Association of 10 VEGF Family Genes with Alzheimer's Disease Pathology at Single Cell Resolution

Background: The role of the vascular endothelial growth factors (VEGFs) in the pathogenesis of Alzheimer's disease (AD) has been recently described, including notable changes along the VEGFB/FLT1 signaling pathway. However, cell-type specific alterations are yet to be characterized in depth. In this study, we utilized a large single-nucleus RNA sequencing dataset (N = 424) to investigate the effect of 10 VEGF gene expression (VEGFA, VEGFB, VEGFC, VEGFD, PGF, FLT1, FLT4, KDR, NRP1, and NRP2) on cognitive performance and AD pathology, as well as on the associated VEGF signaling pathways in 8 cell types from postmortem human brains. Methods: The single-nucleus transcriptomes, derived from Dorsolateral Prefrontal Cortex (DLFPC) tissues of 424 unique donors from the Religious Orders Study and Memory and Aging Project (ROS/MAP; AD Knowledge Portal syn2580853), were collected by the Rush Alzheimer's Disease Center and processed at Columbia University Medical Center. Mean age of death of the cohort was 89 years, among which 68% were females, and 52% were clinical AD cases. Negative binomial mixed models implemented in Nebula R package were used for differential expression analysis between autopsy confirmed AD dementia and normal cognition groups, and for association analysis with amyloid burden, tangle burden, and both cross-sectional and longitudinal global cognitive function. Intercellular VEGF-associated communication pattern among cell types was also profiled using CellChat. Results: Higher microglia expressed FLT1, endothelial FLT4, astrocyte VEGFD, and oligodendrocyte precursor cell (opc) NRP1 expression associated with greater beta-amyloid burden. Higher oligodendrocyte VEGFB expression associated with greater beta-amyloid burden and worse cognitive trajectories, whereas higher VEGFB expression in inhibitory neurons was associated with lower beta-amyloid burden. Higher astrocyte NRP1 was associated with lower tangle burden. Higher expression of microglia and endothelial FLT1 associated with worse cognitive trajectories and lower cognition scores at the last clinic visit before death. As for association with diagnosis, prefrontal cortical FLT1 expression was upregulated in clinical AD patients compared to cognitively normal controls in both endothelial and microglial cells. For VEGF-associated intercellular communication, VEGFA-mediated signals contributed the most to the communication in both AD and normal cognition groups. Interestingly, although FLT1 expression was significantly elevated in AD endothelial cells, these cells still showed comparable VEGFA-FLT1 communication strength to the cognitively normal controls. Conclusions: Consistent with our previously reported results from bulk omics data, prefrontal cortical expression of FLT1 and FLT4 were associated with cross-sectional global cognitive function, longitudinal cognitive trajectories, and AD neuropathology, and our study showed these associations appear to be driven by endothelial and microglial cells. In contrast, VEGFB expression seems to have opposing effects on amyloid burden depending on the cell types, suggesting its more dynamic role in AD pathology.