EPCO-11. BIASES IN HEALTHY BRAIN SINGLE-CELL DATASETS: FINDING THE BEST COMPARISON FOR GLIOBLASTOMA STUDIES

Abstract

Abstract Tumor cells undergo metabolic alterations that support their proliferation and simultaneously modify immune populations, resulting in an immunosuppressive tumor microenvironment. This study aims to compare the metabolic expression of immune cells within the tumor microenvironment to those in a healthy environment. However, there is a lack of single-cell transcriptomic data for normal brain cells, necessitating an analysis of different methods to compare immune cells in tumors with those in a healthy brain. To address this, we explored cell-to-cell metabolic variability using public single-cell RNA-seq (scRNA-seq) data of glioblastoma (n=338564), and from immune cells in the brains of post-mortem individuals (n=14177), fetuses (n=40000), and epilepsy patients (n=466), as well as from immune blood cells (n=329762). We employed ssGSEA to generate activity scores for 70 key metabolic pathways from KEGG for each individual cell. Known marker genes were utilized to identify normal cell populations (macrophages, T cells, oligodendrocytes) in datasets lacking cell type annotations. Our results revealed that blood cells exhibited high metabolic activity in macrophages but showed moderate activity in other cell types. Immune blood cells also demonstrated high oxidative phosphorylation (OXPHOS) but low fatty acid activity. Fetal brain cells displayed a lack of heterogeneity and showed high fatty acid activity with low OXPHOS activity. Brain cells from post-mortem individuals displayed heterogeneity but exhibited low metabolic activity across nearly all cells and pathways. Additionally, the hierarchy of pathway activity differed from the other datasets. Epilepsy data revealed a metabolic activity pattern similar to tumor-infiltrating immune cells, with comparable activity hierarchy and heterogeneity, although the sample size was limited for detailed comparison. Understanding the differences between types of datasets is important to choose the most appropriate comparison, allowing us to observe the metabolic alterations in immune cells caused by glioblastoma and to develop better immunotherapy strategies.