Integrated bulk and single-cell transcriptomic analyses identify transcriptome-defined groups and EGFR-associated microenvironmental programs in glioma
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Updated: May 9, 2026
Quantitative Immunohistochemistry of the Cellular Microenvironment in Patient Glioblastoma Resections
Published on: July 31, 2017
Yuanhan Wang1, Long Li2, Xing Hu1
1Department of Thoracic Surgery, The Affiliated Cancer Hospital of Guizhou Medical University, No.1 Beijing West Road, Yunyan District, Guiyang City, 550004, Guizhou Province, China.
Background:
Glioma exhibits significant molecular heterogeneity, necessitating improved understanding of molecular subtypes for personalized treatment strategies.
Methods:
This study integrated bulk RNA sequencing (GSE35169) to derive transcriptome-defined groups and single-cell RNA sequencing (GSE131928) to characterize cellular heterogeneity and EGFR-associated malignant cell programs. Differential gene expression analysis identified subtype-specific biomarkers. Single-cell analysis included cell-type annotation, pseudotime trajectory, and cell-cell communication inference, with malignant cells stratified by EGFR expression to interrogate EGFR-associated programs. Key findings were validated by qRT-PCR in glioma cell lines (LN229, U251) and normal astrocytes (NHA).
Results:
Two transcriptome-defined groups were identified from bulk RNA-seq. In scRNA-seq, the EGFR-high malignant cell state showed enrichment of ECM-related genes (IGFBP2, COL1A1) and enhanced PI3K-AKT, focal adhesion, and angiogenic signaling, with predominant stromal-to-tumor communication (EGF/AREG→EGFR, TGFB1→TGFBR2). The EGFR-low malignant cell state exhibited higher expression of immune-related genes (CXCL10, IL6, STAT1). Functional enrichment analysis based on differentially expressed genes (FDR < 0.05) indicated significant enrichment of interferon signaling and JAK-STAT pathway-related gene sets in the EGFR-low group. Pseudotime analysis revealed gradual transcriptional transitions between proliferation, hypoxia, and immune programs. qRT-PCR validation confirmed elevated EGFR, IGFBP2, and COL1A1 in U251 cells, and higher CXCL10, IL6, and STAT1 in LN229 cells.
Conclusion:
This study identifies bulk transcriptome-defined groups and reveals EGFR-associated malignant cell programs linked to distinct microenvironmental interaction patterns. The EGFR-high malignant cell state features proliferative and angiogenic programs, while the EGFR-low malignant cell state shows enhanced immune infiltration. These findings provide molecular evidence for precision classification and subtype-specific therapeutic strategies.
