Reactive astrocyte subpopulations with high Gfap and C4b expression in different Alzheimer’s disease mouse models: Single-cell nuclear transcriptome analysis

Understanding the cellular landscape underlying the heterogeneity of Alzheimer’s disease and the cell type-specific molecular perturbations is essential for identifying novel, targeted therapeutic strategies. However, previous bulk transcriptomic studies have failed to capture the unique contributions of individual cell populations to the early pathogenesis of the disease, and the functional diversity of key cell types in driving Alzheimer’s disease progression remains insufficiently characterized. In this study, we examined transcriptional changes in hippocampal tissue during early Alzheimer’s disease stages in two mouse models of Alzheimer’s disease: the apolipoprotein E4 knock-in and amyloid precursor protein/presenilin 1 mice. We performed single-cell nuclear transcriptome sequencing on hippocampal tissue from three 8-month-old amyloid precursor protein/presenilin 1 mice and one 6-monthold apolipoprotein E4 knock-in mouse, with one 6-month-old apolipoprotein E3 knock-in mouse serving as the control. Analyses of intergroup differential expression and functional enrichment indicated that Alzheimer’s disease-associated genes in different cell types were involved in synapse-related pathways. When we re-analyzed astrocytes, we found a group linked to Alzheimer’s disease that had high levels of Gfap and C4b, which was confirmed by immunofluorescence. Gene Ontology enrichment analysis indicated that this subpopulation may promote disease through RNA splicing. Further pseudotime trajectory and functional enrichment analyses showed that cells from different Alzheimer’s disease mouse models had different development paths, functions, and gene expression patterns. Similar re-clustering and functional enrichment analyses of excitatory neurons uncovered a distinct excitatory neuron subpopulation that may affect Alzheimer’s disease progression through mRNA processing and RNA splicing mechanisms. Gene set variation analysis further revealed functional differences between models within this subpopulation. Using single-cell sequencing, we identified a subgroup of astrocytes with high Gfap/C4b and a diseaserelated subgroup of excitatory neurons that are involved in RNA splicing. Together, these results provide a cellular and molecular basis for further research and a potential resource for future targeted treatments.