Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [scRNA-Seq]
Brain tumors are the leading cause of cancer-related death in children. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of pediatric brain cancer are limited and hard to establish. We present a protocol that enables efficient generation, expansion and biobanking of pediatric brain cancer organoids. Utilizing our protocol, we have established patient-derived organoids (PDOs) from ependymomas, medulloblastomas, low-grade glial tumors and patient-derived xenograft organoids (PDXOs) from medulloblastoma xenografts. PDOs and PDXOs recapitulate histological features, DNA methylation profiles and intratumor heterogeneity of the tumors from which they were derived. We also showed that PDOs can be xenografted. Most interestingly, when subjected to the same routinely applied therapeutic regimens, PDOs respond similarly to the patients. Taken together, our study highlights the potential of PDOs and PDXOs for research and translational applications for personalized medicine. Overall design: Cells from the three different samples (tumor and 2 PDOs) have been next integrated based on the reciprocal PCA (“RPCA”) approach, performed with FindIntegrationAnchors (settings: 5000 genes selected for data integration) and IntegrateData function in Seurat. Unsupervised cluster analysis was performed by exploiting the shared nearest neighbor (SNN) modularity clustering algorithm implemented in Seurat function FindClusters. Differentially expressed genes across the cell clusters were annotated using the wilcox test in Seurat function FindAllMarkers.