Therapy-resistance in AT/RT is driven by epithelial-mesenchymal transition, extracellular matrix changes, and enrichment of CD1A+ CD207+ dendritic cells [RNA-seq_cell_lines]

Atypical teratoid/rhabdoid tumors (AT/RT) are the most common malignant brain tumors during infancy and associated with a dismal prognosis. 50% of the patients suffer from progressions or recurrences, but the underlying mechanisms remain largely unknown. To identify mechanisms of progression and recurrence, we performed single-nucleus RNA sequencing of eight primary-recurrence pairs. Tumor cells and cells of the tumor microenvironment (TME) were analysed separately. Therapy-resistant tumor cells were identified through the comparison of global gene expression profiles between primary and recurrent tumor cell populations using CIBERSORT. Histology, in vitro experiments, bulk RNA sequencing, and survival analyses were performed to validate our findings. Paired primary and recurrent AT/RT tumor samples showed significant differences in their gene expression profiles. The TME of AT/RT recurrences was characterized by enrichment of CD1A+ CD207+ dendritic cells (DCs), which were per se associated with inferior survival in relapsed patients. Differentially expressed genes of AT/RT-MYC primary tumor cells that potentially persist after therapy, were involved in the organization of the extracellular matrix (ECM), developmental processes, and diverse immune signalling pathways. In addition, recurrences demonstrated a significantly higher proportion of cells undergoing partial epithelial-mesenchymal transition (pEMT) compared to primary tumors, a feature that we confirmed following treating AT/RT-MYC tumor cells in vitro. Finally, patients with primary tumors strongly expressing respective genes displayed a significantly worse survival. We identified pEMT, ECM remodeling, and enrichment of CD1A+ CD207+ DCs as potential mechanisms of therapy resistance in AT/RT which could be employed to improve therapy in the future.