Identification of TNFRSF12A as a key regulator of stemness and immunosuppression in a novel glioma subtype via multi-omics analysis and experimental validation.

Glioma stem cells (GSCs) drive tumor heterogeneity, therapy resistance, and immunosuppression. This study identified molecular subtypes of glioma based on stemness-related genes and validated a key hub gene through bioinformatics and experiments. A stemness gene set was compiled from single-cell data, GeneCards, and MSigDB. Consensus clustering (NMF) on 157 glioma samples from GSE4290 revealed two subtypes (C1 and C2), with C1 showing higher stemness scores. C1 exhibited enriched DNA repair, proliferation, and metabolic pathways, plus greater temozolomide (TMZ) resistance and M2 macrophage infiltration. WGCNA and differential expression identified 43 genes; machine learning (LASSO, SVM-RFE, RF) selected TNFRSF12A as the core hub gene. TNFRSF12A knockdown in GSCs inhibited proliferation and stemness markers (CD133, OLIG2, SOX2), enhanced TMZ sensitivity, and suppressed M2 macrophage polarization. In vivo, TNFRSF12A silencing reduced tumor growth and synergized with TMZ. TNFRSF12A represents a potential therapeutic target for aggressive gliomas.