Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. We generated isogenic CRISPR–Cas9 knockouts (∆) of 43 genes in human induced pluripotent stem cells, cultured them in the absence of added DNA damage and performed whole-genome sequencing of 173 subclones. ∆OGG1, ∆UNG, ∆EXO1, ∆RNF168, ∆MLH1, ∆MSH2, ∆MSH6, ∆PMS1 and ∆PMS2 produced marked mutational signatures indicative of them being critical mitigators of endogenous DNA modifications. Detailed analyses revealed mutational mechanistic insights, including how 8-oxo-2′-deoxyguanosine elimination is sequence context specific while uracil clearance is sequence context independent. Mismatch repair (MMR) deficiency signatures are engendered by oxidative damage (C > A transversions) and differential misincorporation by replicative polymerases (T > C and C > T transitions), and we propose a reverse template slippage model for T > A transversions. ∆MLH1, ∆MSH6 and ∆MSH2 signatures were similar to each other but distinct from ∆PMS2. Finally, we developed a classifier, MMRDetect, where application to 7,695 whole-genome-sequenced cancers showed enhanced detection of MMR-deficient tumors, with implications for responsiveness to immunotherapies.

突变特征是通过肿瘤发生产生的病理生理过程的印记。我们在人类诱导多能干细胞中生成了 43 个基因的等基因 CRISPR-Cas9 敲除 (Δ)，在没有额外 DNA 损伤的情况下培养它们，并对 173 个亚克隆进行了全基因组测序。∆ OGG1 , ∆ UNG , ∆ EXO1 , ∆ RNF168 , ∆ MLH1 , ∆ MSH2 , ∆ MSH6 , ∆ PMS1和 ∆ PMS2产生了显着的突变特征，表明它们是内源性 DNA 修饰的关键缓和剂。详细分析揭示了突变机制的见解，包括 8-oxo-2'-脱氧鸟苷消除如何是序列上下文特定的，而尿嘧啶清除是序列上下文独立的。错配修复 (MMR) 缺陷特征是由氧化损伤（C > A 颠换）和复制聚合酶的差异错误掺入（T > C 和 C > T 转换）引起的，我们提出了 T > A 颠换的反向模板滑动模型。∆ MLH1 , ∆ MSH6和 ∆ MSH2签名彼此相似但不同于 ∆ PMS2. 最后，我们开发了一个分类器 MMRDetect，该分类器应用于 7,695 个全基因组测序的癌症显示增强了对 MMR 缺陷肿瘤的检测，对免疫疗法的反应具有影响。