Targeted Exome Sequencing of Krebs Cycle Genes Reveals Candidate Cancer–Predisposing Mutations in Pheochromocytomas and Paragangliomas

Abstract

Purpose: Mutations in Krebs cycle genes are frequently found in patients with pheochromocytomas/paragangliomas. Disruption of SDH, FH or MDH2 enzymatic activities lead to accumulation of specific metabolites, which give rise to epigenetic changes in the genome that cause a characteristic hypermethylated phenotype. Tumors showing this phenotype, but no alterations in the known predisposing genes, could harbor mutations in other Krebs cycle genes.Experimental Design: We used downregulation and methylation of RBP1, as a marker of a hypermethylation phenotype, to select eleven pheochromocytomas and paragangliomas for targeted exome sequencing of a panel of Krebs cycle-related genes. Methylation profiling, metabolite assessment and additional analyses were also performed in selected cases.Results: One of the 11 tumors was found to carry a known cancer-predisposing somatic mutation in IDH1. A variant in GOT2, c.357A>T, found in a patient with multiple tumors, was associated with higher tumor mRNA and protein expression levels, increased GOT2 enzymatic activity in lymphoblastic cells, and altered metabolite ratios both in tumors and in GOT2 knockdown HeLa cells transfected with the variant. Array methylation-based analysis uncovered a somatic epigenetic mutation in SDHC in a patient with multiple pheochromocytomas and a gastrointestinal stromal tumor. Finally, a truncating germline IDH3B mutation was found in a patient with a single paraganglioma showing an altered a-ketoglutarate/ isocitrate ratio.Conclusions: This study further attests to the relevance of the Krebs cycle in the development of PCC and PGL, and points to a potential role of other metabolic enzymes involved in metabolite exchange between mitochondria and cytosol. Clin Cancer Res; 23(20); 6315-24. Ó2017 AACR.

Paraganglioma of the tongue with SDHB gene mutation in a patient with Graves’ disease

“…Metabolomics allowed to group PGLs into two clusters depending on pathogenesis and catecholamine phenotype (Table ). Cluster 1 PGLs have an “immature” biochemical phenotype while cluster 2 PGLs have a “differentiated” phenotype . This clustering provided new strategies for treatment of malignant and metastatic PGLs .…”

“…[20][21][22] In addition, succinate can also promote a particular CpG island methylation phenotype (CIMP) by impairment of histone demethylation. 21 Metabolomics allowed to group PGLs into two clusters depending on pathogenesis and catecholamine phenotype (Table 2). Cluster 1 PGLs have an "immature" biochemical phenotype while cluster 2 PGLs have a "differentiated" phenotype.…”

“…Cluster 1 PGLs have an "immature" biochemical phenotype while cluster 2 PGLs have a "differentiated" phenotype. 1,7,20,21 This clustering provided new strategies for treatment of malignant and metastatic PGLs. 22 The multikinase inhibitor sunitinib has been tested in several patients obtaining partial responses in some cases.…”

Molekuláris genetikai vizsgálatok az örökletes endokrinológiai tumor szindrómák klinikai diagnosztikájában

“…Az SDHB-, SDHC-és SDHD-génen kívül az elmúlt 8 évben további 9 gén betegségokozó mutációit azonosí-tották örökletes paragangliomákban (SDHA-, SDHAF2-, FH-, KIF1B-, PHD2-, MAX-, TMEM127-, MDH2-és GOT2-gén-mutációk) [27][28][29][30][31][32][33][34][35]. A lehetséges betegség-okozó gének nagy száma jelentően megnövelheti a genetikai vizsgálatok költségét és a munkaidőt, ezért elengedhetetlen az egyes gének vizsgálatának racionális megtervezése.…”

“…Az utóbbi évtizedben megjelent új generációs szekvenálási (NGS) módszerek a Phaeo és a PGL-ek tekintetében igazi sikertörténetek, hiszen a legutóbb azonosí-tott 3 Phaeo/PGL gén (MAX, FH és MDH2) felfedezése is ilyen technológiát alkalmazó exomszekvenálással történt [32][33][34][35].…”