Cultured ex vivo human brain tissue maintains cell-type transcriptional identities

There is growing recognition of the need for human-based models of the nervous system and its diseases. Studies have investigated the electrophysiological properties of neurons in ex vivo human brain tissue, but the maintenance of other cell types remains unclear. We therefore used single-nucleus RNA sequencing of six patient samples to determine how well various cell types maintain their transcriptional identities over two weeks in organotypic slice culture (day 0, with 83 501 nuclei, and day 14, with 45 738). For each patient sample (two pediatric temporal lobectomies, one adult frontal cortex, two glioblastomas, and one medulloblastoma), we generated correlations between each day 0 and day 14 cell type using the extent of up- and down-regulation of all significantly variable genes. We found generally high correlations, especially in tumour cells (glioblastoma tumour cells r = 0.81, medulloblastoma tumour cells r = 0.90), with microglia (r = 0.72), oligodendrocytes (r = 0.76), and endothelial cells (r = 0.75). This holds significant promise for this model's use in both mechanistic studies and therapeutic screens, with its high degree of molecular and cellular relevance to the in vivo human brain.