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

AbstractBackgroundThe 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 genes’ expression (VEGFA,VEGFB,VEGFC,VEGFD,PGF,FLT1,FLT4,KDR,NRP1, andNRP2) on cognitive performance and AD pathology, as well as on the associated VEGF signaling pathways in 8 cell types from postmortem human brains.MethodsThe 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.ResultsHigher microglia expressedFLT1, endothelialFLT4, astrocyteVEGFD, and oligodendrocyte precursor cell (opc)NRP1expression associated with greater β-amyloid burden. Higher oligodendrocyteVEGFBexpression associated with greater β-amyloid burden and worse cognitive trajectories, whereas higherVEGFBexpression in inhibitory neurons was associated with lower β-amyloid burden. Higher astrocyteNRP1was associated with lower tangle burden. Higher expression of microglia and endothelialFLT1associated with worse cognitive trajectories and lower cognition scores at the last clinic visit before death. As for association with diagnosis, prefrontal corticalFLT1expression 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.ConclusionsConsistent with our previously reported results from bulk omics data, prefrontal cortical expression ofFLT1andFLT4were 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,VEGFBexpression seems to have opposing effects on amyloid burden depending on the cell types, suggesting its more dynamic role in AD pathology.