Systematic mapping of genetic interactions for de novo fatty acid synthesis

Abstract

28The de novo synthesis of fatty acids has emerged as a therapeutic target for various 29 diseases including cancer. While several translational efforts have focused on direct 30 perturbation of de novo fatty acid synthesis, only modest responses have been associated 31 with mono-therapies. Since cancer cells are intrinsically buffered to combat metabolic 32 stress, cells may adapt to loss of de novo fatty acid biosynthesis. To explore cellular 33 response to defects in fatty acid synthesis, we used pooled genome-wide CRISPR 34 screens to systematically map genetic interactions (GIs) in human HAP1 cells carrying a 35 loss-of-function mutation in FASN, which catalyzes the formation of long-chain fatty acids. 36FASN mutant cells showed a strong dependence on lipid uptake that was reflected by 37 negative GIs with genes involved in the LDL receptor pathway, vesicle trafficking, and 38 protein glycosylation. Further support for these functional relationships was derived from 39 additional GI screens in query cell lines deficient for other genes involved in lipid 40 metabolism, including LDLR, SREBF1, SREBF2, ACACA. Our GI profiles identified a 41 potential role for a previously uncharacterized gene LUR1 (C12orf49) in exogenous lipid 42 uptake regulation. Overall, our data highlights the genetic determinants underlying the 43 cellular adaptation associated with loss of de novo fatty acid synthesis and demonstrate 44 the power of systematic GI mapping for uncovering metabolic buffering mechanisms in 45 human cells. 65cells adapt to perturbation of de novo fatty acid synthesis could help identify new 66 targetable vulnerabilities that may inform novel therapeutic strategies or biomarker 67 approaches. 69Mapping genetic interaction (GI) networks provides a powerful approach for identifying the 70 functional relationships between genes and their corresponding pathways. The systematic 71 exploration of pairwise GIs in model organisms revealed that GIs often occur among 72 4 functionally related genes and that GI profiles organize a hierarchy of functional modules 73 (Costanzo et al, 2016; Fischer et al, 2015). Thus, GI mapping has become an effective 74 strategy for identifying functional modules and annotating the roles of previously 75 uncharacterized genes. Model organism GI mapping has also provided insight into the 76 mechanistic basis of cellular plasticity or phenotypic switching that occurs as cells evolve 77 within their environments (Harrison et al, 2007; Szappanos et al, 2011). Accordingly, the 78 insights gained through systematic interrogation of GIs have fuelled significant interest to 79 leverage these approaches towards functionally annotating the human genome. 81Recent technological advances using CRISPR-Cas enable the systematic mapping of GIs 82 in human cells (Wright et al, 2016; Doench, 2018). Here, we explore genome-wide GI 83 screens within the context of human query mutant cells defective for de novo fatty acid 84 synthesis. We systematically mapped genome-wide GI profiles for six genes involved in ...