Fusion transcriptome landscape in glioblastoma: Incidence and therapeutic implications

Glioblastoma (GBM) lacks effective therapies for recurrent disease. Unlike cancers with successful fusion-targeted treatments (eg BCR-ABL1 in CML), the incidence and therapeutic potential of gene fusions in GBM remain unclear. We analyzed a large genomic database to define fusion frequency and molecular associations.

4800 IDH-wildtype GBM samples (WHO 2021) underwent NextGen DNA sequencing (592-gene panel/whole exome) and Whole Transcriptome Sequencing for fusions at Caris Life Sciences. Fisher-Exact/Chi-Square tests, adjusted by Benjamini-Hochberg (q < 0.05), assessed significance.

Pathogenic fusions occurred in 428 (8.9%) samples, primarily FGFR3 (37%, n = 159; FGFR3: TACC3, n = 134), MET (21%, n = 92), and EGFR (20%, n = 87). Pathogenic or likely pathogenic fusions included NTRK2 (n = 27), PDGFRA (n = 23), ROS1 (n = 14), and BRAF (n = 10). Fusion-positive tumors had higher MET (7.5% vs. 0.7%), FGFR3 (5% vs. 0.2%), CDK4 (17% vs. 11%), and MDM2 (12% vs. 7.5%) amplifications, but lower EGFR mutations (6.1% vs. 18%), amplifications (6.1% vs. 18%), and EGFRvIII (11.9% vs. 22.5%) (all q < 0.05). Median survival was 16.6 months (fusion-positive) vs. 15.5 months (fusion-negative) (P = 0.043). Tyrosine kinase inhibitor (TKI)-treated fusion-positive patients (n = 37) showed no significant survival benefit (18.4 vs. 16.5 months, P = .971).

Approximately 9% of GBMs harbor targetable fusions, with five genes (FGFR3, MET, EGFR, NTRK2, PDGFRA) comprising 8%. These findings support multi-arm clinical trials to evaluate targeted therapies, potentially improving outcomes for molecularly defined GBM subgroups.