LAUSR

Discovery Kevin Lou,*,† Luke A. Gilbert,‡,§,∥ and Kevan M. Shokat†,⊥ †Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States ‡Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, United States Department of Urology, University of California, San Francisco, San Francisco, California 94158, United States Innovative Genomics Institute, University of California, San Francisco, San Francisco, California 94158, United States Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States S the connection between oncogenic molecular features and specific genetic vulnerabilities was initially made between the Philadelphia chromosome and the fusion oncoprotein BCR-ABL, inhibitors directed against these selective dependencies have been successfully applied in multiple therapeutic development efforts for the treatment of cancer. These inhibitors are both effective and relatively well tolerated by patients because cancer cells require the function of these driver oncogenes to a greater degree than normal tissue, creating a therapeutic window. This targeted therapeutic approach has largely relied upon the initial recognition of cancer-associated genetic perturbations followed by an investigation of the functions of these proteins and consequences of their inhibition. Functional genomics inverts this framework by first systematically assessing the functional relevance of perturbing (e.g., using CRISPR-Cas9) any gene in the genome of a particular cancer cell. Phenotypes determined from multiple large-scale screens can then be associated with specific oncogenic molecular features to identify potentially tractable targets. Behan et al. tackled the challenge of target prioritization by performing genome-scale CRISPR knockout screens in 324 human cancer cell lines representing 30 different cancer types. The authors developed a computational framework to integrate their functional genomics data with genetic biomarker information to identify both broadly required (“pan-cancer”) and highly specific (“cancer-type-specific) genetic dependencies. The authors then assigned each of 628 priority targets to one of three tractability groups (Figure 1). Tractability group 1 (40 genes) contained genes that had already been targeted by clinically approved or advanced clinical/preclinical compounds. Group 2 (277 genes) encompassed genes with some features that supported their tractability despite not having compounds in clinical development. Genes without strong evidence of tractability were placed in group 3 (311 genes). These efforts nominated a large number of potentially interesting targets, and the authors further investigated a selected example to validate their approach and highlight a novel cancer vulnerability uncovered by their functional genomics data. The RecQ helicase family member WRN, a tractability group 2 gene, was shown to be selectively essential in the context of microsatellite instability (MSI) in multiple cancer types. MSI results from a deficiency in DNA mismatch repair, which can promote the accumulation of pro-oncogenic mutations that support tumor growth and survival. Functional genomics screens are well equipped to determine synthetic lethal (SL) interactions, such as those between WRN and MSI, which formally occur when perturbation of either of two genes alone remains viable, but perturbation of both results in a loss of viability. In this case, MSI is not itself a specific gene but a molecular marker reflective of a particular cancer cell state. Genetic knockout (protein removal), however, is fundamentally distinct from pharmacological inhibition (typically occupancy of an active site), and the authors provided further evidence to bolster WRN’s attractiveness as a drug target in MSI cancers. They demonstrated that expression of point mutant variants of WRN that were helicase deficient was insufficient to rescue knockout of WRN in MSI cells, offering a rationale for the development of chemical inhibitors against the specific functional domain of relevance (Figure 2). The authors concluded by validating the essentiality of WRN in an in vivo xenograft model. Notably, a related manuscript from Chan et al. also nominated WRN as a SL vulnerability in MSI cancers through a large-scale functional genomics approach, and