Health + Life Science Alliance Heidelberg Mannheim

Cancers must rewire their metabolism to support their rapid proliferation and adapt to new environments in the body when they spread to distant organs. These metabolic adaptations, however, often introduce vulnerabilities that are unique to the cancer and present new therapeutic opportunities. Ewing sarcoma (EwS) is an aggressive malignancy that arises primarily in adolescents and young adults and has frequently already metastasised by the time patients are diagnosed. It is known that the fusion gene that drives EwS alters the expression of many genes involved in metabolism, but until this project, this had not been comprehensively studied at the level of the metabolome in physiologically refined cell line models or in primary and metastatic tumours from animal models of EwS.

We cultured a range of EwS cell lines in human plasma-like media and as 3D spheroids to better recapitulate the nutrient- and oxygen-limiting conditions of tumours in the body, as well as with high or low levels of the EwS driver fusion to study the effect of the fusion on the EwS cell metabolome. Further, we collected primary, metastatic, and matched normal tissue from mouse models of EwS in order to study metabolic changes that EwS cells undergo during metastasis. Using the biocrates MxP® Quant 500 XL kit, the largest combination of lipids and small molecules profiled in a single quantitative metabolomics kit, we comprehensively characterize the metabolome of these cell line and tumour models.

We found numerous, significant changes in metabolites between tumours and normal tissue, demonstrating cancer-specific metabolic changes, as well as between matched primary and metastatic tumours, highlighting metastatic-specific changes. These metabolites included amino acid and amino acid derivatives, biogenic amines, carboxylic acids, and a host of lipid species. Further, compared to the findings in tumours, there were both overlapping and unique metabolic changes in the cell lines upon lowering of the fusion driver gene. Together, this revealed metabolites whose abundance is, at least in part, regulated by the EwS fusion driver as well as metabolites whose abundance is driven more by an environmental context than the fusion driver. This has opened a number of lines of investigation into understanding how fusion-driven metabolic changes may support EwS development and how environmental-driven changes may support EwS metastasis, with potential to identify new therapeutic targets for both primary and metastatic EwS.