Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Department of Surgery, University of Cambridge, Cambridge, UK.
Nat Genet. 2022 Sep;54(9):1406-1416. doi: 10.1038/s41588-022-01147-3. Epub 2022 Aug 11.
We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide resolution. We used genome sequencing data from two large hiPSC repositories involving 696 hiPSCs and daughter subclones. We find ultraviolet light (UV)-related damage in ~72% of skin fibroblast-derived hiPSCs (F-hiPSCs), occasionally resulting in substantial mutagenesis (up to 15 mutations per megabase). We demonstrate remarkable genomic heterogeneity between independent F-hiPSC clones derived during the same round of reprogramming due to oligoclonal fibroblast populations. In contrast, blood-derived hiPSCs (B-hiPSCs) had fewer mutations and no UV damage but a high prevalence of acquired BCOR mutations (26.9% of lines). We reveal strong selection pressure for BCOR mutations in F-hiPSCs and B-hiPSCs and provide evidence that they arise in vitro. Directed differentiation of hiPSCs and RNA sequencing showed that BCOR mutations have functional consequences. Our work strongly suggests that detailed nucleotide-resolution characterization is essential before using hiPSCs.
我们探索了源自不同组织的人类诱导多能干细胞（hiPSC），以深入了解单核苷酸分辨率下的基因组完整性。我们使用了两个大型 hiPSC 库的基因组测序数据，其中包含 696 个 hiPSC 和子克隆。我们发现约 72%的皮肤成纤维细胞来源的 hiPSC（F-hiPSC）中存在与紫外线（UV）相关的损伤，偶尔会导致大量突变（每个兆碱基高达 15 个突变）。我们证明了由于寡克隆成纤维细胞群体，在同一轮重编程过程中产生的独立 F-hiPSC 克隆之间存在显著的基因组异质性。相比之下，血液来源的 hiPSC（B-hiPSC）突变较少，没有 UV 损伤，但获得性 BCOR 突变的发生率很高（26.9%的系）。我们揭示了 F-hiPSC 和 B-hiPSC 中 BCOR 突变的强烈选择压力，并提供了它们在体外发生的证据。hiPSC 的定向分化和 RNA 测序表明，BCOR 突变具有功能后果。我们的工作强烈表明，在使用 hiPSC 之前，必须进行详细的核苷酸分辨率特征描述。
