Molecular profiling of SDHA-deficient GIST guides preclinical disease modeling based on induced Pluripotent Stem Cells

Gastrointestinal stromal tumors (GIST) are the most common mesenchymal tumors of the gastrointestinal tract, arising from the interstitial cells of Cajal (ICCs) or their precursors. While the vast majority of GISTs harbor KIT or PDGFRA mutations, 10 – 15% of GIST do not show any of these driver mutations. Among them, 20% to 40% carry mutations in one of the four SDH-complex subunits, with SDHA mutations as the most frequent event. Representative features of SDH-deficient GISTs are gastric localization, frequent lymph node metastases and an indolent clinical course despite advanced disease status. This study was aimed at uncovering the specific gene expression profile of SDHA-deficient GIST and at developing a cellular model of this disease to allow preclinical drug testing. We analyzed 36 GIST tumor samples including SDH-deficient and KIT-mutant GISTs by gene expression arrays or RNA sequencing. SDHA-deficient GISTs displayed a very homogeneous gene expression profile, different from that of KIT-mutant GIST, characterized by an increased expression of neural markers and by the activation of the hypoxia signature and of the fibroblast growth factor pathway. This specific molecular signature was used to validate a SDHA-deficient GIST cellular model obtained from induced Pluripotent Stem Cells (iPSC). Patient-derived cells were reprogrammed to pluripotency then differentiated towards the mesodermal layer, as shown by lineage marker expression (T, MIXL1, NCAM), and treated with an irreversible chemical inhibitor of succinate dehydrogenase at concentrations that inhibit mitochondrial activity (3-Nitropropionic acid, 3-NPA). Pluripotent and mesoderm-committed iPSC exposed to 3-NPA showed a statistically significant upregulation of hypoxia-related genes such as HIF1α, EPAS1 and VEGF and of neural lineage markers (LHX2, CDH2 and NEFL) whose overexpression was previously found to characterize SDHA-mutant GIST. Notably, succinate dehydrogenase inhibition in iPSC also significantly increased expression of IGF1R, a characteristic marker of SDH-deficient GISTs. Overall, this study revealed the gene expression landscape of SDHA-deficient GISTs and provided evidence that the iPSC model has the potential to mimic the molecular phenotype of the disease, therefore providing a useful tool for preclinical pharmacological testing.