DNA Methylation-Based Deconvolution Study of Glioblastoma Heterogeneity and Cell Types Associated with Patient Survival

Background: IDH-wildtype glioblastoma (GBM) is an aggressive, heterogeneous brain tumor with limited treatment options. This study tries to improve our understanding of GBM by applying DNA methylation-based deconvolution to define its cellular composition and its association with patient outcomes. Methods: We generated oligodendroglial precursor cells at various developmental stages from enriched human neural progenitor cultures and used their DNA methylation signatures, along with published signatures of cells types relevant to brain tumors and the tumor microenvironment, to deconvolve 263 adult GBMs (Heidelberg cohort). Tumor purity was estimated using RF_Purify. An independent cohort of 199 GBMs from TCGA and GEO, all treated with standard-of-care therapy, was similarly deconvolved, followed by Kaplan–Meier survival analysis to assess the prognostic value of the proportions of the neoplastic components. Results: Deconvolution uncovered distinct cellular compositions that differed between the neoplastic and non-neoplastic components of GBM. Tumor purity analysis showed that the neoplastic fractions averaged 70% of the tumor bulk: they were predominantly oligodendrocyte-like (43%), along with oligodendrocyte precursor-like (27%), astrocyte-like (19%), and mesenchymal stem cell-like (11%) populations. The non-neoplastic fractions were enriched for macrophages, vascular cells, and immune cell populations. A higher oligodendrocyte-like signature was linked to poorer survival (median survival 14.3 vs. 15.3 months; p = 0.017), while a higher astrocyte-like signature correlated with improved survival (15.3 vs. 13.4 months; p = 0.044). The astrocyte-to-oligodendrocyte ratio emerged as a strong prognostic marker, with a higher ratio predicting significantly longer survival (15.8 vs. 11.9 months; p < 0.00011). Conclusions: The methylation-based deconvolution data provided insight into GBM heterogeneity, highlighting the prognostic relevance of the astrocyte-to-oligodendrocyte ratio and its potential to guide personalized treatment strategies.