Differential endothelial cell remodeling in Down syndrome and APP duplication drives distinct blood brain barrier dysfunction

An extra copy of the amyloid precursor protein gene (APP) is present in Down syndrome (DS) and APP duplication (APPdup), increasing the risk of Alzheimer disease (AD) and cerebral amyloid angiopathy (CAA). However, we reported greater vascular Aβ deposition in APPdup than in DS with AD, suggesting that other triplicated chromosome 21 genes may mitigate CAA severity. We investigated endothelial cell (EC) function and blood brain barrier (BBB) integrity in DS and APPdup using human induced pluripotent stem cell-derived ECs (iECs), assessing their morphology, junctional proteins, Aβ peptide secretion, barrier function, and transcriptomic profiles. Both DS and APPdup iECs secreted more Aβ40 Aβ42 compared with their respective isogenic controls but exhibited distinct Aβ peptide profiles. DS iECs showed increased junctional protein expression and reduced permeability, whereas APPdup iECs displayed increased permeability. Transcriptomic analysis revealed extensive dysregulation in DS iECs, with enrichment of junctional, adhesion, angiogenic, immune, and apoptosis pathways, and reduced cell-cycle, proliferative, and membrane-targeting signatures. APPdup iECs showed milder changes, including impaired protein targeting and reduced adhesion-related pathways. Despite comparable APP dosage, DS iECs maintained greater junctional integrity and lower permeability than APPdup iECs, potentially contributing to differential CAA vulnerability. However, impaired proliferation and altered angiogenesis may reduce BBB resilience during ageing.