Dissecting the intra- and inter-tumoral heterogeneity underlying glioblastoma pathogenesis utilizing multi-omics analysis

Abstract Glioblastoma (GBM) is the most common malignant brain tumor with a dismal prognosis. Considering its extensive molecular diversity underlies therapeutic resistance to multimodal treatment, it is imperative to reveal intra- and inter-tumoral heterogeneity, leading to further understanding of GBM pathogenesis. We analyzed 289 whole-genome sequencing data (WGS) including 159 unpublished deep WGS (≥ ×120 coverage) along with RNA-seq, DNA methylation array, whole-genome bisulfite sequencing, and assay for transposase-accessible chromatin with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) to uncover the multi-omics molecular heterogeneity of GBM. Along with inter-tumoral heterogeneity of genetic driver alterations, deep WGS enables us to delineate a fine view of clonal architecture where mutational signatures differ across clonal and subclonal mutations, supporting that different mutational processes contribute to GBM pathogenesis depending on the developmental stage. As well, tumor cell differentiation status detected by transcriptional deconvolution analysis is associated with multi-layer profiles including genome, transcriptome, epigenome, and chromatin status. ATAC-seq demonstrated distinct features of genome-wide chromatin accessibility associated with gene expression subtypes of GBM. Motif enrichment analysis detects the differentially accessible regions where the proneural subtypes are enriched with the SOX10 motif, known as a transcription factor for mesenchymal transition whereas the mesenchymal and classical subtypes are enriched with the CREB/ATF motif, a regulator of TGF beta associated with a poor prognosis. Our findings support a model in which GBM evolves through generating genetic and epigenetic intra-tumoral heterogeneity suggesting that specific cell states may have distinct vulnerability to mutational processes and epigenetic modifications. Our analysis reveals the molecular mechanisms underlying the progression of GBM enhancing our understanding of the pathogenesis.