Single cell RNA sequencing reveals immunomodulatory effects of stem cell factor and granulocyte colony-stimulating factor treatment in the brains of aged APP/PS1 mice

Abstract

Alzheimers disease leads to progressive neurodegeneration and dementia. Alzheimers disease primarily affects older adults with neuropathological changes including amyloid beta deposition, neuroinflammation, and neurodegeneration. We have previously demonstrated that systemic treatment with stem cell factor, SCF, and granulocyte colony stimulating factor, GCSF, reduces amyloid beta load, increases amyloid beta uptake by activated microglia and macrophages, reduces neuroinflammation, and restores dendrites and synapses in the brains of aged APP–PS1 mice. However, the mechanisms underlying SCF–GCSF–enhanced brain repair in aged APP–PS1 mice remain unclear. This study used a transcriptomic approach to explore the mechanisms by which SCF–GCSF treatment alters the functions of microglia and macrophages in the brains of 28–month–old APP–PS1 mice. After 5–day injections of SCF–GCSF, single–cell RNA sequencing was performed on CD11b positive microglia and macrophages isolated from the brain. Flow cytometry was used for identifying CD11b positive microglia and macrophages in the brain. Both transcriptional profiling and flow cytometry data demonstrated dramatic increases in the population of macrophages in the brain following SCF–GCSF treatment. SCF–GCSF treatment robustly increased the transcription of genes implicated in activated immune cells, including gene sets that regulate inflammatory processes and cell migration. SCF–GCSF treatment also increased a cell population coexpressing microglial and macrophage marker genes. This cell cluster aligned with a disease–associated microglial profile linked with amyloid beta restriction and phagocytosis. S100a8 and S100a9 were the most robustly enhanced genes in both microglial and macrophage clusters following SCF–GCSF treatment. Furthermore, the topmost genes differentially expressed after SCF–GCSF treatment were largely upregulated in S100a8–9 positive microglia and macrophages, suggesting a largely well–conserved transcriptional profile related to SCF–GCSF treatment in cerebral immune cells. This S100a8–9–associated transcriptional profile contained genes related to pro– and anti–inflammatory responses, neuroprotection, and amyloid beta plaque inhibition or clearance. This study sheds new light on the cellular and molecular mechanisms of SCF–GCSF–mitigated Alzheimers disease neuropathology in the aged brain.