CRISPR/Cas9-based Genetic Screens Reveal Novel Cancer Cell Mechanisms for Evading Metabolic and Immunological Stress

Genetic screening technologies with the CRISPR-Cas system have greatly expanded our ability to annotate the function of genes in mammalian models at a systems-level. While this has provided novel insight into the genetic basis for diseases such as cancer, the use of this technology remains in its infancy. Through an exploration of the contemporary CRISPR screening literature, we identified a paucity of data informing our understanding of the emerging cancer hallmarks of reprogrammed metabolism and immune evasion. To circumvent these knowledge gaps, we developed and employed CRISPR/Cas9-based genetic screening approaches to reveal new biological insight into how cancer cells adapt to metabolic stress and evade T-cell killing. This included the mapping of genetic interactions (GI) for the de novo fatty acid synthesis pathway, which identified the previously uncharacterized gene, C12orf49 (named herein as Lipid Uptake Regulator; LUR1), as a strong negative GI partner of fatty acid synthase (FASN). We demonstrate LUR1 as being required for the optimal induction of the sterol-regulatory-element binding protein 2 (SREBP2) transcriptional response following intracellular lipid depletion. Furthermore, we identify a core set of genes whose perturbation renders cancer cells more sensitive or resistant to T-cell killing across diverse genetic backgrounds. We subsequently organize these genes into a functional hierarchy through genetic co-essentiality analysis and GI mapping, revealing the power of systematically applying CRISPR screens for uncovering the genetic determinants of complex phenotypes such as immune evasion. Collectively, our data underscore core principles in applying CRISPR/Cas-based genetic screens for interrogating the genotype to phenotype relationship of cancer.Ph.D