A Re-visit of Glioblastoma Molecular Subtypes Utilizing the 2021 WHO Classification of CNS Tumors Framework
Geraldine Lee Wen She, M Tarek Elghetany, John Myseros, Seok-Gu Kang, Xiaonan Li, Wan-Yee TeoAbstract
Background
The three-subtype transcriptional framework is an established approach for classifying glioblastoma (GBM). The 2021 World Health Organization (WHO) Classification re-defined GBM as an IDH-wildtype (IDH-WT) tumor. We evaluated the three-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.
Methodology
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 four-subtype assignments, cross-platform reproducibility, overall survival and subtype-specific molecular characteristics were evaluated.
Results
Among WHO-2021-defined GBMs, the three-subtype framework demonstrated good concordance with legacy TCGA four-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 three-subtypes among WHO-2021-defined GBMs.
Conclusion
This study provides an updated evaluation of the three-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.