Systemic screening identifies GABRD, a subunit gene of GABAA receptor as a prognostic marker in adult IDH wild-type diffuse low-grade glioma

Abstract

Currently, no reliable prognostic biomarkers have been identified for adult IDH wild-type (WT) diffuse low grade glioma (LGG). With data from The Cancer Genome Atlas (TCGA)-LGG, we examined the prognostic value of GABAA receptor subunits in adult IDH WT LGG. Using 2016 WHO CNS tumor classification, we re-classified the TCGA-LGG and identified 95 IDH WT patients. Among 16 GABAA receptor subunit genes with RNA-seq data, eight genes showed significantly different expression in IDH WT LGG compared with IDH mutant (MT) cases. Among these genes, only GABRD expression was related to overall survival (OS) status. Preserved GABRD expression was independently associated with longer OS (HR: 0.799, 95%CI: 0.691-0.925, p = 0.003) in IDH WT LGG. GABRD expression showed a moderately negative correlation with tumor infiltration macrophage (TIM) and CSF1 expression. The methylation status of 34 CpG sites across GABRD gene was checked and only cg13916816 showed a moderately negative correlation with GABRD expression. In conclusion, GABRD expression might serve as a potential independent prognostic marker in patients with IDH WT LGG. Meanwhile, its expression was negatively correlated with the extent of TIM, which might help to explain the favorable survival outcome. Cg13916816 might be a critical CpG site influencing GABRD expression in IDH WT LGG.