Metabolome-guided genomics to identify pathogenic variants in isocitrate dehydrogenase, fumarate hydratase, and succinate dehydrogenase genes in pheochromocytoma and paraganglioma

Purpose: Metabolic aberrations have been described in neoplasms with mutations in the Krebs cycle genes encoding succinate dehydrogenase (SDH), fumarate hydratase (FH) and isocitrate dehydrogenase (IDH). In turn, accumulation of oncometabolites succinate, fumarate, and 2-hydroxyglutarate can be employed to identify tumors with those mutations. Additionally, such metabolic readouts may aid in genetic variant interpretation and improve diagnostics. Methods: Using liquid-chromatography-mass-spectrometry, 395 pheochromocytomas and paragangliomas (PPGLs) from 391 patients were screened for metabolites to indicate Krebs cycle aberrations. Multi-gene panel-sequencing was applied to detect driver mutations in cases with indicative metabolite profiles but undetermined genetic drivers. Results: Aberrant Krebs cycle metabolomes identified rare cases of PPGLs with germline mutations in FH and somatic mutations in IDHx and SDHx, including the first case of a somatic IDH2 mutation in PPGL. Metabolomics also reliably identified PPGLs with SDHx loss-of-function (LOF) mutations. Therefore we utilized tumor metabolite profiles to further classify variants of unknown significance in SDHx, thereby enabling missense-variants associated with SDHx LOF to be distinguished from benign variants. Conclusion: We propose incorporation of metabolome data into the diagnostics algorithm in PPGLs to guide genetic testing and variant interpretation and to help identify rare cases with mutations in FH and IDHx.