Single nucleus RNA sequencing unveils relationship between microglia and endothelial cells in mixed Alzheimer's disease and vascular pathology

Single-nucleus RNA sequencing (snRNAseq) allows for the dissection of cell type-specific transcriptional profiles. We evaluated differential gene expression using snRNAseq data generated from hippocampal region tissue donated by 11 Boston University Alzheimer's Disease Research Center (BU-ADRC) participants with neuropathologically confirmed Alzheimer's disease (AD) with or without co-existing pathology (AD only = 3, AD+vascular disease (Vas) = 6, AD+Lewy body disease (LBD) = 2). Expression of 19,893 genes was compared between AD+Vas and other AD groups for each cell type. Co-expression modules were identified in a set of 174 bulk RNAseq hippocampal samples from BU-ADRC. Modules enriched in differentially expressed genes (DEGs) were identified using Fisher's exact tests. The overlap between DEGs and co-expression modules was incorporated into quantitative gene set analysis. AD+Vas subjects showed decreased expression of genes related to immune activation in microglia (t = -2.67, p = 2.72 × 10^-2). Expression of these genes was negatively associated with expression of receptors P2RY12 and CX3CR1 (r = -0.87, p = 1.70 × 10^-2), which have been linked to microglial migration and activation, respectively. Expression of genes that negatively regulate angiogenesis in endothelial cells was decreased (t = -4.84, p = 1.49 × 10^-3) and associated with expression of the microglial activation genes in the BU-ADRC dataset (r = 0.68, p = 1.63 × 10^-2). This association and the finding of upregulation of P2RY12 in AD+Vas samples were replicated in 393 ROSMAP Study dorsolateral prefrontal cortex snRNAseq samples (r = 0.34, p = 8.37 × 10^-12 and z = 5.82, p_FDR = 8.73 × 10^-6, respectively). In summary, we found an expression profile in brain tissue from individuals with AD+Vas pathology that is associated with reduced activation and increased migration in microglia and angiogenesis in endothelial cells.