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Integrated analysis of multiple methods reveals characteristics of the immune microenvironment in medulloblastoma

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Abstract

To explore the characteristics of the immune microenvironment (IME) of medulloblastoma (MB) by four methods: flow cytometry (FCM), immunohistochemical (IHC), bulk RNA expression and single cell RNA sequencing (scRNA-seq), we collected the intraoperative specimens of MB, ependymoma (EPN), high-grade glioma (HGG), and low-grade glioma (LGG) to make a cross-cancer comparison. The specimens were subjected to FCM and IHC respectively, and deconvolution from bulk RNA expression data and scRNA-seq analysis were performed in MB from the GEO database. FCM and IHC analysis found that the proportion of lymphocytes (LC) and T cells between MB and other brain tumors were significantly different. The deconvolution of bulk RNA expression data showed that only the proportion of cell types in MCPCOUNTER changed greatly. scRNA-seq found that the proportion of various immune cells in the IME of MB differed between different subtypes. Techniques such as FCM, IHC, bulk RNA expression, and scRNA-seq can sort out different immune cell subsets to a certain extent and quantify their proportions. The four methods have their own strengthens and limitations, but for highly heterogeneous tumor such as MB, integrated analysis of multiple methods is a better choice.

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Data availability

The data that support the findings of this study are available from the corresponding author, Jian Gong, upon reasonable request.

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Funding

This work was funded by National Natural Science Foundation of China (Grant No. 62276027).

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Authors and Affiliations

  1. Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China

    Kaiyu Fan, Yunwei Ou & Jian Gong

  2. MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China

    Yifan Wei

  3. China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China

    Kaiyu Fan, Yunwei Ou & Jian Gong

  4. Beijing Neurosurgical Institute, Beijing, 100070, China

    Yunwei Ou & Jian Gong

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  1. Kaiyu Fan
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Correspondence to Jian Gong.

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Fan, K., Wei, Y., Ou, Y. et al. Integrated analysis of multiple methods reveals characteristics of the immune microenvironment in medulloblastoma. Brain Tumor Pathol 40, 191–203 (2023). https://doi.org/10.1007/s10014-023-00467-4

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