MULTIDIMENSIONAL PROFILING OF TUMOR CELL HETEROGENEITY REVEALS CELL-LINEAGE SPECIFIC FUNCTIONS IN SUPRATENTORIAL EPENDYMOMAS

Abstract Supratentorial ependymomas (ST-EPN) are aggressive pediatric brain tumors that are categorized into distinct molecular subgroups. However, the developmental origins, tumor microenvironment, and phenotypic characteristics of tumor subpopulations across these subgroups are still poorly understood. In this study, we explored the human developmental signatures, global spatial organization, and the morphological and migratory tumor cell state behaviors in ST-EPN tumors at unprecedented resolution. We profiled 42 ST-EPN patients encompassing ZFTA-RELA (n = 20), ZFTA-Clusters 1 to 4 (n=20), and ST-YAP1 (n=4) subgroups by single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and live-cell imaging. We identified recurrent tumor cell states across tumors, that cover both generic cell processes (including cycling and mesenchymal/hypoxia) and human embryonic and fetal brain developmental signatures. ST-EPN subgroups displayed distinct developmental signatures, mapping to two separate temporally restricted progenitors-neuroepithelial-like and embryonic-like cells. Additionally, tumors showed diverging patterns of neuronal or ependymal differentiation, with ZFTA-Cluster 3 tumors as especially distinct from other subgroups in both developmental origin and differentiation. Furthermore, by utilizing 10X Xenium and novel algorithms we discovered that mesenchymal/hypoxia is critical for driving global tissue architecture to become more organized. Notably, recurrent tumors exhibited higher proportion of mesenchymal/hypoxia cells and greater structure than primary tumors. Lastly, by superimposing molecular and functional assays in both in vivo and in vitro models, we found that cell states exhibit distinct morphological and migratory behaviors, with neuronal-like cells being the most invasive. Neuronal-like cells especially exhibited distinct behavioral patterns reminiscent of neuronal migration during development. Moreover, we demonstrated the crucial role of neuronal microenvironment in promoting plasticity of cells toward this neuronal lineage. Taken together, we present a multidimensional framework for investigating cellular states within ST-EPN tumors, offering novel insights into their developmental origins, patterns of spatial organization, and cellular behavioral characteristics.