Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [10x Spatial]

Glioblastoma (GBM) remains an untreatable disease. Understanding of GBM's infiltrative biology at the resection margin is limited, despite causing disease recurrence and progression. To address this, we generated a high-throughput single-nucleus (sn)RNA-seq and snATAC-seq multi-omic dataset from six tumors with distinct genomic drivers and combined it with spatial transcriptomics to characterize the unique molecular phenotype of GBM near the margin. By contrasting GBM-specific biology in matching “Core” vs. “Margin” dissections, we define unique, shared “GBM infiltration” and chromatin accessibility signatures near the margin. We prioritize EGFR as a top differentially expressed and accessible “Margin” marker across GBM subtypes, show its dynamic expression along a core-to-margin infiltration trajectory, and validate its role in migration through CRISPR/Cas9 deletion in two patient-derived models. ChIP-seq studies furthermore corroborate preferential TEAD1 binding at EGFR's accessible regulatory elements. This validated multi-omic dataset enables further studies into tumor and microenvironment biology in the context of residual GBM disease. Overall design: Surgical glioma tissue was collected from 2 patients with confirmed diagnosis of glioblastoma, WHO grade 4 (2021 diagnostic criteria), representing diverse genetic backgrounds and of each sex. Tissue procurement was coordinated with neurosurgery to include contrast-enhancing tumor “Core” (C) and FLAIR-hyperintense infiltrative “Margin” (M) representing the distal extent of gross supratotal resection and having a “normal brain” appearance on fresh tissue inspection. Tissues were fixed in 10% formalin for spatial transcriptomics (n=2). Serial formalin-fixed and paraffin embedded (FFPE) sections from samples were kept for histological analysis.