Combinatorialin vivogenome editing identifies widespread epistasis during lung tumorigenesis

Abstract

ABSTRACTLung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable tumorigenesisin vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and multiplexed manner. Here, we employed a novel platform to generate tumors with all pairwise inactivation of ten tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast,Apcinactivation showed positive epistasis with the inactivation of several other genes, including dramatically synergistic effects on tumor fitness in combination withLkb1orNf1inactivation. This approach has the potential to expand the scope of genetic interactions that may be functionally characterizedin vivo, which could lead to a better understanding of how complex tumor genotypes impact each step of carcinogenesis.