Squalene accumulation in cholesterol auxotrophic lymphomas prevents oxidative cell death

Cholesterol is essential for cells to grow and proliferate. While normal mammalian cells meet their need for cholesterol through its uptake or de novo synthesis(1), the extent to which cancer cells rely on each of these pathways remains poorly understood. Here, using a competitive proliferation assay on a pooled collection of DNA-barcoded cell lines, we identified a subset that is auxotrophic for cholesterol and thus highly dependent on its uptake. Metabolic gene expression analysis pinpointed loss of squalene monooxygenase (SQLE) expression as a cause of the cholesterol auxotrophy, particularly in ALK+ anaplastic large cell lymphoma (ALCL) cell lines and primary tumors. SQLE catalyzes the oxidation of squalene to 2,3-oxidosqualene in the cholesterol synthesis pathway and its loss results in accumulation of the upstream metabolite squalene, which is normally undetectable. In ALK+ ALCLs, squalene alters the cellular lipid profile and protects cancer cells from ferroptotic cell death, providing a growth advantage under conditions of oxidative stress and in tumor xenografts. Finally, a CRISPR-based genetic screen identified cholesterol uptake by the low-density lipoprotein receptor (LDLR) as essential for the growth of ALCL cells in culture and as patient-derived xenografts. This work reveals that the cholesterol auxotrophy of ALCLs is a targetable liability, and, more broadly, that systematic approaches are useful for identifying nutrient dependencies unique to individual cancer types.