Comprehensive Characterization of Somatic Mutations and Gene Expression on TP53/PTEN DKO Murine Glioblastoma Cell Lines: Insights from Whole-Exome and RNA-seq Analysis

Glioblastoma (GBM) is an aggressive brain tumor characterized by genomic instability and transcriptional plasticity. To investigate the somatic evolution of GBM, we performed an integrated analysis using Whole-Exome Sequencing (WES) and RNA-seq on a murine glioblastoma model representing two stages: early-stage transformed neural stem cells (tNSC) and late-stage malignant GBM (mGB). The comparative analysis of mutational signatures provides evidence of a two-phase evolutionary path for tNSC and mGB. Variant calling in tNSCs revealed mutations in Pfdn2, Oip5, Trmt10a, Nabp2, Man2b1 with mGBs acquiring additional putative progression-associated genes such as Cdk4, Ubap2, Ccdc11, Errfil, and Tead2 associated with malignancy and Temozolomide (TMZ) resistance. Samples in tNSCs exhibited signatures associated with stress-(SBS4) and development-associated (SBS40) processes. In contrast, mGB samples exhibited an increase inmutation signatures, specifically associated with replication- (SBS5) and mismatch repair (MMR) processes (SBS26). Notably, SBS26 consistently ranked in the top five mutational signatures across all samples, indicating that there may have been an early, and sustained, loss of MMR. Ti/Tv ratio also revealed elevated transversions in tNSCs supporting early instability post TP53/PTEN knockout, while mGB demonstrated normal transition-to-transversion ratio. Gene ontology reveals activities in neurodevelopmental pathways in tNSCs such as neurogenesis, axon guidance, and synapse regulation while in mGB it shifts to cellular transformation and invasion, and epidermal development. Moreover, differential expression analysis showed extreme downregulation against control neural stem cells (ctrlNSCs) indicating genomic instability and then the partial restoration of expression in mGB, resembling ctrlNSCs but with a bias toward malignant upregulations. Together this suggests, early genomic instability disrupting developmental programs and blocking differentiation, and later on replication-driven mutations and cytoskeletal remodeling reprograms the tumor into a proliferative, invasive, and therapy-resistant state.