Unbiased global proteomic profiling of patient-derived meningiomas of all grades to identify molecular signatures of differentially expressed proteins and phosphoproteins.
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Meningioma is the most frequent primary intracranial tumour. Surgical resection remains the main therapeutic option as pharmacological intervention is still hampered by the poor knowledge of the molecular signature of these tumours. In order to elucidate the proteomic profiling of meningiomas and identify proteins involved in their pathogenesis, we completed a comparative mass spectrometry analysis of meningioma tissue of all WHO grades, analysing global proteins, phosphoproteins and phosphopeptides. We performed differential expression analyses and functional annotation studies to identify commonly upregulated proteins and phosphoproteins in all grades of meningioma compared to meningeal tissue as well as grade-specific candidates relevant for tumour progression. Top candidates were validated by Western blotting and immunohistochemistry in an independent sample set, confirming for example significant overexpression of proteins including EGFR, STAT2 and EPS8L2 across all grades, as well as the aberrant activation of the PI3K/AKT/mTOR pathway. Further, we validated upregulation in all grades of the total and activated phosphorylated form of the NIMA-related kinase, NEK9, involved in mitotic progression and of the transmembrane protein CKAP4. Novel proteins identified in meningioma and validated as commonly overexpressed in all grades were the nuclear proto-oncogene SET and the splicing factor SF2/ASF, while another newly identified protein that was specific for high-grade meningiomas was the glycolytic enzyme hexokinase-2, involved in cellular metabolism. In summary, we generated a proteomic thesaurus of meningiomas in order to decipher aberrantly expressed proteins and activated pathways; this body of knowledge will eventually lead to the identification of relevant biomarkers and possible novel therapeutic targets.