Fig. 6

Between non-NP and NP, neuronal system, transmission across chemical synapse, and Ca-dependent event pathway are upregulated in NP and downregulated in non-NP microenvironment. a Volcano plot shows non-NP and NP spatial transcriptomic differences. Low AD cases lack p-tau + NP and removed from the analysis. SYNPR is most upregulated in NP microenvironment suggesting NP are pre-synaptic and axonal in origin. Top 25 DEGs in both non-NP and NP microenvironments that are above the set threshold (P-value = 0.05, log2 FC = 0.2) are highlighted/labelled. b Volcano plot shows genes involved in neuronal system are more downregulated in non-NP microenvironment. GLUL and MYO6 were upregulated in non-NP and SNAP25 and SYT1 were upregulated in NP. Top DEGs are labelled. c Top 20 pathways that are upregulated in both non-NP and NP microenvironment. The blue color represents pathways that are upregulated in NP or downregulated in Non-NP. The red color represents pathway that are upregulated in Non-NP. Pathway analysis shows that Ca-dependent events (adj p-value = 0.006), Transmission across Chemical Synapses (adj p-value = 0.006), and Neuronal system (adj p-value = 0.006) are upregulated in NP and downregulated in non-NP