Drug resistance is a principal limitation to the long-term efficacy of cancer therapies. Cancer genome sequencing can retrospectively delineate the genetic basis of drug resistance, but this requires large numbers of post-treatment samples to nominate causal variants. Here we prospectively identify genetic mechanisms of resistance to ten oncology drugs from CRISPR base editing mutagenesis screens in four cancer cell lines using a guide RNA library predicted to install 32,476 variants in 11 cancer genes. We identify four functional classes of protein variants modulating drug sensitivity and use single-cell transcriptomics to reveal how these variants operate through distinct mechanisms, including eliciting a drug-addicted cell state. We identify variants that can be targeted with alternative inhibitors to overcome resistance and functionally validate an epidermal growth factor receptor (EGFR) variant that sensitizes lung cancer cells to EGFR inhibitors. Our variant-to-function map has implications for patient stratification, therapy combinations and drug scheduling in cancer treatment.

耐药性是癌症治疗长期疗效的主要限制因素。癌症基因组测序可以回顾性地描述耐药性的遗传基础，但这需要大量的治疗后样本来指定因果变异。在这里，我们使用预测在 11 个癌症基因中安装 32,476 个变异的向导 RNA 文库，从四种癌细胞系中的 CRISPR 碱基编辑诱变筛选中前瞻性地确定了对 10 种肿瘤药物耐药的遗传机制。我们确定了调节药物敏感性的蛋白质变体的四种功能类别，并使用单细胞转录组学来揭示这些变体如何通过不同的机制发挥作用，包括引发药物成瘾细胞状态。我们确定了可以用替代抑制剂靶向以克服耐药性的变体，并在功能上验证了使肺癌细胞对 EGFR 抑制剂敏感的表皮生长因子受体 （EGFR） 变体。我们的变异到功能图对癌症治疗中的患者分层、治疗组合和药物调度有影响。