DENND2D serves as a novel prognostic biomarker with paradoxical protumorigenic effects in glioma

Glioma, especially glioblastoma (GBM), has a dismal prognosis with current therapies. In this study, we aimed to identify potential novel molecular targets for GBM by analyzing RNA sequencing.

RNA-seq data from TCGA, CGGA, and GTEx were analyzed to assess DENND2D expression across glioma grades and molecular subtypes. Survival analysis, methylation/copy number profiling, weighted gene co-expression network analysis (WGCNA), functional enrichment (GO/KEGG), and immune infiltration deconvolution (CIBERSORT) were performed.

By multi-cohort analysis, 5 upregulated genes and 23 downregulated genes demonstrated prognostic significance in GBM. DENND2D was upregulated in high-grade gliomas (GBM > LGG; p < 0.05) and correlated with poor prognostic features (IDH-wildtype, non-1p/19q-codeletion). High DENND2D levels predicted worse survival (HR > 1, p < 0.001) in TCGA and CGGA cohorts. Expression was inversely correlated with promoter methylation (sites cg00619207/cg24641737) and was modulated by copy number alterations. WGCNA revealed co-expression with immune regulators (RAC2/TLR2/ITGB2/PTPRC/HLA-DPA1) and enrichment in leukocyte activation pathways (p < 0.01). CIBERSORT showed that DENND2D^high tumors had elevated immunosuppressive infiltrates: M1/M2 macrophages and γδ T cells in LGG, and M2 macrophages in GBM (p < 0.05).

DENND2D acts as an oncogene in glioma, driving aggressiveness and shaping an immunosuppressive microenvironment. It represents a novel prognostic biomarker and therapeutic target for overcoming immunotherapy resistance.