Loss of SDHB manifests differently in the proteomes of neuroendocrine tumors and a tumor-derived cell line model hPheo-1

Pheochromocytomas and paragangliomas (PPGL) are rare neuroendocrine tumors derived from chromaffin cells. PPGL with germline mutations in the succinate dehydrogenase subunit B (SDHB), an enzyme participating in the TCA cycle and electron transport chain (ETC), are associated with a high rate of malignancy and metastasis.

Unfortunately, the absence of a reliable in vitro or in vivo human PPGL model limits functional research, including drug testing. Only a single stable cell line of human PPGL origin—hPheo1—is currently available. An SDHB knockout cell sub-line hPheo-1 SDHB KO has been recently generated as a model of human SDHB-mutated PPGL. To evaluate its relevance, we asked whether this model recapitulates the specific proteome changes found in SDHB-mutated human PPGL tumors.

Using 2D-LC-MS/MS with TMT-based quantitation, we performed proteomic analysis of 1) hPheo1 cells vs. hPheo-1 cells SDHB KO and b) human PPGL samples, including tumors with and without SDHB mutation.

In the cell line model, we identified and quantified over 7200 proteins. The SDHB loss was associated with almost 250 differentially expressed proteins, including marked downregulation of the remaining succinate dehydrogenase subunits SDHC and SDHD but not SDHA. In addition to the complex II of ETC, most observed components of complex I, III, and IV were downregulated in the SDHB KO cell model. However, no marked changes were observed in the expression of the other TCA cycle enzymes.

The overlap between the changes caused by SDHB deficiency in cell line versus human PPGL was rather limited. Arginase 2 and ornithine aminotransferase upregulation was associated with SDHB defect in both tumors and cells, along with upregulated monofunctional C1-tetrahydrofolate synthase and bifunctional methylenetetrahydrofolate dehydrogenase. This may suggest a compensatory metabolic remodeling of amino acid utilization and of the folate cycle. While the SDHB-deficient cell line downregulated the expression of all ETC complexes, SDHB mutation in tumors was generally associated with the opposite effect- mildly upregulated ETC components (except for SDHB-containing Complex II). Similarly, in contrast to the cell model, SDHB-deficient tumors showed increased expression of enzymes of pyruvate metabolism and TCA cycle (except SDHB). These energo-metabolic changes seem to point toward different modes of metabolic compensation for the SDHB loss in the complex tumor environment versus cell media in the cell line model. Alternatively, it may indicate some residual SDHB activity in the tumors (missense mutations of SDHB) compared to the effect of the complete SDHB knock-out in the cell model. Based on our observations, we conclude that any in vitro studies with hPheo-1 SDHB KO cells as a model of human SDHB-mutated PPGL should be interpreted with caution, considering the molecular differences between the model and the human PPGL.