Single-cell transcriptomics of resected human traumatic brain injury tissues reveals acute activation of endogenous retroviruses in oligodendroglia

Traumatic brain injury (TBI) is a leading cause of chronic brain impairment and results in a robust, but poorly understood, neuroinflammatory response that contributes to the long-term pathology. We used snRNA-seq to study transcriptomic changes in different cell populations in human brain tissue obtained acutely after severe, life-threatening TBI. This revealed a unique transcriptional response in oligodendrocyte precursors and mature oligodendrocytes, including the activation of a robust innate immune response, indicating an important role for oligodendroglia in the initiation of neuroinflammation. The activation of an innate immune response correlated with transcriptional upregulation of endogenous retroviruses in oligodendroglia. This observation was causally linked in vitro using human glial progenitors, implicating these ancient viral sequences in human neuroinflammation. In summary, this work provides a unique insight into the initiating events of the neuroinflammatory response in TBI, which has new therapeutic implications. To investigate changes in cell-type composition and cell-type specific transcriptional responses after severe, acute TBI in humans, we performed single-nucleus RNA sequencing (snRNA-seq) from fresh frozen human brain tissue. We recruited 12 severe TBI patients, defined as post resuscitation Glasgow Coma Scale (GCS) score ≤ 8. The mean age of TBI patients (10 males, 2 females) was 49.5 ± 18.2 years. In these patients decompressive surgery was a life-saving measure to remove injured and swollen space-occupying brain tissue causing marked mass effect or increased intracranial pressure (ICP) refractory to conservative, medical neurointensive care treatment. The injured and contused brain regions (typically the injured part of a temporal or frontal lobe) were surgically removed between 4 hours and 8 days after injury 20. The raw data of these patients is not included in the GEO repository as these are alive individuals protected by GDPR, processed files are available. As control tissue, we used five fresh-frozen post-mortem samples from the frontal and temporal lobe obtained from three non-neurological deaths aged 69, 75 and 87 years. We isolated nuclei from frozen human brain tissue using ultracentrifugation and FACS (see methods for details) and performed snRNA-seq using the 10X Genomics pipeline. To investigate a mechanistic link between interferon activation and ERV expression we decided to perform in vitro experiments in human glial progenitor cells (hGPCs). We differentiated human embryonic stem cells (hESCs) into hGPCs using a 135-day differentiation protocol. The hGPCs were treated with interferon gamma (IFN?, 5ng/ml) for 48 hours before harvested for 2×150 bp paired-end, strand-specific bulk RNA-seq analysis. ***Raw data not provided for GSM6376811-GSM6376826 due to patient privacy concerns*** The records have been updated with the following files on Sep 5, 2023: TBI_gene_count_matrix_2.csv hGPC_gene_count_matrix_2.csv