Skip to main content
. Author manuscript; available in PMC: 2022 Feb 5.
Published in final edited form as: Nature. 2021 Apr 28;593(7858):255–260. doi: 10.1038/s41586-021-03489-0

Figure 3 |. Gene-set analysis uncovers a link between impaired meningeal lymphatic vasculature and microglial activation in Alzheimer’s disease.

Figure 3 |

a, Single nucleotide polymorphisms in the 1 Mb region of genes highly expressed in meningeal LECs are in cis-expression quantitative expression loci (cis-eQTL) in microglia from the parietal cortex of human brains (non-AD and sporadic AD cases only). Violin plots with the distribution of gene expression and the first, median and third quantiles depicted for each genotype. b, tSNE plots showing the segregation of microglia from human donors or 5xFAD mice into 5 distinct clusters upon cross-species RNA-seq data integration and analysis (see also Extended Data Fig. 10). c, d, Violin plots with expression levels of c) homeostatic genes and d) activation genes in the different human microglia clusters. e, Graph showing the cluster proportions in the human non-AD, presymptomatic AD, familial AD, sporadic AD microglia groups, and in the 5xFAD mouse Vis. plus mIgG and Vis./photo. plus mIgG microglia groups. Statistically significant differences were observed between the Vis. plus mIgG and Vis./photo. plus mIgG groups regarding the proportions of microglia clusters 1 (P = 0.00026), 2 (P = 0.00191) and 3 (P = 0.03535). f, tSNE representation of the scaled average expression (range in scale bar) of the module of 54 human gene orthologs of the 5xFAD microglial gene signature of meningeal lymphatic dysfunction, subtracted by an aggregated expression of randomly chosen control feature gene-sets. g, Violin plot showing each microglia cluster’s signature score obtained by partial residuals from linear mixed models. Data in b-g were obtained from the integrated analysis of a total of 5,462 non-AD, 618 presymptomatic AD, 4,548 familial AD and 6,461 sporadic AD microglia (single-nucleus RNA-seq data) from human brain parietal lobes, and from a total of 781 and 770 microglia (single-cell RNA-seq data) from the brains of 5xFAD mice of the Vis. plus mIgG and the Vis./photo. plus mIgG groups, respectively; results involving human microglia were corrected for age of death, sex and disease status; statistically significant differences were calculated by two-proportion Z-test in e and by linear mixed models in g (individual comparisons between the score in cluster 1 and the other scores).