Cancer Cell’s Seven Achilles Heels: Considerations for design of anti-cancer drug combinations.

Loss of function screens using shRNA and CRISPR are routinely used to identify genes that modulate responses of tumor cells to anti-cancer drugs. Here, by integrating GSEA and CMAP analyses of multiple published shRNA screens, we identified a core set of pathways that affect responses to multiple drugs with diverse mechanisms of action. This suggests that these pathways represent “weak points” or “Achilles heels”, whose mild disturbance should make cancer cells vulnerable to a variety of treatments. These “weak points” include proteasome, protein synthesis, RNA splicing, RNA synthesis, cell cycle, Akt-mTOR, and tight junction-related pathways. Therefore, inhibitors of these pathways are expected to sensitize cancer cells to a variety of drugs. This hypothesis was tested by analyzing the diversity of drugs that synergize with FDA-approved inhibitors of the proteasome, RNA synthesis, and Akt-mTOR pathways. Indeed, the quantitative evaluation indicates that inhibitors of any of these signaling pathways can synergize with a more diverse set of pharmaceuticals, compared to compounds inhibiting targets distinct from the “weak points” pathways. Our findings described here imply that inhibitors of the “weak points” pathways should be considered as primary candidates in a search for synergistic drug combinations. We used microarray to identify genetic interaction partners of 2 drugs Samples were collected at different time points after infection with the 90k shRNA libraries and probes were prepared to hybridize to microarray chips to identify GI partners of 2 drugs.

基于短发卡RNA（shRNA）和成簇规律间隔短回文重复序列（CRISPR）的功能缺失筛选，是当前用于鉴定调控肿瘤细胞对抗癌药物应答相关基因的常规实验手段。本研究通过整合多项已发表的shRNA筛选的基因集富集分析（Gene Set Enrichment Analysis，GSEA）与连通性图谱（Connectivity Map，CMAP）数据，鉴定出一组核心通路，这些通路可影响肿瘤细胞对多种作用机制各异的抗癌药物的应答反应。这表明这些通路可被视为肿瘤细胞的"薄弱环节"或"阿喀琉斯之踵"，对其进行轻度扰动即可使癌细胞对多种治疗手段产生敏感性。这些"薄弱环节"涵盖蛋白酶体、蛋白质合成、RNA剪接、RNA合成、细胞周期、Akt-mTOR以及紧密连接相关通路。因此，靶向这些通路的抑制剂有望增强癌细胞对多种药物的敏感性。本研究通过分析与美国食品药品监督管理局（Food and Drug Administration，FDA）批准的蛋白酶体、RNA合成及Akt-mTOR通路抑制剂具有协同作用的药物多样性，对上述假说进行了验证。定量评估结果证实，相较于靶向"薄弱环节"通路以外靶点的化合物，上述任意信号通路的抑制剂均可与更多种类的药物产生协同效应。本研究结果表明，在筛选协同药物组合的研究中，靶向"薄弱环节"通路的抑制剂可作为优先候选对象。我们采用基因芯片（microarray）技术鉴定两种药物的遗传互作伴侣（genetic interaction partners，GI partners）：实验中，我们在感染90k shRNA文库后的不同时间点收集样本，制备探针并与基因芯片进行杂交，以此鉴定两种药物的遗传互作伴侣。