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A single-cell transcriptomic atlas of all cell types in the entire 5xFAD mouse brain in response to dietary inulin supplementation

ABSTRACT: Alzheimer’s disease (AD) is a progressive neurodegenerative disease that becomes a major threat to the aging population. Due to lack of effective therapy, preventive treatments are important strategies to limit AD onset and progression, of which dietary patterns have been implicated as a key influencer. Diet with high fiber content is known to have beneficial effects on cognitive decline in AD. However, a global survey on brain cell dynamics in response to high fiber intake at single-cell resolution is still missing. Here, we show that dietary inulin supplementation synergized with AD progression to specifically increase the abundance of Akkermansia muciniphila in gut microbiome of the 5x Familial AD (FAD) mice. By performing single-nucleus RNA sequencing on different regions of the whole brain with three independent biological replicates, we reveal region-specific changes in the proportion of neuron, astrocyte and granule cell subpopulations upon inulin supplementation in 5xFAD mice. Intriguingly, such dietary change only marginally alleviated astrogliosis and microgliosis, without affecting the amyloid-beta plaque burden. These results provide a comprehensive overview on the transcriptomic changes in individual cells of the entire mouse brain in response to high fiber intake, which provides a resourceful foundation for future mechanistic studies on related topics

ORGANISM(S): Mus musculus

PROVIDER: GSE262881 | GEO | 2025/04/28

REPOSITORIES: GEO

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Project description:Roseburia inulinivorans is a recently identified motile representative of the Firmicutes that contributes to butyrate formation from a variety of dietary polysaccharide substrates in the human large intestine. Microarray analysis was used here to investigate substrate-driven gene expression changes in R. inulinivorans A2-194. A cluster of fructo-oligosaccharide (FOS)/inulin utilisation genes induced during growth on inulin included one encoding a b-fructofuranosidase protein that was prominent in the proteome of inulin-grown cells. This cluster also included a 6-phosphofructokinase and an ABC transport system, while a distinct inulin-induced 1-phosphofructokinase was linked to a fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS II transport enzyme). Real-time PCR analysis demonstrated that the b-fructofuranosidase and adjacent ABC transport protein showed greatest induction during growth on inulin, whereas the 1-phosphofructokinase enzyme and linked PTS II transport system were most strongly up-regulated during growth on fructose, indicating that these two clusters play distinct roles in the utilization of inulin. The R. inulinivorans B-fructofuranosidase was over-expressed in E. coli and shown to hydrolyse fructans ranging from inulin down to sucrose, with greatest activity on fructo-oligosacharides. Genes induced on starch included the major extra-cellular a-amylase and two distinct a-glucanotransferases together with a gene encoding a flagellin protein. The latter response may be concerned with improving bacterial access to insoluble starch particles. RNA was purified from mid-exponential phase (OD650 = 0.4) cultures of R. inulinivorans grown on basal YCFA supplemented with a single substrate of either starch or inulin using the RNeasy RNA purification kit (Qiagen), and the mRNA component enriched using the MICROBExpress system (Ambion). The purified RNA (1 ug) was labelled by reverse transcription (Amersham), employing random nonamer extension incorporating either dCTP-Cy3 or dCTP-Cy5 dyes. In order to ensure reproducibility, and to obtain statistically significant results, the dye labelling was swapped for a second hybridisation. RNA purified from a separate biological replicate was labelled and hybridised twice in the same way.

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A single-cell transcriptomic atlas of all cell types in the entire 5xFAD mouse brain in response to dietary inulin supplementation

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