High-density in vivo profiling of metastatic double knockouts through CRISPR-Cpf1

Metastasis is the major lethal factor of solid cancers. However, the genetic interactions that influence metastatic potential have been challenging to investigate in a systematic manner. A streamlined approach for constructing maps of metastasis gene networks is key to understanding metastasis at the systems level. Here we developed MCAP (massively-parallel Cpf1-crRNA array profiling), an approach for high-throughput interrogation of genetic combinations in vivo. We designed a barcoded, high-density, high-redundancy MCAP library with 11,934 crRNA arrays targeting 325 pairwise combinations of genes implicated in metastasis, and functionally interrogated the metastatic potential of all combinations in parallel in mice. Enrichment, synergy and clonality analyses unveiled a quantitative landscape of genetic interactions in metastasis. We subsequently validated the synergistic effect of Nf2 and Trim72 mutations in promoting lung metastasis in vivo.