Abstract 4971: Integrated spatial multiomic mapping of glioblastoma microenvironments via proteomic and transcriptomic profiling

Abstract Glioblastoma (GBM) progression is characterized by striking spatial heterogeneity across tumor and adjacent normal brain regions, driven by complex gradients in immune activity, angiogenesis, and cellular state transitions. Conventional bulk and single-cell molecular profiling methods provide valuable insights but typically lose the spatial context critical for understanding the glioma microenvironment. To address this challenge, we leveraged the highly multiplexed Bruker Multiomic GeoMx® Digital Spatial Profiler (DSP) in combination with the Neural Proteome Atlas (NPA) and Immune Profiling Atlas (IPA) collectively referred to as the Discovery Proteome Atlas (DPA) alongside the Whole Transcriptome Atlas (WTA) panel. This integrated approach enables simultaneous spatial quantification of multiplex protein targets and more than 18,000 protein-coding transcripts within human GBM tissue slides. Regions of interest were selected along the continuum areas of each tissue, allowing for a comprehensive, multiplexed spatial proteomic and transcriptomic characterization of GBM invasive front. Using immunofluorescence-guided images, we defined normal tissue region, tumor cores, and invasive borders, generating high-resolution spatial proteomic maps that revealed region-specific alterations in transcriptome and proteome expressions between these regions. We identified several distinct molecular signatures that emerged between GBM-infiltrated areas with increased expression related to tumor growth, angiogenesis pathways, whereas normal brain regions retained baseline neuronal (NEFL), astrocytic (GFAP), and vascular integrity markers. The NPA framework further enabled fine-grained classification of cellular niches and functional states, distinguishing immunologically active versus suppressed microenvironments. These analyses highlighted the capacity of DSP to dissect localized activation of oncogenic pathways. Together, these findings underscore the power of an unprecedented high-plex spatial multi-omic profiling to elucidate region-specific molecular programs within complex tumor ecosystems. GeoMx DSP provides an advanced analytical framework for biomarker discovery, disease stratification, and evaluation of therapeutic strategies in glioblastoma and other heterogeneous brain pathologies. Citation Format: Chia-Ying Lee, Arya Bahrami, Yi Cui, Megan Vandenberg, Michael McKenna, Shanshan He, Mirko Corselli, Joseph M. Beechem. Integrated spatial multiomic mapping of glioblastoma microenvironments via proteomic and transcriptomic profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4971.