A CRISPR knockout screen highlighting dependencies on acetate metabolism for fatty acid biosynthesis reveals a role for SLC16A13 in acetate import into cancer cells

The connection between cancer progression and deregulated cell metabolism is well established, as metabolites act as biomass sources and signaling modulators. Acetate is a major alternative nutrient source of acetyl-CoA and consequently influences oxidative respiration, lipid metabolism, and epigenetic regulation. While the role of acetatemetabolizing enzymes in cancer is an area of active study, a mechanistic and quantitative understanding of how acetate crosses the plasma membrane to contribute to compartmentalized cell metabolism is currently under-investigated and focused mostly on the activity the monocarboxylate transporters SLC16A1 and SLC16A3. To address this, we developed and applied an LC-MS metabolomics platform to quantitatively assess net metabolic consumption fluxes through the plasma membrane on a large panel of established cancer cell line models. We report on the relative contribution of each downstream functional pathway to acetate consumption, describing the larger quantitative role that fueling of the TCA cycle takes in comparison to biosynthesis and acetylation. By analyzing the landscape of transporter gene expression in cancer, we associate the poorly studied transporter SLC16A13 to acetate metabolism. Moreover, by designing and validating a CRISPR KO screen methodology that identifies genetic dependencies on acetate metabolism to sustain cell proliferation we directly link SLC16A13 to acetate import inside the cell. These findings open the opportunity of investigating the mechanism of acetate transport in multiple cancer types using the same methodology, while shedding light on a previously poorly characterized solute carrier transporter. A quantitative and mechanistic description of acetate transport is in general critical for increasing our understanding of cancer metabolism and human physiology, but targeting acetate transport in particular has translational potential for treating cancer in tissue-specific contexts, taking into account the role of acetate metabolism for immune responses. Elucidating the contribution of different transporters to acetate import is thus what we sought to address with this thesis.