Uncovering conditional vulnerabilities in human cancer cells

Abstract

Forward genetic screens based on either RNAi or CRISPR make it possible to systematically identify genes required for the survival and growth of mammalian cells, and thus offer a powerful approach to characterize protein function and identify potential cancer vulnerabilities. Nonetheless, fitness genes can be context‐dependent, and indeed, CRISPR screens across hundreds of human cell lines have revealed that genetic dependencies can vary with natural cell‐intrinsic diversity. However, while the impact of environmental factors on cell physiology has become better appreciated, there has been little investigation into how nutrient availability affects gene essentiality and, further, most forward genetic screens are performed in vitro using culture media with little relevance to human physiology. We previously developed Human Plasma‐Like Medium (HPLM) – the first systematically designed physiologic medium, which contains over 60 components at concentrations that reflect their average values in human blood. To test the hypothesis that medium composition influences gene essentiality, we performed CRISPR‐based loss‐of‐function screens of blood cancer lines HPLM versus traditional media. Analysis of these data revealed that sets of conditionally essential genes are involved in several biological processes and can vary with both cell‐intrinsic diversity and the combination of basal and serum components that comprise typical media. Moreover, our approach allows for the downstream identification of gene‐nutrient interactions that underlie conditional CRISPR phenotypes, which can in turn uncover conditionally essential protein roles.Additionally, most preclinical therapies fail to achieve translation – a major problem attributed in part to the limited physiologic relevance of existing models. Nonetheless, there has been similarly little systematic investigation into how the composition of culture media might affect drug efficacy. Further, virtually all drug screens, initial hit validation efforts, and studies of drug activity are performed in vitro using traditional media as well. Therefore, we with collaborators at NCATS used a library of approved and (pre)‐clinical drugs to screen blood cancer lines in HPLM versus conventional media. Remarkably, we identified many whose killing activity varied with medium composition, including drugs approved for non‐oncology indications. Indeed, neither the drug‐nutrient interaction nor the mechanism of drug activity in cancer cells is immediately apparent in many such cases.