Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towards in vivo malignant cell states

In the malignant brain tumour, sonic hedgehog medulloblastoma the properties of cancer cells are influenced by their microenvironment, but the nature of those effects and the phenotypic consequences for the tumour are poorly understood. The aim of this study was to identify phenotypic properties of SHH-MB cells that were driven by the non-malignant tumour microenvironment. Human iPSC were differentiated to cerebellar organoids to simulate the non-malignant tumour microenvironment. Tumour spheroids were generated from two distinct, long-established SHH-MB cell lines which were co-cultured with cerebellar organoids. We profiled the cellular transcriptomes of malignant and non-malignant cells by performing droplet-based single cell RNA-seq of thousands of cells. The transcriptional profiles of tumour cells in co-culture were compared with those of malignant cells cultured in isolation and with public SHH-MB datasets of patient tumours and PDX models. Heterogeneity of cell states was observed for SHH-MB cells cultured in isolation and in co-culture. Tumour cells in co-culture activated a key marker of differentiating granule cells, NEUROD1 that was not observed in control tumour cells cultured in isolation. In malignant cells in co-culture, cancer stem cell (CSC)-like states emerged that were not observed in control cultures and closely similar or equivalent cell states could be identified in patient tumours. For both SHH-MB cell lines grown in co-culture, there was a convergence of malignant cell states towards in vivo cell states observed in SHH-MB patient tumours and PDX models that were non-cell autonomously induced by the non-malignant microenvironment.