Liu, Jefferey

Abstract Glioblastoma (GBM) progression and recurrence are often driven by therapy-resistant cellular states emerging within hypoxic tumor niches. While hypoxia is a hallmark of GBM, the spatial transcriptomic heterogeneity that underpins resistance in these regions remains poorly characterized. Here, we employ pimonidazole labeling in conjunction with high-resolution spatial and single cell transcriptomics across 29 primary, treatment-naive human GBM samples, syngeneic mouse models, and patient-derived glioma-initiating cells exposed to hypoxia to define the hypoxia-specific tumor microenvironment and its associated cellular programs. We reveal spatially organized sub-niches within hypoxic regions, each supporting diverse cellular programs yet coexisting tumor lineage states with minimal transitions between cell states. Phylogenetic reconstruction based on inferred copy number variations demonstrates consistent evolutionary trajectories from non-hypoxic to hypoxic tumor loci. Specific copy number alterations were enriched in hypoxic regions and associated with immune infiltration and poor prognosis in MGMT-methylated tumors. Cross-species analyses confirmed the conservation of hypoxia-associated gene programs and spatial architectures. Together, our study delineates the cellular, evolutionary, and spatial complexity of hypoxia in GBM, identifies hypoxia-induced genomic alterations that may promote tumor fitness, and offers insights into new therapeutic vulnerabilities within hypoxic niches.