Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective

Treatment failure for the lethal brain tumor glioblastoma (GBM) is attributed to intratumoral heterogeneity and tumor evolution. We utilized 3D neuronavigation during surgical resection to acquire samples representing the whole tumor mapped by 3D spatial coordinates. Integrative tissue and single-cell analysis revealed sources of genomic, epigenomic, and microenvironmental intratumoral heterogeneity and their spatial patterning. By distinguishing tumor-wide molecular features from those with regional specificity, we inferred GBM evolutionary trajectories from neurodevelopmental lineage origins and initiating events such as chromothripsis to emergence of genetic subclones and spatially restricted activation of differential tumor and microenvironmental programs in the core, periphery, and contrast-enhancing regions. Our work depicts GBM evolution and heterogeneity from a 3D whole-tumor perspective, highlights potential therapeutic targets that might circumvent heterogeneity-related failures, and establishes an interactive platform enabling 360° visualization and analysis of 3D spatial patterns for user-selected genes, programs, and other features across whole GBM tumors. [Display omitted] •Deep evolutionary roots of individual GBMs suggest tumor-wide therapeutic targets•Whole-tumor transcriptome and chromatin analysis reveals divergent cells of origin•3D analysis depicts GBM and microenvironmental programs with regional specificity•An interactive 3D platform enables whole-tumor analysis of user-selected GBM features An integrative 3D spatial analysis provides a whole-tumor perspective on human glioblastoma, mapping out regional specificity in tumor and microenvironment programs while highlighting tumor-wide features as promising targets for future therapeutic development.