Abstract 1206: Large-scale spatial molecular profiling uncovers distinct macrophage activation states across meningioma methylation classes.

Abstract Recent advances in neuro-oncology have highlighted the meninges as a key immunological hub at the interface between systemic immunity and the central nervous system (CNS). While meningiomas are primarily benign, ∼20% exhibit high-grade features including brain invasion, recurrence, and treatment resistance. Macrophages in the tumor microenvironment are of particular interest due to their high abundance and phenotypic plasticity. While many studies have investigated macrophage diversity in cancer, this study spatially resolves myeloid activation programs in their native tissue context, exploring correlates with clinical parameters including meningioma molecular subtypes and recurrence. We combine spatial transcriptomics (Xenium) with multiplexed ion beam imaging (MIBI), integrating gene expression and high-dimensional protein data at single-cell resolution. Our large multi-center retrospective cohort of 368 FFPE samples includes cases with detailed molecular and clinical annotations. To enable scalable spatial analysis, we sampled pathologist-annotated regions and imaged tissue-micro-arrays (TMAs). Myeloid activation programs were discovered using cNMF. Delaunay algorithms delineated niches in Xenium data, while CellCharter discovered tissue niches in MIBI data. Spatial protein and transcriptomic data from consecutive sections reveal spatially segregated biological processes. The myeloid compartment in meningioma makes up a significant part of the tumor bulk, especially in low-grade tumors. Protein-level analysis shows clear tissue zonation marked by specific metabolic marker expression such as MCT1 and differential infiltration by microglia-like macrophage subsets. Spatial transcriptomics revealed at least 5 nuanced transcriptional myeloid activation programs that differ across methylation classes of over 320 cases. These differential enrichments were accompanied by distinct infiltration patterns and cell-type co-localization suggesting interaction-driven activation of myeloid programs. Overall, tumor-associated macrophages (TAMs) exhibit context-dependent prognostic significance across cancer types, most evidence supports their association with poor prognosis. In meningiomas, dense TAM infiltration is a key feature of benign subtypes. This study provides spatial context to meningioma methylation classes and addresses critical questions regarding the microenvironmental cues that shape TAM diversity and whether specific TAM activation programs have prognostic value, potentially revealing novel therapeutic avenues. Citation Format: Domenico Calafato, Yiheng Tang, Gleb Rukhovich, Elyas Heidari, Leonille Schweizer, Michael Weller, Christine Haberler, Till Acker, Bhuvic Patel, Abigail Suwala, Felix Sahm, Felix Hartmann, Moritz Gerstung. Large-scale spatial molecular profiling uncovers distinct macrophage activation states across meningioma methylation classes [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 1206.