Investigating the cellular landscape of glioblastoma brain tumours, and how it changes through treatment

Glioblastoma (GBM) is the most aggressive primary malignancy of the central nervous system. Despite standard treatment, comprising surgical resection, followed by concomitant radiation and chemotherapy, it is incurable. This devastating prognosis stems from complex multi-layered heterogeneity, which enables GBM tumour cells to resist treatment and reoccur. Advances in genomic technologies have classified GBM tumours at the single-cell resolution, revealing that malignant GBM cells occupy distinct neoplastic cell states which resemble neuro-developmental hierarchies and wound healing programs. These states are supported by complex interactions which include immune, healthy brain and vasculature cells.

To investigate how the cellular landscape of GBM tumours changes through treatment, I utilised an extensive dataset of paired (pre- and post-treatment) GBM tumour patient samples. These samples were profiled using bulk RNA sequencing (RNA-seq) and thus characterising their cell type composition in silico, necessitated the use of cellular deconvolution techniques. Benchmarking of such methods has shown that accuracy and interpretability are highly dependent on the specificity of the cell type reference used. Therefore, I developed a set of GBM-specific cell type markers and used these to validate the optimal deconvolution method, which I also released as a publicly available web application, GBMDeconvoluteR. Using this tool, I characterised 219 paired GBM samples and uncovered consistent cell type changes through treatment. These changes were associated with survival outcomes and aligned with our previously described patient stratification, based on treatment-resistance mechanisms.

To complement these findings, I then applied a novel spatial proteomics method and found that hypoxia drives the layered organisation of the GBM tumour microenvironment (TME) pre-treatment, but post-treatment the GBM TME is less structured, driven instead by reactive astrocytes and infiltrating lymphocytes. Collectively, this work highlights some key shifts in the cellular landscape of GBM through treatment, which may hold therapeutic potential.