Segovia Romulo, Shen Yaoqing, Lujan Scott A, Jones Steven J M, Stirling Peter C
Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada V5Z1L3.
Michael Smith Genome Sciences Centre, Vancouver, BC, Canada V5Z4S6.
Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):2663-2668. doi: 10.1073/pnas.1618555114. Epub 2017 Feb 21.
Gene-gene or gene-drug interactions are typically quantified using fitness as a readout because the data are continuous and easily measured in high throughput. However, to what extent fitness captures the range of other phenotypes that show synergistic effects is usually unknown. Using and focusing on a matrix of DNA repair mutants and genotoxic drugs, we quantify 76 gene-drug interactions based on both mutation rate and fitness and find that these parameters are not connected. Independent of fitness defects, we identified six cases of synthetic hypermutation, where the combined effect of the drug and mutant on mutation rate was greater than predicted. One example occurred when yeast lacking were exposed to cisplatin, and we characterized this interaction using whole-genome sequencing. Our sequencing results indicate mutagenesis by cisplatin in Δ cells appeared to depend almost entirely on interstrand cross-links at GpCpN motifs. Interestingly, our data suggest that the following base on the template strand dictates the addition of the mutated base. This result differs from cisplatin mutation signatures in XPF-deficient and supports a model in which translesion synthesis polymerases perform a slippage and realignment extension across from the damaged base. Accordingly, DNA polymerase ζ activity was essential for mutagenesis in cisplatin-treated Δ cells. Together these data reveal the potential to gain new mechanistic insights from nonfitness measures of gene-drug interactions and extend the use of mutation accumulation and whole-genome sequencing analysis to define DNA repair mechanisms.
基因与基因或基因与药物的相互作用通常使用适应性作为读数来进行量化，因为这些数据是连续的，并且易于在高通量条件下测量。然而，适应性在多大程度上反映了其他具有协同效应的表型范围通常是未知的。我们以DNA修复突变体和基因毒性药物的矩阵为研究对象，基于突变率和适应性对76种基因与药物的相互作用进行了量化，发现这些参数并无关联。在不考虑适应性缺陷的情况下，我们鉴定出6例合成性超突变，即药物和突变体对突变率的联合效应大于预期。其中一个例子是，缺乏[具体基因]的酵母暴露于顺铂时出现了这种情况，我们使用全基因组测序对这种相互作用进行了表征。我们的测序结果表明，顺铂在Δ细胞中诱导的诱变似乎几乎完全依赖于GpCpN基序处的链间交联。有趣的是，我们的数据表明模板链上的后续碱基决定了突变碱基的添加。这一结果与XPF缺陷型[具体细胞]中的顺铂突变特征不同，并支持了一个模型，即跨损伤合成聚合酶在受损碱基对面进行滑移和重新排列延伸。因此，DNA聚合酶ζ活性对于顺铂处理的Δ细胞中的诱变至关重要。这些数据共同揭示了从基因与药物相互作用的非适应性测量中获得新的机制性见解的潜力，并扩展了突变积累和全基因组测序分析在定义DNA修复机制方面的应用。
