Title: Defining the molecular impact of extrachromosomal oncogenes on cellular interactions in the glioblastoma microenvironment
Funder: The Academy of Medical Sciences

Abstract: Glioblastoma (GBM) is the most common primary brain tumour, and has a devastating prognosis. Precision medicine has failed to make an impact in this cancer largely due to intratumour heterogeneity and the immunosuppressive tumour microenvironment (TME). Oncogenes can drive recruitment of immune cells in the TME, including tumour associated microglia/macrophages (TAMs). Extrachromosomal DNA (ecDNA)-encoding driver oncogenes are present in 55% of GBMs, and drive resistance to therapy and tumour evolution. Their stochastic inheritance and highly dynamic nature likely contribute to the failure of targeted therapies to measurably improved outcomes in GBM. Understanding common mechanisms by which ecDNAs promote oncogenesis may yield new therapeutic avenues. Given their high copy-number, we hypothesize that ecDNA oncogenes affect cancer and TAM cell behaviour through driving production of factors for intercellular communication, potentially representing a powerful way of driving GBM evolution. Here, we will apply new spatial transcriptomic technology, Slide-seq, for measuring genome-wide expression at single-cell spatial resolution in human GBMs, allowing definition of cell states in their native spatial position and of their cellular interactions. In particular, ligand-receptor pairs between neighbouring cancer cells and TAMs can be identified, which drive cell-cell communication and whose expression may be dependent on oncogene expression. Next, we will perform functional in vivo studies to determine the effects of ecDNA-encoded oncogenes on cellular interactions, and validate novel ligand-receptor pairs driving GBM intercellular communication through CRISPR knockout of targets in orthotopic xenograft tumours. Our work has potential to elucidate fundamentally new insights into GBM biology and ecDNA-dependent therapeutic targets.

Lay abstract: Recent work has shed light on the importance of DNA circles in cancer cells; these DNA circles were long regarded as a curiosity, as they float in the cell but outside of chromosomes where DNA is normally found. It is now recognized that these DNA circles, termed extrachromosomal DNA (or ecDNA), can quickly grab or release genes responsible for tumour growth, allowing cancers to evade treatment. In essence, these DNA circles can explain why some cancers are so hard to cure, including the most common form of brain cancer (glioblastoma, GBM) which has a very poor survival rate. Much is unknown about how DNA circles affect the behaviour of cancer cells. We believe that cancer genes on DNA circles can determine how cancer cells communicate with one another and with other cells, such as immune cells. To explore in this in unprecedented detail, we will use a combination of human patient GBM samples and animal models. We will deploy a powerful new technology, Slide-seq – unlike previous technologies, this tool enables us to determine all genes that are switched on or off in every single cell of a tumour and also tells us precisely where each cell is in relation to others. As such, Slide-seq will allow us to determine how cancer and immune cells communicate with one another by highlighting signals sent between cells. This is important as it may lead to the discovery of new drug treatments for this lethal cancer that work by blocking lines of communication.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS