SLC25A11, a Novel Gene Associated With Carney-Stratakis Syndrome

Abstract

Background: Carney-Stratakis syndrome (CSS), a rare condition characterized by paragangliomas and/or pheochromocytomas and gastrointestinal stromal tumors (GIST), is caused by germline heterozygous pathogenic variants in the succinate dehydrogenase subunit genes (SDHB, SDHC, SDHD).

Methods: Histological, genetic, and functional analyses were conducted in a 59-year-old female with CSS (9 cm left pheochromocytoma, 4.8 cm paraganglioma, and 9.3 cm GIST). Whole-exome sequencing (WES) of germline DNA paired with tumor DNA was performed.

Results: WES identified a rare 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). WES of pheochromocytoma, paraganglioma, and GIST did not reveal somatic pathogenic variants in genes previously associated with these tumors. A significant reduction in SLC25A11 expression was observed in the tumors of this patient with the SLC25A11 c.293G>A variant (0.69 ± 0.003) compared to tumors from cluster 1 (1.39 ± 0.45; P = 0.0229) and cluster 2 (1.79 ± 0.71; P = .0154). Consistent with the mRNA findings, SLC25A11 protein levels were markedly reduced in the pheochromocytoma and paraganglioma compared to other tumors. Negative staining for 5-hydroxymethylcytosine in all 3 tumors suggests a DNA hypermethylation profile characteristic of cluster 1A, despite normal SDHB expression levels. However, genome-wide copy number variation analysis did not reveal any loss of heterozygosity at the SLC25A11 locus.

Conclusion: The loss of SLC25A11 expression in tumors, the absence of somatic drivers, and the hypermethylation status strongly support the role of SLC25A11 in CSS pathogenesis.

Keywords: Carney-Stratakis syndrome; genetics; paraganglioma; pheochromocytoma.

Figure 1.

(A) Magnetic resonance images of a patient with Carney-Stratakis syndrome. Axial T2-weighted magnetic resonance imaging (MRI) shows a left solid-cystic pheochromocytoma (PHEO; white arrow), an axial T2-weighted MRI depicts a para-aortic paraganglioma (PGL; white arrow), and MRI scans illustrate a gastrointestinal stromal tumor (GIST; white arrow) originating from the gastric body and fundus. (B) Whole-exome sequencing results reveal a key germline variant in the DNA of the patient with CSS.

Figure 2.

(A) Analysis of SDHB transcript levels in PPGL tumor samples using RT-qPCR. Bars represent the mean ± SD between replicates. CSS sample (patient sample): Refers to the RNA obtained from the paraganglioma (PGL) and pheochromocytoma (PHEO) of a patient with Carney-Stratakis syndrome harboring the novel heterozygous germline variant c.293G>A (p.R98H) in SLC25A11. SDHB Controls: Includes tumor samples from patients carrying pathogenic SDHB variants, specifically p.R230C (c.688C>T) and c.201-2A>G (near the canonical splice site). Other PPGL samples: Includes tumor samples from patients harboring pathogenic variants in Cluster 1B (VHL, n = 2) and Cluster 2 (RET, n = 5; TMEM127, n = 2). The ACTB gene was used as an endogenous control. (B) Western blot analysis of total SDHB protein levels in PPGL tumor samples, including both PHEO and PGL samples from the patient with CSS. Three SDHB-deficient tumor samples were used as controls. The specific gene variant for each sample is indicated in the figure. β-Tubulin protein was used as a loading control.

Figure 3.

(A) Reduced mRNA levels of SLC25A11 in tumor samples from the patient with Carney-Stratakis syndrome (CSS). Bars represent the mean ± SD from replicates. CSS sample (patient sample): Refers to the RNA obtained from the paraganglioma (PGL) of the CSS patient. Other samples: Includes pheochromocytoma (PHEO) and PGL from patients harboring pathogenic variants in Cluster 1 (SDHB, n = 2; SDHD, n = 1; VHL, n = 1) and Cluster 2 (RET, n = 5; TMEM127, n = 2). The ACTB gene was used as an endogenous control. (B) Western blot analysis of SLC25A11 protein levels in PHEO and PGL samples from the CSS patient. The gene variant for each sample is indicated in the figure. β-Actin was used as a loading control, and protein loading was further verified by Ponceau S staining.

Figure 4.

Immunohistochemical analysis of SDHB and 5-hydroxymethylcytosine (5hmC) in tumor samples from a patient with Carney-Stratakis syndrome, including pheochromocytoma (PHEO), paraganglioma (PGL), and gastrointestinal stromal tumors (GIST). The samples were stained with hematoxylin and eosin (HE), and images were captured at a magnification of 400×.