An in vivo genome-wide CRISPR/Cas9 screen in mice identifies genes that control lung metastasis.

  • Major finding: An in vivo genome-wide CRISPR/Cas9 screen in mice identifies genes that control lung metastasis.

  • Concept: The primary tumor growth advantage conferred by loss-of-function mutations correlates with metastasis.

  • Impact: CRISPR/Cas9 screens can be used to assess the role of genes in cancer-related phenotypes in vivo.

The genomic landscape of cancer cells is complex, harboring a mixture of driver and passenger mutations. Genetic screens have been essential in determining causal links between genetic alterations and cancer phenotypes, including tumor growth and metastasis. To identify loss-of-function mutations that promote primary tumor growth and metastasis in vivo, Chen, Sanjana, and colleagues performed a genome-wide CRISPR/Cas9–mediated screen using a nonmetastatic mouse non–small cell lung cancer (NSCLC) line. Introduction of a pooled genome-scale mouse CRISPR knockout library containing 67,405 single-guide RNAs (sgRNA) targeting 20,611 protein-coding genes and 1,175 microRNAs enhanced primary tumor growth and the formation of lung metastasis compared with uninfected cells. Deep sequencing of early- and late-stage primary tumors and lung metastases revealed dynamic changes in sgRNA representation during tumor evolution; less than half of sgRNAs were retained in early primary tumors, with only 8% of these sgRNAs detected in late-stage tumors and ≤1.1% of these sgRNAs selected for in corresponding lung metastases. Importantly, late primary tumors and metastases were enriched in sgRNAs targeting proapoptotic genes and tumor suppressors that are mutated or downregulated in human NSCLC. Furthermore, lung metastases were enriched in only a small number of sgRNAs, which were highly correlated with the sgRNAs enriched in late primary tumors, suggesting that mutant cells with a proliferative advantage in late-stage tumors preferentially seed metastases. In vivo validation of top-scoring genes using individual sgRNAs or sgRNA minipools revealed that loss-of-function mutations in genes including Nf2, Pten, Trim72, Cdkn2a, Fga, miR-152, and miR-345 were sufficient to enhance lung metastasis and that accelerated primary tumor formation correlated with increased metastatic incidence. Together, this work identifies specific loss-of-function mutations that drive tumor growth and metastasis and highlights the use of CRISPR/Cas9 screening technology to characterize the functional role of genes in cancer cell phenotypes in vivo

Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 2015;160:1246–60.

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