Proteo-metabolomics and patient tumor slice experiments point to amino acid centrality for rewired mitochondria in fibrolamellar carcinoma

Fibrolamellar carcinoma (FLC) is a rare, lethal, early-onset liver cancer with a critical need for new therapeutics. The primary driver in FLC is the fusion oncoprotein, DNAJ-PKAc, which remains challenging to target therapeutically. It is critical, therefore, to expand understanding of the FLC molecular landscape to identify druggable pathways/targets. Here, we perform the most comprehensive integrative proteo-metabolomic analysis of FLC. We also conduct nutrient manipulation, respirometry analyses, as well as key loss-of-function assays in FLC tumor tissue slices from patients. We propose a model of cellular energetics in FLC pointing to proline anabolism being mediated by ornithine aminotransferase hyperactivity and ornithine transcarbamylase hypoactivity with serine and glutamine catabolism fueling the process. We highlight FLC’s potential dependency on voltage-dependent anion channel (VDAC), a mitochondrial gatekeeper for anions including pyruvate. The metabolic rewiring in FLC that we propose in our model, with an emphasis on mitochondria, can be exploited for therapeutic vulnerabilities. [Display omitted] •Proteo-metabolomics predicts SDS dependency that is validated in patient tumor slices•OAT, GLS, and ALDH18A1 form an axis central to mitochondrial rewiring in FLC•Profiling and functional studies show a lack of dependency on glycolysis•Erastin administration in tumor tissue slices demonstrates potential dependency on VDAC Fibrolamellar carcinoma (FLC) is a rare but lethal liver cancer lacking effective therapeutics. Long, Jr. et al. provide the most comprehensive map to date of rewired metabolism in FLC. The study leverages multi-omics, nutrient manipulation, respirometry analyses, and functional studies in patient tumor tissue slices. The results reveal potential therapeutic vulnerabilities.