Proteomic and Metabolomic Analysis of PCK2-Dependent Alterations in Group 3 Medulloblastoma Cells

Group 3 medulloblastoma (G3MB) is an aggressive pediatric brain tumor subtype accounting for 20-25% of cases and characterized by poor prognosis and frequent metastasis. This subgroup frequently exhibits MYC amplification, driving oncogenic transcription, biosynthesis, and metabolic reprogramming, which is crucial for the rapid growth of tumor cells. Prior proteomic analysis of G3MB samples showed disrupted glucose and pyruvate metabolism, with notable overexpression of mitochondrial phosphoenolpyruvate carboxykinase (PCK2). This links the TCA cycle and pyruvate metabolism, aiding metabolic flexibility under nutrient stress. Consistent with this observation, we observed PCK2 overexpression in two independent patient data sets. To investigate its functional role, we performed shRNA-mediated knockdown of PCK2 in HD-MB03 and G3MB cells. Quantitative proteomics using Evosep-Tims TOF revealed dysregulation of metabolic interactors along with enrichment of ribosomal and RNA processing pathways. Complementary metabolomic profiling showed alterations in phosphocholine, carnitine, and metabolites related to redox imbalance upon PCK2 loss. Together, these findings provide insights into PCK2's role in Group 3 MB cells and expose vulnerabilities for therapeutic targeting.