12510 SLC25A11 As A Novel Gene For Carney-stratakis Syndrome

Abstract

Abstract Disclosure: F. Freitas-Castro: None. L.S. Santana: None. G.F. Fagundes: None. A.F. Afonso: None. E.C. Lobato: None. F.L. Ledesma: None. I.C. Soares: None. B.B. Mendonca: None. M.C. Fragoso: None. A. Latronico: None. C.A. Stratakis: None. M.Q. Almeida: None. Background: Carney-Stratakis syndrome (CSS, OMIM #606864), also reported as “paraganglioma and gastrointestinal stromal tumor syndrome” or Carney-Stratakis dyad, is an autosomal dominant rare syndrome with incomplete penetrance, characterized by the association of paragangliomas (PGL) and/or pheochromocytomas (PHEO) and gastrointestinal stromal tumors (GIST). CSS is mainly caused by germline heterozygous pathogenic variants (PVs) in the succinate dehydrogenase subunit genes (SDHB, SDHC, SDHD), with SDHB and SDHD being the most frequently affected. Aim: To investigate a novel genetic etiology for CSS not associated with germline SDHx defects. Methods: Genetic investigation using SANGER sequencing and multiplex ligation-dependent probe amplification (MLPA) rule out germline defects for SDHx in a 59-year-old woman diagnosed with a 9 cm left PHEO, 4.8 cm PGL and 9.3 cm GIST. Thus, we performed whole exome sequencing of germline DNA (paired with tumor DNA from PHEO, PGL, and GIST) and applied a targeted analysis with the enrichment of 3,485 potential neuroendocrine tumors susceptibility genes associated with cellular response to hypoxia, mitochondrion, Krebs cycle, and tumorigenesis (MAPK, mTOR, ERK, and Wnt signaling). Additionally, we performed RT-qPCR to determine SLC25A11 expression levels in PHEO and PGL samples, stratified into three groups: tumors from the case harboring the SLC25A11 variant, Cluster 1 (n= 4), and Cluster 2 (n= 8). Tumor DNA methylation status was assessed using immunostaining for 5-hydroxymethylcytosine (5hmC). Results: Exome sequencing revealed a new heterozygous germline variant (c.293G>A / p.Arg98His) in the mitochondrial 2-oxoglutarate/malate carrier gene (SLC25A11). This variant, located in a highly conserved residue of the SLC25A11 mitochondrial carrier domain, is predicted to be deleterious in silico (REVEL score= 0.81). Exome sequencing of the PHEO and PGL did not reveal somatic PVs in genes previously associated with PHEO and PGL. Moreover, somatic c-KIT and PDGFRA PVs were not identified in GIST. Notably, a significant downregulation of SLC25A11 expression was observed in tumor samples harboring the SLC25A11 p.Arg98His variant (0.57 ± 0.13) compared with tumors from cluster 1 (1.39 ± 0.45; p = 0.025) and cluster 2 (1.79 ± 0.71; p < 0.001). Interestingly, immunostaining for 5hmC was negative in all tumors (PHEO, PGL and GIST), indicating tumor hypermethylation. Conclusion: A rare germline deleterious variant in SLC25A11 was identified in a patient with CSS. Moreover, the absence of somatic drivers, hypermethylation status and loss of SLC25A11 expression in the CSS tumors support the involvement of this gene with CSS. Support: Sao Paulo Research Foundation (FAPESP) grant 2019/15873-6 (to M.Q.A.), and FAPESP post-doctoral fellowship 2021/11240-9 (to F.F-C.). Presentation: 6/1/2024