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Unsupervised Clustering Reveals Noncanonical Myeloid Cell Subsets in the Brain Tumor Microenvironment

ABSTRACT: Unsupervised Clustering Reveals Noncanonical Myeloid Cell Subsets in the Brain Tumor Microenvironment

PROVIDER: PRJNA1055892 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27330815_1.fastq.gz	Fastqsanger.gz
	SRR27330815_2.fastq.gz	Fastqsanger.gz
	SRR27330816_1.fastq.gz	Fastqsanger.gz
	SRR27330816_2.fastq.gz	Fastqsanger.gz
	SRR27330817_1.fastq.gz	Fastqsanger.gz

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Unsupervised Clustering Reveals Noncanonical Myeloid Cell Subsets in the Brain Tumor Microenvironment

Project description: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 via data-driven approaches to dissect a diverse TiME and uncover noncanonical immune cell types in human CNS tumors. 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 validated with an independent dataset, suggesting that our DNT phenotype represents γδ T cells. 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 and reveal the mosaic of immune cell types constituting TiME.

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Project description: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.

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