Challenges and opportunities for drug repurposing in cancers based on synthetic lethality induced by tumor suppressor gene mutations

Abstract

Although two-thirds of cancers arise from loss-of-function mutations in tumor suppressor genes, there are few approved targeted therapies linked to these alterations. Synthetic lethality offers a promising strategy to treat such cancers by targeting vulnerabilities unique to cancer cells with these mutations. To identify clinically relevant synthetic lethal interactions, we analyzed genome-wide CRISPR/Cas9 knock-out (KO) viability screens from the Cancer Dependency Map and evaluated their clinical relevance in patient tumors through mutual exclusivity, a pattern indicative of synthetic lethality. Indeed, we found significant enrichment of mutual exclusivity for interactions involving cancer driver genes compared to non-driver mutations. To identify therapeutic opportunities, we integrated drug sensitivity data to identify inhibitors that mimic the effects of CRISPR-mediated KO. This approach revealed potential drug repurposing opportunities, including BRD2 inhibitors for bladder cancers with ARID1A mutations and SIN3A-mutated cell lines showing sensitivity to nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. However, we discovered that pharmacological inhibitors often fail to phenocopy KO of matched drug targets, with only a small fraction of drugs inducing similar effects. This discrepancy reveals fundamental differences between pharmacological and genetic perturbations, emphasizing the need for approaches that directly assess the interplay of loss-of-function mutations and drug activity in cancer models. Author SummarySynthetic lethality is an emerging approach for targeting a biological dependency in cancer cells that does not harm normal cells. This strategy is particularly valuable for targeting loss-of-function mutations in tumor suppressor genes, which are more challenging to directly target. In an effort to accelerate treatments for cancer patients, we aimed to map out these dependencies and overlap them with responses to available drugs. We discovered different outcomes when a protein is targeted by a drug versus when that same target is disrupted genetically. Thus, if a drug is to be effectively repurposed as synthetic lethal agent, feasibility studies must capture drug biology, ideally by test the drug empirically in relevant cancer models. A second notable discovery is that in vitro synthetic lethal interactions involving cancer driver genes are significantly more likely to exhibit consistent patterns, such as mutual exclusivity in human tumor samples. This is important since selection of relevant cell lines is often critical in drug development to maximize potential for translation to clinical responses.