Combinatorial CRISPR/Cas9 Screening Reveals Epistatic Networks of Interacting Tumor Suppressor Genes and Therapeutic Targets in Human Breast Cancer.
Combinatorial CRISPR/Cas9 Screening Reveals Epistatic Networks of Interacting Tumor Suppressor Genes and Therapeutic Targets in Human Breast Cancer.
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DOI：
10.1158/0008-5472.can-21-2555
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发表时间：
2021-12-15
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影响因子：
11.2
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中科院分区：
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这项研究为从基于单驱动基因分析的发现和治疗策略的开发到基于多个驱动基因之间的相互作用的发现提供了路线图。大多数癌症是由多种基因改变驱动的，但这些改变在肿瘤发生过程中如何协同作用在很大程度上仍不清楚。为了从机制上深入了解肿瘤抑制基因(TSG)之间的致癌基因相互作用，我们在人乳腺上皮细胞中进行了组合CRISPR筛选和单细胞转录图谱分析。正如预期的那样，乳腺上皮细胞中不同的驱动基因改变影响了能够诱导肿瘤形成的肿瘤抑制基因改变的谱系。更令人惊讶的是，TSG相互作用网络由许多集团组成--由三到四个基因组成的集合，使得集团内的每个TSG都显示出与集团中所有其他基因的致癌合作。遗传互作图谱表明，主要合作的TSG共享重叠功能，而不是截然不同或互补的功能。CRISPR双基因敲除的单细胞转录图谱显示，在促进肿瘤发生和生长因子独立方面协同的TSG表现出转录上位性，而不协同的TSGs则没有。这些上位性转录变化，包括缓冲和协同作用，影响了致癌介质和治疗靶点的表达，包括CDK4、SRPK1和DNMT1。重要的是，在这个系统中，由于TSG的双重失活引起的上位性表达变化，如PTEN和TP53，也在患者肿瘤中观察到，建立了这些发现与人类乳腺癌的相关性。据估计，乳腺癌中50%的差异表达基因是由上位性相互作用控制的。总体而言，我们的研究表明转录上位性是多基因乳腺癌进展的一个中心方面，并概述了在其他人类癌症中发现驱动基因上位性网络的方法。这项研究为从基于单驱动基因分析的发现和治疗策略的开发到基于多个驱动基因之间的相互作用的发现提供了路线图。见Fong等人的相关评论，第6078页
This study provides a roadmap for moving beyond discovery and development of therapeutic strategies based on single driver gene analysis to discovery based on interactions between multiple driver genes. The majority of cancers are driven by multiple genetic alterations, but how these changes collaborate during tumorigenesis remains largely unknown. To gain mechanistic insights into tumor-promoting genetic interactions among tumor suppressor genes (TSG), we conducted combinatorial CRISPR screening coupled with single-cell transcriptomic profiling in human mammary epithelial cells. As expected, different driver gene alterations in mammary epithelial cells influenced the repertoire of tumor suppressor alterations capable of inducing tumor formation. More surprisingly, TSG interaction networks were comprised of numerous cliques—sets of three or four genes such that each TSG within the clique showed oncogenic cooperation with all other genes in the clique. Genetic interaction profiling indicated that the predominant cooperating TSGs shared overlapping functions rather than distinct or complementary functions. Single-cell transcriptomic profiling of CRISPR double knockouts revealed that cooperating TSGs that synergized in promoting tumorigenesis and growth factor independence showed transcriptional epistasis, whereas noncooperating TSGs did not. These epistatic transcriptional changes, both buffering and synergistic, affected expression of oncogenic mediators and therapeutic targets, including CDK4, SRPK1, and DNMT1. Importantly, the epistatic expression alterations caused by dual inactivation of TSGs in this system, such as PTEN and TP53, were also observed in patient tumors, establishing the relevance of these findings to human breast cancer. An estimated 50% of differentially expressed genes in breast cancer are controlled by epistatic interactions. Overall, our study indicates that transcriptional epistasis is a central aspect of multigenic breast cancer progression and outlines methodologies to uncover driver gene epistatic networks in other human cancers. This study provides a roadmap for moving beyond discovery and development of therapeutic strategies based on single driver gene analysis to discovery based on interactions between multiple driver genes. See related commentary by Fong et al., p. 6078