Extended Data Fig. 9: Neuroinflammatory signature in hippocampus with advancing age.
a, The proportion of spots enriched with IFN-γ signature is increased in the old hippocampus (young: 2.4%; middle-age: 2.5%; old: 5.9%). b, Pictogram illustration of inflammatory spots (IS) and their nearest neighbor spots (NNS). c, Volcano plot showing the differentially expressed genes between IS and their NNS. For all dots shown in color by an adjusted P < 0.05, DESeq2 differential test. d, Gene Ontology terms enriched in IS and their NNS. All GO terms shown by an adjusted P < 0.05 with Benjamini–Hochberg correction. e, Representative images showing the spatial correlation between T cells, IFN-γ signature (STAT1+ cells) and reactive microglia. f, Quantitation of the coverage of IBA-1 signal in hippocampus between young (3 MO), middle-age (10 MO) and old (18MO) animals (young: 7.0 ± 0.4%; middle-age: 7.8 ± 0.4%; old: 14.5 ± 1.1%; two-tailed unpaired t-test with Welch’s correction, NS, P = 0.2103 between young and middle-age, ***P = 0.0004 between middle-age and old, ***P = 0.0002 between young and old). g, PCA plot of in silico aggregated Visium spots of (left) the whole hippocampus, DG and (right) CA in the old mouse brain. h, Hierarchical clustering of in silico aggregated Visium spots showing distinct transcriptional structure among all three types of spots in (left) the whole hippocampus, DG and (right) CA of the old mouse brain. i, Module scores of CAS and expression of selected genes among all three types of spots. Upper: (most left) CAS-UP score (two-tailed unpaired t-test with Welch’s correction; t = 14.99, ****P < 0.0001 between IS and NNS, t = 10.35, ****P < 0.0001 between NNS and ENS1, t = 8.256, ****P < 0.0001 between ENS1 and ENS2; IS, n = 299 spot, NNS, n = 967 spots, ENS1, n = 1163 spots, ENS2, n = 1005 spots) and (the rest) H2-D1, C4b, Vim and Vcam1 among all three types of spots. Lower: (most left) CAS-DOWN score (two-tailed unpaired t-test with Welch’s correction; t = 12.29, ****P < 0.0001 between IS and NNS, t = 12.62, ****P < 0.0001 between NNS and ENS1, t = 7.295, ****P < 0.0001 between ENS1 and ENS2; IS, n = 299 spot, NNS, n = 967 spots, ENS1, n = 1163 spots, ENS2, n = 1005 spots) and (the rest) Syn2, Snca, Prdm3 and Pcdh20 among all three types of spots. Box plots depict the median and interquartile range, with whiskers indicating minimum and maximum values. Scale bars, 100 μm.
