Profiling of rare immune cell populations and integrative analysis identify immune ecotypes in newly diagnosed meningiomas.

Meningiomas (MGMs) are the most common primary intracranial tumors in adults with a substantial subset exhibiting aggressive clinical behavior. Immunotherapy represents a potential alternative treatment option, even though MGMs have traditionally been considered “immunologically cold” tumors. This study explored less characterized immune cell subsets —B cells, natural killer (NK) cells, and granulocytes— and their associations with major immune cell populations as well as their prognostic implications. For this purpose, we performed tissue cytometry analysis in a clinically well-annotated multi-center cohort of 97 newly diagnosed MGMs encompassing all WHO grades (1, 2, 3) and DNA methylation classes (benign, intermediate, malignant). Resulting infiltration data were integrated with previously published data on tumor-associated macrophages (TAMs) and tumor-infiltrating T lymphocytes (TILs) to identify MGM immune ecotypes. Overall, infiltration rates of B cells, NK cells, neutrophils, and eosinophils showed lower frequencies and varied widely across tumors. Notably, we observed significantly lower numbers of B cells in MGM with losses in chromosomal arms 10q and 22q, while lower number of T cells were found in patients with a loss of chromosomal arm 1p. In addition, NK cells and eosinophils were enriched in grade 1 and benign tumors, whereas neutrophils predominated in malignant cases. Despite their relatively low abundance, elevated neutrophil frequencies turned out to be an independent of prognostic factor for poor survival. Importantly, subsequent integration of TAM and TIL data derived from the same patient cohort unraveled five distinct immune ecotypes, each displaying characteristic immune cell infiltration patterns and differential survival outcomes. Altogether, this study provides an expanded overview of various rare immune cell subtypes in MGM and demonstrates their integration into different prognostic immune ecotypes, enabling better stratification in future clinical studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40478-026-02276-0.