10064-GGE-6 A MULTI-OMIC LANDSCAPE OF GLIOBLASTOMA, IDH-WILD TYPE

Abstract

Abstract Glioblastoma (GBM) is the most common and highly resistant malignant brain tumor. Although the previous large-scale genomic analyses identified numerous driver genes, limited progress has been achieved in the development of novel treatments. To obtain further insights into the molecular mechanisms underlying the development of GBM, an integrated analysis including epigenetic and transcriptomic analyses, known to regulate malignant tumor progression, is imperative. We analyzed 289 whole-genome sequencing (WGS) including 159 unpublished deep WGS (≥ ×120 coverage) along with RNA-seq, DNA methylation array, whole-genome bisulfite sequencing, and assay for transposase-accessible chromatin with sequencing (ATAC-seq).Mutational analysis identified known driver alterations exhibiting inter-tumoral heterogeneity. Deep WGS enables us to delineate a fine view of clonal architecture demonstrating distinct mutational signatures between clonal and subclonal mutations, suggesting different mutational processes contribute to GBM pathogenesis depending on the developmental stage. Genetic alterations are strongly associated with gene expression subtypes and DNA methylation patterns. Transcriptional deconvolution analysis reveals the heterogeneous proportion of differentiated and stem-like cell states among cases. Tumors predominantly comprised of differentiated cells display genetic and epigenetic profiles that align with the classical subtype, whereas tumors predominantly composed of stem-like cells exhibit profiles consistent with the proneural subtype. Genome-wide chromatin accessibility patterns are well associated with expression subtypes of GBM. Motif enrichment analysis of open chromatin sites identified specific transcription factor binding sites, such as the SOX10 motif in the proneural subtype, known to regulate cell states, and the CREB motif in the mesenchymal and classical subtypes, which promote cell proliferation and angiogenesis through TGF-beta regulation. These findings support a model in which the difference in chromatin structure also regulates the progression of GBM.Our analysis encompassing multilayer molecular mechanisms reveals that GBM evolves through harboring genetic alterations and epigenetic modifications depending on the tumor initiation stage and cellular differentiation status.