SnRNA-seq analysis of hippocampus in TAFE3 and TAFE4 mice

The apolipoprotein E (APOE) gene is the strongest genetic risk factor for Alzheimer disease (AD). In addition to effects of apoE on amyloid-β, results have shown that apoE markedly influences pathological forms of tau and tau-mediated neurodegeneration with apoE4 having a strong deleterious effect on both parameters. In the brain, apoE is produced and secreted primarily from astrocytes and also by activated microglia though the cell-specific role of each form of apoE in the setting of neurodegeneration has not been determined. We utilized a well- characterized mouse model of tauopathy, P301S Tau transgenic mice expressing floxed APOE-e4 or APOE-e3 alleles. We crossed these mice with Aldh1l1-CreERT2 mice and at 5.5 months of age, after the onset of tau pathology, administered tamoxifen or vehicle. We then compared mice with or without inducible knockout of astrocyte APOE at 9.5 months of age. Single nucleus RNA sequencing analysis revealed striking gene expression changes in all cell types in P301S mice with astrocytic APOE4 playing a role in modulating neuron, astrocyte, and microglial gene expression to a more homeostatic state. Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers.