A comprehensive study of the effect of IDH1 mutation in glioblastoma multiforme progression combining proteome, transcriptome and clinical data

Glioblastoma multiforme (GBM), an aggressive type of cancer, is known to occur in the brain or spinal cord. A genome-wide mutational analysis revealed a common mutation, IDH1 mutation, shown in GBM patients to interestingly show association with survival increase. Despite its importance, difficulties in IDH1 mutation cell line construction have limited extensive proteomic research. In this study, we performed comprehensive global and phosphoproteome profiling on successfully constructed IDH1 R132H point mutated cell-lines to investigate the effect of the mutation on the progression of GBM. With wild type U-87, early (day1) and late (day 6) samples of two successful IDH1 mutated U-87 cell-line batches, three replicates of 6-plex TMT labeled peptides were obtained.

Proteome profiling using DO-NCFC-RP/RP-MS/MS platform [2016, Lee et al] resulted in averages of 51,595 distinct phosphopeptides with 41,603 phosphorylation sites, corresponding to 7,352 phosphoprotein groups, and 259,061 distinct peptides corresponding to 11,868 protein groups. Along with gene ontology patterning analysis of the proteome data, RNA-seq expression results were combined to seek overlap of differentially expressed proteins/genes. These genes were compared with selected signature genes from GBM patient subtyping from TCGA public data and analyzed microarray results regarding TMZ resistance in GBM patients to extract 12 core genes, for a network model construction. From these results, our model centered in the decrease of TGF-beta signaling pathway and DNA damage response to explain the better survival of GBM patients with IDH1 mutation, hoping to provide insight for future GBM treatments.