BIOM-67. DIFFERENTIAL DNA METHYLATION PATTERNS IN THE CSF OF PATIENTS WITH DIFFUSE GLIOMAS

Abstract

Abstract Studies have shown that different central nervous system (CNS) tumor types exhibit unique DNA methylation profiles. DNA methylation-based machine learning classification of CNS tumor tissue has been demonstrated to be highly-accurate in differentiating between tumor types, including between diffuse glioma subtypes. While similar analyses have been performed using cell-free DNA (cfDNA) from blood, few studies have looked at the potential of DNA methylation as a biomarker for diffuse gliomas using CSF-derived cfDNA. In this study, we analyzed CSF cfDNA methylation patterns in diffuse glioma patients. DNA methylation profiling of CSF of patients with glioblastoma, IDH-wildtype (GBM) (n=37), IDH-mutant diffuse gliomas (n=12), and non-neoplastic conditions (n=5) was performed using cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq). Methylation quantification was estimated for each genomic region. Significance testing was performed between diagnostic groups to discover differentially-methylated regions (DMRs). The 300 most differentially-methylated regions (DMRs) for each comparison (IDH-wildtype vs. IDH-mutant, IDH-mutant vs. control, IDH-wildtype vs. control), for a total of 900 DMRs, were utilized as features in dimensionality reduction analysis and machine learning. Out of ~1×107 defined genomic regions, there were ~7×105 DMRs between GBM and control samples and ~1.5×106 DMRs between GBM and IDH-mutant samples, accounting for ~7% and ~15% of the genome, respectively. Uniform manifold approximation and projection (UMAP) and hierarchical clustering analysis revealed that samples were mostly clustered by diagnosis. Random forest analysis of the 900 DMRs with an 80/20 train/test split resulted in an overall accuracy of 0.815. In conclusion, CSF cfDNA methylation profiles of diffuse glioma patients exhibit differential methylation patterns between IDH-mutant and IDH-wildtype tumors, as well as between tumor and control, and could be informative biomarkers for the diagnosis of patients with diffuse gliomas.