TMOD-02. Cultured ex vivo human brain tissue maintains cell-type transcriptional identities

Abstract There is growing recognition of the need for human-based models of the nervous system and its diseases. The maintenance of other cell types within explanted human brain tissue, including tumor cells, remains unclear. We therefore sought to use single-nucleus RNA sequencing to determine how well ex vivo human brain tissues maintain their transcriptional identities over two weeks in organotypic slice culture. With 83,501 nuclei from day 0 and 45,738 nuclei from day 14, we systematically compared the transcriptional profiles of patient tissue collected immediately after surgical resection (day 0) to tissue from that same patient collected after fourteen days in culture (day 14). We used two pediatric temporal lobectomy samples, an adult frontal cortex sample, two IDH wild-type glioblastoma samples, and one medulloblastoma sample. For each cell type in a given sample, we compared the extent of up- or down-regulation of all significantly variable genes between the paired day 0 and day 14 tissues to generate cell type correlations. We found generally high correlations of day 14 transcriptional identities to day 0 tissue. Strikingly high correlations were found especially in tumor cells (glioblastoma tumor cells r = 0.89, medulloblastoma tumor cells r = 0.93), with microglia (r = 0.86), oligodendrocytes (r = 0.80), pericytes (r = 0.77), endothelial cells (r = 0.78), and fibroblasts (r = 0.76) showing the strongest preservation of their transcriptional profiles. Astrocytes and excitatory neurons showed moderate preservation (r = 0.66 and 0.47, respectively). This holds significant promise for the model’s use in both mechanistic studies and therapeutic screens. Broad uptake of this more representative model, which is highly accessible to neurosurgeons, should prompt advances in our understanding of many uniquely human diseases for which resected tissue is available, leading to more reliable clinical trial performance, and ultimately yielding better therapies for our patients.