Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19

Abstract

Background Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We sought to further our understanding of the relationship between brain tropism, neuro-inflammation, and host immune response in acute COVID-19 cases. Methods Three brain regions (dorsolateral prefrontal cortex, medulla oblongata, and choroid plexus) from 5 patients with severe COVID-19 and 4 controls were examined. The presence of the virus was assessed by western blot against viral spike protein, as well as viral transcriptome analysis covering > 99% of SARS-CoV-2 genome and all potential serotypes. Droplet-based single-nucleus RNA sequencing (snRNA-seq) was performed in the same samples to examine the impact of COVID-19 on transcription in individual cells of the brain. Results Quantification of viral spike S1 protein and viral transcripts did not detect SARS-CoV-2 in the postmortem brain tissue. However, analysis of 68,557 single-nucleus transcriptomes from three distinct regions of the brain identified an increased proportion of stromal cells, monocytes, and macrophages in the choroid plexus of COVID-19 patients. Furthermore, differential gene expression, pseudo-temporal trajectory, and gene regulatory network analyses revealed transcriptional changes in the cortical microglia associated with a range of biological processes, including cellular activation, mobility, and phagocytosis. Conclusions Despite the absence of detectable SARS-CoV-2 in the brain at the time of death, the findings suggest significant and persistent neuroinflammation in patients with acute COVID-19.

Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets

“…We further assessed Portal’s ability to integrate across data types when no cell type, or very few cell types are shared. In this scenario, we applied Portal to integrate one human PBMC scRNA-seq dataset [50] with two human brain snRNA-seq datasets [51, 52], respectively, as two examples. In the first example (Fig.…”

Neurological sequela and disruption of neuron-glia homeostasis in SARS-CoV-2 infection

“…However, RNA analysis from bulk brain tissue does not allow localization of the RNA to specific cell types, and the virus detected in the brain may be more prevalent in endothelial cells versus neurons or glia ( Nuovo et al, 2021 ; Wenzel et al, 2021 ). However, this possibility requires further investigation and single-cell sequencing of brain autopsy tissue may be one path forward ( Fullard et al, 2021 ).…”

“…Peripheral T cell infiltration is present along with resident microglia, which have adopted a phenotype reminiscent of neurodegenerative disease. Another transcriptomic analysis of three distinct brain areas ( n = 5 COVID-19; n = 4 controls) found an influx of monocytes and macrophages in the choroid plexus along with a signature in cortical microglia linked to cellular activation, mobility, and phagocytosis ( Fullard et al, 2021 ). In both instances, molecular traces of SARS-CoV-2 were not detected ( Fullard et al, 2021 ; Yang et al, 2021 ), possibly suggestive of persistent inflammation and longer-lasting neural injury, even after the virus has cleared.…”

“…Another transcriptomic analysis of three distinct brain areas ( n = 5 COVID-19; n = 4 controls) found an influx of monocytes and macrophages in the choroid plexus along with a signature in cortical microglia linked to cellular activation, mobility, and phagocytosis ( Fullard et al, 2021 ). In both instances, molecular traces of SARS-CoV-2 were not detected ( Fullard et al, 2021 ; Yang et al, 2021 ), possibly suggestive of persistent inflammation and longer-lasting neural injury, even after the virus has cleared. Using a paradigm of spatial profiling by imaging mass cytometry at single-cell resolution, an evaluation was performed of autopsy brain stem and olfactory bulb ( Schwabenland et al, 2021 ).…”

Application of omics technology to combat the COVID‐19 pandemic

“…In the postmortem human brain tissue of COVID‐19 patients, monocytes and macrophages infiltrate to choroid plexus across the blood–brain barrier and lead to IRF8‐, ATF5‐, SPI1‐, and TAL1‐mediated activation of microglia inflammatory responses, including cellular activation, mobility, and phagocytosis. 154 Peripheral T cells can infiltrate to the parenchyma, and astrocyte cluster is marked by established inflammation and astrogliosis, lead to significant dysregulation of neurotransmission and synaptic organization. 155 In the frontal cortex tissue of COVID‐19 patients, downregulation of genes associated to HIF was observed, which may inhibit the capacity of defense system during infection and oxygen deprivation, showing that hypoxia is also marked in the brain of COVID‐19 patients.…”