# Single-cell RNA sequencing reveals disease associated changes in brain endothelial cells in the 5XFAD mouse

## TL;DR

This study uses single-cell RNA sequencing to uncover changes in brain endothelial cells in a mouse model of Alzheimer's disease.

## Contribution

The study provides a detailed molecular profile of endothelial cell changes in the 5XFAD mouse model using scRNAseq.

## Key findings

- Differentially expressed genes in 5XFAD mice are linked to DNA damage, immune reactivity, and inflammation.
- Transcriptomic changes are zonated along the arteriovenous axis and involve AD GWAS risk genes.
- The study offers a resource to better understand vascular dysfunction in Alzheimer's disease.

## Abstract

Vascular dysfunction is a key contributor to Alzheimer’s disease (AD) pathology, where changes to the endothelium and its crucial role in maintaining blood-brain barrier (BBB) integrity have been of particular emphasis. The transgenic 5XFAD (5X Familial Alzheimer’s Disease) mouse model, which exhibits AD-related amyloidosis through FAD associated mutations in amyloid precursor protein (APP) and presenilin-1 (PS1), has become a widely adopted preclinical model in AD-related research studies. The need for cross-study standardization, accessibility, and data reproducibility has led to the widespread implementation of the C57BL/6J genetic background for maintaining this model. However, its reliability for studying vascular dysfunction and BBB alterations has been questioned due to conflicting reports in the literature. This variation is often attributed to the previously documented protective nature of the C57BL/6J background and loss of genetic background diversity. Since prior studies have mostly relied on imaging or functional assays, we herein utilized single-cell RNA sequencing (scRNAseq) to investigate AD-related molecular changes to endothelial cell populations in the 5XFAD mouse model. To initially build this resource, we focused on 12-month-old male mice, which revealed differentially expressed genes between 5XFAD and wildtype animals that mapped to signaling pathways involved in DNA damage, immune reactivity, and inflammation, among others. Many of these transcriptomic changes were zonated along the arteriovenous axis and occurred in AD genome-wide association study (GWAS) risk-associated genes. Overall, we anticipate this resource will help clarify the use of the 5XFAD model for studying AD-associated vascular changes and provide the foundation for expanded molecular profiling of brain endothelial cells under AD-associated conditions.

The online version contains supplementary material available at 10.1186/s12987-026-00766-w.