Fig. 5

Spatial transcriptomic analysis shows neuronal system and Ca-dependent event pathway is downregulated in amyloid plaque microenvironment. a Gene expression differences between control (no plaque microenvironment) and amyloid plaque (NP + non-NP) in volcano plot. Top 25 DEGs in both microenvironments that are above the set threshold (P-value = 0.05, log2 FC = 0.3) are highlighted/labelled. Plaque-induced Genes (PIGs) and Disease associated microglia (DAM) genes are more distributed towards amyloid plaque microenvironment. b Neuronal system related gene expression differences between control (no plaque microenvironment) and amyloid plaque (NP + non-NP) in volcano plot. Neuronal system related genes are downregulated in amyloid plaque microenvironment compared to control (no plaque) microenvironment. Top DEGs are labelled. P-value = 0.05, log2 FC = 0.2. c Top 20 Pathways of control (no plaque) and amyloid plaque microenvironment in postmortem brain sample. The blue color represents pathways that are upregulated in Control (no plaque) or downregulated in amyloid plaque microenvironment. Neuronal system (adj p-value = 0.003), Ca-dependent events (adj p-value = 0.003) and Transmission across Chemical Synapses pathway (adj p-value = 0.003) are more downregulated in amyloid plaque microenvironment