Integrated genomic and transcriptomic profiling uncovers spatial and evolutionary dynamics in astrocytoma

Intratumoral genomic heterogeneity in glioblastoma arises through clonal evolution and may contribute to treatment resistance and poor outcomes, yet the interplay between subclonal diversity and transcriptional states remains incompletely understood. We utilized multi-sampled whole-genome sequencing (WGS), bulk RNA sequencing, and single-cell RNA sequencing (scRNA-seq) to comprehensively map the layers of intratumoral transcriptomic and genomic heterogeneity and trace the evolutionary lineages across twelve spatially distinct tumor regions in two glioblastoma and one IDH mutant high-grade astrocytoma patients. In the IDH mutant astrocytoma, tumor evolution was characterized by early whole-genome duplication followed by a rare chromothripsis between chromosomes 2 and X, as well as region-specific hypermutation enriched for short insertions and deletions. In contrast, both glioblastomas exhibited linear evolution facilitated by early clonal copy number alterations and single-nucleotide variants, and in one patient, extensive loss of heterozygosity, extrachromosomal DNA structures, and high ploidy. Single-cell copy number analysis validated WGS-defined clones in this patient and uncovered additional subclones with distinct copy number alterations undetectable in bulk sequencing, refining the tumor's phylogenetic tree. Transcriptomic profiling revealed region- and clone-specific differences in glioblastoma cell states, while IDH mutant tumor regions generally exhibited neural progenitor-like activity in addition to astrocytoma-like programs. Glioblastoma samples were dominated by astrocytoma-like states but frequently displayed mesenchymal and endothelial-like transcriptional activity, with rarer and more heterogeneous niches of neural progenitor-like or oligodendrocyte precursor-like cells along with elevated proliferation and distinct maturation signatures. Moreover, scRNA-seq-derived subclones showed differences in mesenchymal-like expression and similar transcriptional branching with state differences observed in bulk RNA-seq, reflecting WGS-based clones. Together, these results demonstrate that intratumoral heterogeneity in adult diffuse astrocytomas arises from both genomic divergence and substantial transcriptional plasticity, while inter-patient diversity remains high across these aggressive tumors. By linking single-cell and bulk transcriptional profiles to evolutionary lineages, our multi-omic framework provides detailed insight into diffuse astrocytoma evolution and malignant cell-state organization.