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

Susan Richter, Laura Gieldon, Ying Pang, Mirko Peitzsch, Thanh Huynh, Rocio Leton, Bruna Viana, Tonino Ercolino, Anastasios Mangelis, Elena Rapizzi, Mario Menschikowski, Daniela Aust, Matthias Kroiss, Felix Beuschlein, Volker Gudziol, Henri Jlm Timmers, Jacques Lenders, Massimo Mannelli, Alberto Cascon, Karel Pacak, Mercedes Robledo, Graeme Eisenhofer, Barbara Klink

Journal: Genetics in medicine : official journal of the American College of Medical Genetics 2019;21(3):705-717

PMID: 30050099

Abstract

PURPOSE

Metabolic aberrations have been described in neoplasms with pathogenic variants (PV) 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 PV . 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. Multigene panel sequencing was applied to detect driver PV in cases with indicative metabolite profiles but undetermined genetic drivers.

RESULTS

Aberrant Krebs cycle metabolomes identified rare cases of PPGLs with germline PV in FH and somatic PV in IDHx and SDHx, including the first case of a somatic IDH2 PV in PPGL. Metabolomics also reliably identified PPGLs with SDHx loss-of-function (LOF) PV. 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 PV in FH and IDHx.

Address: Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany. [email protected].; Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA.; Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.; Hereditary Endocrine Cancer Group, CNIO, Madrid, Spain and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.; Azienda Ospedaliero-Universitaria Careggi, Endocrinology Unit, Florence, Italy.; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.; Institute of Pathology, Tumor and Normal Tissue Bank of the UCC/NCT Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.; Department of Internal Medicine, Division of Endocrinology, University Hospital, University of Würzburg, Würzburg, Germany.; Medizinische Klinik and Poliklinik IV, Ludwig-Maximilians-Universität München, Munich, Germany.; Department for Endocrinology, Diabetology and Clinical Nutrition, UniversitätsSpital Zürich, Zurich, Switzerland.; Departments of Otorhinolaryngology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.; Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands.; Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands.; Department of Medicine III, University Hospital Dresden, Dresden, Germany.; Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.; Department of Medicine III, University Hospital Dresden, Dresden, Germany.
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