RNA-Sequencing and immunohistochemistry reveal ZFN7 as a stronger marker of survival than molecular subtypes in G-CIMP-negative glioblastoma

Esteve-Codina, Anna; Alameda Quitllet, Francisco; Arpí Llucià, Oriol; Gut, Marta; Dabad, Marc; Balana, Carmen

doi:http://dx.doi.org/10.1158/1078-0432.CCR-20-2141

RNA-Sequencing and immunohistochemistry reveal ZFN7 as a stronger marker of survival than molecular subtypes in G-CIMP-negative glioblastoma

Citation

Esteve-Codina A, Alameda F, Carrato C, Pineda E, Arpí O, Martinez Garcia M et al. RNA-Sequencing and immunohistochemistry reveal ZFN7 as a stronger marker of survival than molecular subtypes in G-CIMP-negative glioblastoma. Clin Cancer Res. 2021;27(2):645-55. DOI: 10.1158/1078-0432.CCR-20-2141

Abstract

Purpose: Glioblastoma is the most aggressive brain tumor in adults and has few therapeutic options. The study of molecular subtype classifications may lead to improved prognostic classification and identification of new therapeutic targets. The TCGA subtype classification has mainly been applied in USA clinical trials, while the IGS has mainly been applied in European trials. Experimental design: From paraffin-embedded tumor samples of 432 uniformly treated, newly diagnosed glioblastoma patients, we built tissue microarrays for immunohistochemical analysis and applied RNA-Sequencing to the best samples in order to classify them according to the TCGA and IGS subtypes. Results: We obtained transcriptomic results from 124 patients. There was a lack of agreement among the three TCGA classificatory algorithms employed, which was not solely attributable to intratumoral heterogeneity. There was overlapping of the TCGA mesenchymal subtype with IGS cluster 23 and of the TCGA classical subtype with IGS cluster 18. Molecular subtypes were not associated with prognosis, but levels of expression of 13 novel genes were identified as independent prognostic markers in G-CIMP-negative patients, independently of clinical factors and MGMT methylation. These findings were validated in at least one external database. Three of the 13 genes were selected for immunohistochemical validation. In particular, high ZNF7 RNA expression and low ZNF7 protein expression were strongly associated with longer survival, independently of molecular subtypes. Conclusions: The TCGA and IGS molecular classifications of glioblastoma have no higher prognostic value than individual genes and should be refined before being applied to clinical trials.