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Updated: Oct 19, 2026
Evaluation of Biomarkers in Glioma by Immunohistochemistry on Paraffin-Embedded 3D Glioma Neurosphere Cultures
Published on: January 9, 2019
A re-visit of glioblastoma molecular subtypes utilizing the 2021 WHO classification of central nervous system tumors
Geraldine Wen She Lee1,2, M Tarek Elghetany3,4, John Myseros5
1Pediatric Brain Tumor Research Office, SingHealth-Duke-NUS Academic Medical Center, Singapore.
Background:
The 3-subtype transcriptional framework is an established approach for classifying glioblastoma (GBM). The 2021 World Health Organization (WHO) Classification redefined GBM as an isocitrate dehydrogenase-wildtype (IDH-WT) tumor. We evaluated the 3-subtype framework in context of the new diagnostic criteria of WHO-2021 Classification which defined GBM to be IDH-WT only, to establish subtype concordance, cross-platform reproducibility, and subtype-associated molecular characteristics.
Methods:
The Cancer Genome Atlas (TCGA) RNA-seq (n = 233) and Affymetrix HGU133A (n = 330) cohorts fulfilling WHO-2021 criteria for IDH-WT GBMs were classified using the published 500-gene classifier. Concordance with legacy TCGA 4-subtype assignments, cross-platform reproducibility, overall survival, and subtype-specific molecular characteristics were evaluated.
Results:
Among WHO-2021-defined GBMs, the 3-subtype framework demonstrated good concordance with legacy TCGA 4-subtype assignments (79.7%, Cohen's κ = 0.69) and cross-platform reproducibility between RNA-seq and Affymetrix platforms (81.6%; κ = 0.72). Legacy proneural (PN; 96.2%) and neural (NE; 70.6%) tumors predominantly mapped to the PN/NE subtype, whereas mesenchymal (MES) tumors largely retained their original subtype assignment (95.4%). The Classical (CL) subtype showed the lowest concordance with its original TCGA subtype assignment (59.4%), with frequent subtype-switching towards PN/NE and MES subtypes while retaining canonical molecular characteristics, including EGFR amplification and CDKN2A/CDKN2B homozygous deletion. MES subtype remained enriched for NF1 alterations in the Affymetrix HGU133A cohort. Overall survival did not differ between 3 subtypes among WHO-2021-defined GBMs.
Conclusion:
This study provides an updated evaluation of the 3-subtype framework within WHO-2021-defined IDH-WT GBM. Based on WHO-2021 criteria, the framework preserved principal subtype assignment patterns, cross-platform reproducibility and established subtype-associated molecular characteristics.
