ArticleDiscover oncology2026
Integrated bulk and single-cell transcriptomic analyses identify transcriptome-defined groups and EGFR-associated microenvironmental programs in glioma.
Article in Discover oncology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundGlioma exhibits significant molecular heterogeneity, necessitating improved understanding of molecular subtypes for personalized treatment strategies.
methodsThis 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).
resultsTwo 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.
conclusionThis 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.
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