Introduction and Objectives
Medulloblastoma is the most common pediatric brain cancer of the central nervous system and it accounts for 20% of all pediatric tumors. Earlier transcriptomics based investigations identified 4 subgroups of medulloblastoma namely, SHH, group 3, group 4 (G4), and Wnt, which is incorporated in WHO revised classification. The current study has majorly focused on identifying proteomic alteration associated with medulloblastoma subtypes and understanding mechanisms of group3(G3) tumors.
Methods
The label-free proteomic samples preparation was accomplished using Urea lysis buffer. The extracted proteins were subjected to enzymatic digestion using trypsin followed by c18 based desalting and subjected to Orbitrap fusion for MS/MS analysis. The total number of proteins obtained from the analysis was 5498 using stringent filtering criteria (1%FDR, >2 peptides). The validation of the significant candidates was performed using Multiple Reaction Monitoring (MRM)
Results and Discussion
The initial analysis was focused on the unsupervised clustering of data to investigate whether the proteomics signatures are falling under the existing transcriptomic classification by WHO and the proteomic clusters were reflecting the same. We were able to identify a panel of the classifier proteins which can differentiate between G3 and G4 tumor types. The G3 tumor exhibited differential proteomic profile in metabolic pathways specifically in glycolysis and TCA cycle. The proteins like POSTN was significantly altered in G3 tumor and it usually induced by reduced oxygen tension. MRM results were reflecting the same trend and large scale validation of key findings are ongoing
Conclusions
This comprehensive label free proteome profiling of medulloblastoma using tissue samples will provide an in-depth and mechanistic insight into proteomic alterations associated with medulloblastoma subtype.However, further validation of identified protein targets on a larger cohort of medulloblastoma patients is needed before anticipating their diagnostic impact.
Keywords
Medulloblastoma, Central Nervous System (CNS), World health organization (WHO),