sqc (2025-07-31 23:53):
#paper, 《A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy》, 10.1186/s13073-021-00987-8, 本研究开发了一个名为 Cancer Data Integrator(CanDI)的 Python 框架,用于整合来自 CCLE、DepMap、PICKLES、CORUM 等多源公开数据,实现跨组学(基因组、转录组、蛋白组、代谢组)与功能基因组数据的无缝查询与联合分析。作者通过统一索引与类对象抽象,使用户无需数据库背景即可快速完成复杂条件筛选与可视化。利用 CanDI,研究者在卵巢癌和乳腺癌模型中发现了 BRCA1 突变背景下 Fanconi Anemia 通路的合成致死性;在 KRAS 与 EGFR 突变 NSCLC 模型中评估了基因条件必需性;首次系统揭示了男性与女性 KRAS 突变结直肠癌、胰腺癌和肺癌模型中的性别差异必需基因;并整合外部支气管上皮 RNA-seq 数据,提名了 12 个定位于细胞膜、在 KRAS/EGFR 突变 NSCLC 中显著上调的潜在免疫治疗靶点。CanDI 以灵活、可扩展的方式降低了大规模癌症数据整合门槛,为发现新靶点、解释性别差异及设计联合治疗策略提供了高效工具。
A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy
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Abstract:
AbstractBackgroundAdvances in cancer biology are increasingly dependent on integration of heterogeneous datasets. Large-scale efforts have systematically mapped many aspects of cancer cell biology; however, it remains challenging for individual scientists to effectively integrate and understand this data.ResultsWe have developed a new data retrieval and indexing framework that allows us to integrate publicly available data from different sources and to combine publicly available data with new or bespoke datasets. Our approach, which we have named the cancer data integrator (CanDI), is straightforward to implement, is well documented, and is continuously updated which should enable individual users to take full advantage of efforts to map cancer cell biology. We show that CanDI empowered testable hypotheses of new synthetic lethal gene pairs, genes associated with sex disparity, and immunotherapy targets in cancer.ConclusionsCanDI provides a flexible approach for large-scale data integration in cancer research enabling rapid generation of hypotheses. The CanDI data integrator is available athttps://github.com/GilbertLabUCSF/CanDI.
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