Unsupervised clustering reveals noncanonical myeloid cell subsets in the brain tumor microenvironment.

The tumor immune microenvironment (TiME) of human central nervous system (CNS) tumors remains to be comprehensively deciphered. Here, we employed flow cytometry and RNA sequencing analysis for a deep data-driven dissection of a diverse TiME and to uncover noncanonical immune cell types in human CNS tumors by using seven tumors from five patients. Myeloid subsets comprised classical microglia, monocyte-derived macrophages, neutrophils, and two noncanonical myeloid subsets: CD3 ⁺ myeloids and CD19 ⁺ myeloids. T lymphocyte subsets included double-negative (CD4 ^- CD8 ^- ) T cells (DNTs). Noncanonical myeloids and DNTs were explored on independent datasets, suggesting that our DNT phenotype represents γδ T cells. Noncanonical myeloids were validated using orthogonal methods across 73 patients from three independent datasets. While the proportions of classical myeloids agreed with reported malignancy type-associated TiMEs, unexpectedly high lymphocyte frequencies were detected in gliosarcoma, which also showed a unique expression pattern of immune-related genes. Our findings highlight the potential of data-driven approaches in resolving CNS TiME to reveal the mosaic of immune cell types constituting TiME, warranting the need for future studies on the nonclassical immune cell subsets.
Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests. Ethical approval: The study was performed in accordance with the principles of the Declaration of Helsinki. This prospective study was reviewed and approved by The Regional Ethics Committee of Pirkanmaa Hospital District, currently named as the Ethics Committee of the Wellbeing Services County of Pirkanmaa, with the reference of the approval number R14024. Consent to participate: All patients provided informed consent to the use of tumor material for the applications used in this study. Consent to publish: All the participants of this study provided informed consent for publication of their data according to the legislation and good practice.
(© 2024. The Author(s).)