Biological and therapeutic implications of multisector sequencing in newly diagnosed glioblastomas

Abstract

Background

Diagnostic workflows for glioblastoma (GBM) patients increasingly include DNA sequencing-based analysis of a single tumor site following biopsy or resection. We hypothesized that sequencing of multiple sectors within a given tumor would provide a more comprehensive representation of the molecular landscape and potentially inform therapeutic strategies.

Methods

10 newly diagnosed, IDH1 wildtype GBM tumor samples were obtained from two (n = 9) or four (n = 1) spatially distinct tumor regions. Tumor and matched blood DNA samples underwent whole-exome sequencing.

Results

Across all 10 tumors, 51% of mutations were clonal and 3% were subclonal and shared in different sectors, whereas 46% of mutations were subclonal and private. Two of the 10 tumors exhibited a regional hypermutator state despite being treatment naive, and remarkably, the high mutational load was predominantly limited to one sector in each tumor. Among the canonical cancer-associated genes, only TERT promoter mutations were observed in the founding clone in all tumors. Reconstruction of the clonal architecture in different sectors revealed regionally divergent evolution, and integration of data from two sectors increased the resolution of inferred clonal architecture in a given tumor. Predicted therapeutic mutations differed in presence and frequency between tumor regions. Similarly, different sectors exhibited significant divergence in the predicted neoantigen landscape.

Conclusions

The substantial spatial heterogeneity observed in different glioblastoma tumor sectors, especially in spatially-restricted hypermutator cases, raise important caveats to our current dependence on single-sector molecular information to guide either targeted or immune-based treatments.