Volume 216, November 2025, 107128Author links open overlay panel, , , , , , , , , , Highlights•

Expression of receptors P2RY12 and CX3CR1 is linked to microglial migration and activation, respectively.

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Expression of genes that negatively regulate angiogenesis in endothelial cells was decreased.

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AD+Vas pathology-related expression is associated with reduced activation and increased migration in microglia and angiogenesis in endothelia.

Abstract

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, pFDR = 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.

Keywords

Single-nucleus RNA sequencing

Alzheimer's disease

Lewy body disease

Vascular disease

Microglia

Endothelial cells

Data availabilityRaw and processed single nucleus RNAseq data from the ROSMAP samples can be obtained from the Synapse website (https://www.synapse.org/Synapse:syn31512863). Access to raw data derived from the BU-ADRC samples will be made available upon request.

© 2025 The Authors. Published by Elsevier Inc.