Differential Expression Analysis of Immune-Related Genes in Pediatric High-Grade Brain Tumors using RNA-seq Data

Abstract

[""A better understanding of pediatric brain tumor immune microenvironment is crucial for developing effective immune-based treatments. The primary aim of this research was to compare the immune-related gene expressions of various high-grade pediatric brain tumors compared to Craniopharyngioma, a low-grade tumor. This is due to the absence of control group from healthy tissue at the time of this research. We also aimed to detect clusters of genes that behave similarly and their association with various tumor types.

In addressing our primary objective, we employed differential expression analysis using DESeq2 in R. We observed marked disparities in immunerelated gene expression profiles among tumor types. Medulloblastoma demonstrated a striking 64% downregulation in gene expression. Contrastingly, Ependymoma and Glioma displayed 7.7% and 10% upregulation of gene expression, respectively. Specifically MAGEA3 was top highly expressed gene across all tumor types.

Using Weighted Gene Co-expression Analysis (WGCNA), we identified eight distinct immune-related gene modules, three of which showed a strong correlation with Medulloblastoma. The gene PIAS1 in the module with the highest positive correlation showed a notably significant association with Medulloblastoma.""]