Baccei Anna, Sasaki Takayo, Gilbert David M, Lerou Paul H
1 Department of Pediatric Newborn Medicine and Division of Genetics, Department of Medicine, Brigham and Women's Hospital , Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts.
2 Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine , Mayo Clinic, Rochester, Minnesota.
Stem Cells Dev. 2016 May 1;25(9):740-7. doi: 10.1089/scd.2015.0393. Epub 2016 Apr 11.
Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. We show that following reprogramming the early and late replicating genome is differentially affected by CNVs in ATM-deficient iPSCs relative to wild-type iPSCs. Specifically, the early replicating regions had increased CNV losses during retroviral (RV) reprogramming. This differential CNV distribution was not present after later passage or after episomal reprogramming. Comparison of different reprogramming methods in the setting of defective DDR reveals unique vulnerability of early replicating open chromatin to RV vectors.
基因组不稳定是诱导多能干细胞（iPSC）研究和治疗应用的一个潜在限制。观察到的基因组变异反映了DNA损伤、细胞DNA损伤反应（DDR）以及培养中的选择压力的综合作用。为了了解DDR对iPSC中拷贝数变异（CNV）分布的影响，我们将具有中心DDR基因ATM突变的iPSC的CNV映射到由全基因组复制时间图谱定义的基因组组织景观上。我们表明，重编程后，相对于野生型iPSC，ATM缺陷型iPSC中早期和晚期复制基因组受CNV的影响存在差异。具体而言，在逆转录病毒（RV）重编程期间，早期复制区域的CNV损失增加。在后期传代或游离体重编程后，这种CNV分布差异不存在。在DDR缺陷的情况下对不同重编程方法的比较揭示了早期复制的开放染色质对RV载体具有独特的脆弱性。
