Spatial Transcriptomic Sequencing of a DIPG-infiltrated Brainstem reveals Key Invasion Markers and Novel Ligand-Receptor Pairs contributing to Tumour to TME Crosstalk

Abstract

Emerging spatially-resolved sequencing technologies offer unprecedented possibilities to study cellular functionality and organisation, transforming our understanding of health and disease. The necessity to understand healthy and diseased tissues in its entirety becomes even more evident for the human brain, the most complex organ in the body. The brains cellular architecture and corresponding functions are tightly regulated. However, when intercellular communications are altered by pathologies, such as brain cancer, these microenvironmental interactions are disrupted. DIPG is a brainstem high-grade glioma arising in young children and is universally fatal. Major disease obstacles include intratumoural genetic and cellular heterogeneity as well as a highly invasive phenotype. Recent breakthrough studies have highlighted the vital oncogenic capacity of brain cancer cells to functionally interact with the central nervous system (CNS). This CNS-crosstalk crucially contributes to tumour cell invasion and disease progression. Ongoing worldwide efforts seek to better understand these cancer-promoting CNS interactions to develop more effective DIPG anti-cancer therapies. In this study, we performed spatial transcriptomic analysis of a complete tumour-infiltrated brainstem from a single DIPG patient. Gene signatures from ten sequential tumour regions were analysed to assess disease progression and to study DIPG cell interactions with the tumour microenvironment (TME). We leveraged this unique DIPG dataset to evaluate genes significantly correlated with invasive tumour distal regions versus the proximal tumour initiation site. Furthermore, we assessed novel ligand-receptor pairs that actively promote DIPG tumour progression via crosstalk with endothelial, neuronal and immune cell communities, which can be utilised to support future research efforts in this area of high unmet need.