Identification of Prominent Genes between 3D Glioblastoma Models and Clinical Samples via GEO/TCGA/CGGA Data Analysis

Biology (Basel). 2023 Apr 25;12(5):648. doi: 10.3390/biology12050648.


A paradigm shift in preclinical evaluations of new anticancer GBM drugs should occur in favour of 3D cultures. This study leveraged the vast genomic data banks to investigate the suitability of 3D cultures as cell-based models for GBM. We hypothesised that correlating genes that are highly upregulated in 3D GBM models will have an impact in GBM patients, which will support 3D cultures as more reliable preclinical models for GBM. Using clinical samples of brain tissue from healthy individuals and GBM patients from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Chinese Glioma Genome Atlas (CGGA), and Genotype-Tissue Expression (GTEx) databases, several genes related to pathways such as epithelial-to-mesenchymal transition (EMT)-related genes (CD44, TWIST1, SNAI1, CDH2, FN1, VIM), angiogenesis/migration-related genes (MMP1, MMP2, MMP9, VEGFA), hypoxia-related genes (HIF1A, PLAT), stemness-related genes (SOX2, PROM1, NES, FOS), and genes involved in the Wnt signalling pathway (DKK1, FZD7) were found to be upregulated in brain samples from GBM patients, and the expression of these genes were also enhanced in 3D GBM cells. Additionally, EMT-related genes were upregulated in GBM archetypes (wild-type IDH1R132 ) that historically have poorer treatment responses, with said genes being significant predictors of poorer survival in the TCGA cohort. These findings reinforced the hypothesis that 3D GBM cultures can be used as reliable models to study increased epithelial-to-mesenchymal transitions in clinical GBM samples.

Keywords: 3D culture; CGGA; EMT; Glioblastoma; TCGA; differential expression; therapy resistance.