An integrated Omics analysis to identify mode of action of a metabolically active compound

Succinate dehydrogenase (SDH) is a tetramer complex that enzymatically converts succinate to fumarate and functions as a tumor suppressor. SDH is localized to the mitochondria where it participates in both the tricarboxylic acid cycle and the electron transport chain. Mutations in Sdhb, a nuclear gene that encodes the B subunit, are prevalent in pheochromocytoma, paraganglioma, renal cell carcinoma, and gastrointestinal stromal tumors. A synthetic lethal phenotypic drug screen in vitro identified a compound that selectively targeted Sdhb-deficient mouse-kidney cells but not wild-type ones. We aimed to characterize the mode of action that led to the differential effect of the drug on both genotypes. We devised a two-factor design where we integrated transcriptomics, metabolomics, and phosphoproteomics data using statistically robust methods and network analysis. The analysis flagged an upregulation of Txnip and Arrdc4 expression, both members of the α-arrestin family and inhibitors of GLUT transporters. This upregulation leads to an impairment in glucose uptake, which is essential in the energetically compromised Sdhb-deficient cells. The expression of the α-arrestins is critically regulated by chREBP, a transcription factor activated by dephosphorylation in a dependent manner of the phosphate pentose pathway, which was found to be completely inhibited by the compound. Additionally, we identified the upregulation of a tightly clustered set of genes involved in the cholesterol and fatty acid synthesis in the wild type suggesting a mode of survival that is dependent on Sdhb activity. These results demonstrate the efficacy of multi-omics integration to reconstruct metabolic effects regulated at different levels.