Dysregulation of neuroprotective astrocytes, a spectrum of microglial activation states, and altered hippocampal neurogenesis are revealed by single-cell RNA sequencing in prion disease

Abstract

Prion diseases are neurodegenerative disorders with long asymptomatic incubation periods, followed by a rapid progression of cognitive and functional decline culminating in death. The complexity of intercellular interactions in the brain is challenging to unravel and the basis of disease pathobiology remains poorly understood. In this study, we employed single cell RNA sequencing (scRNAseq) to produce an atlas of 147,536 single cell transcriptomes from cortex and hippocampus of mice infected with prions and showing clinical signs. We identified transcriptionally distinct populations and sub-populations of all the major brain cell-types. Disease-related transcription was highly specific to not only overarching cell-types, but also to sub-populations of glia and neurons. Most striking was an apparent decrease in relative frequency of astrocytes expressing genes that are required for brain homeostasis such as lipid synthesis, glutamate clearance, synaptic modulation and regulation of blood flow. Additionally, we described a spectrum of microglial activation states that suggest delineation of phagocytic and neuroinflammatory functions in different cell subsets. Differential responses of immature and mature neuron populations were also observed, alongside abnormal hippocampal neurogenesis. Our scRNAseq library provides a new layer of knowledge on single cell gene expression in prion disease, and is a basis for a more detailed understanding of cellular interplay that leads to neurodegeneration.

NG2 glia protect against prion neurotoxicity by inhibiting prostaglandin E2 signaling

“…Our previous gene expression analyses of prion-inoculated mice (Sorce, Nuvolone et al 2020) and prion-infected cerebellar organotypic cultured slices (COCS) (Liu, Senatore et al 2022), as well as recent single-cell transcriptomics from other groups (Dimitriadis, Zhang et al 2022, Slota, Sajesh et al 2022), point to possible transcriptional changes in NG2 glia during prion disease. However, it is unclear how these cells respond to prion infections at the cellular level.…”

“…To molecularly characterize PGE2-producing microglia in prion-infected brains, we analyzed a previously generated single-cell RNA sequencing dataset (Slota, Sajesh et al 2022) based on a prion infection model similar to that used in the current study. In normal brains, microglia were largely (∼99%) Cox2 - or Ptges - ; however, the fractions of Cox2 + and Ptges + microglia were increased after prion infection in both the cerebral cortex ( Fig.…”

“…Cerebral cortex and hippocampal single-cell RNA sequencing dataset from prion-infected or control mice (Slota, Sajesh et al 2022) were obtained from the single cell portal at the Broad institute through the following link: https://singlecell.broadinstitute.org/sin-gle_cell/study/SCP1962. After loading the raw single-cell RNA sequencing data into R, doublets and ambient RNA were removed using scrublet (Wolock, Lopez et al 2019) and decontX (Yang, Corbett et al 2020), respectively.…”

“…Recent advances in high resolution gene expression analyses have enabled a deeper understanding of this complex cellular landscape. In addition to confirming the alterations of microglia and astrocytes, single-cell and spatial transcriptomics analyses of brain tissues from patients and animal models have unraveled prominent changes of oligodendrocyte linage cells in multiple neurodegenerative disorders (Mathys, Davila-Velderrain et al 2019, Chen, Lu et al 2020, Pandey, Shen et al 2022, including prion diseases (Dimitriadis, Zhang et al 2022, Slota, Sajesh et al 2022.…”

A single-cell map of antisense oligonucleotide activity in the brain

“…Although astrocytes may contribute to disease by propagating prions [58][59][60] , only neurons degenerate in prion disease, and neurotoxicity is cell autonomous: neurons that do not express PrP are protected even if they are in direct contact with misfolded prions produced by neighboring cells [60][61][62] . In contrast, neuroinflammatory responses from astrocytes and microglia [63][64][65][66] appear to be strictly non-autonomous, requiring neuronal prion infection 60 . That PrP-lowering ASOs extend survival in prion-infected mice 22,41,67 implies that they must lower PrP in neurons; nevertheless, we felt it prudent to further examine this link to determine whether there might ever exist circumstances in which a bulk tissue readout would indicate PrP lowering despite little or no target engagement in neurons.…”