Fig. 2

Identification of female-enriched and disease-associated microglia (FDAMic). A, B Single-cell trajectory analysis with the Monocle 3 algorithm identified an evolutionary relationship among all microglial nuclei in the Mathys et al. cohort. A UMAP plot showing the locations of various microglial subclusters based on existing knowledge from published studies. Numbers inside the blanket represent the number of nuclei. B Three major branches of microglial fates were identified: HomMic, BAMic and ARMic branches. C Violin plots showing marker gene expression of BAMic (black), HomMic (blue), ARMic (red) and DysMic (pink) subtypes. D, E Visualization of all subtypes of microglia on the evolutionary trajectory UMAP plot according to D disease diagnosis or E sex of the samples. F Sex- and disease status-specific cell ratio distribution among all subclusters of microglia. Subcluster numbers are color-labeled according to their branch location on the evolutionary plot, i.e., BAMic (black), HomMic (blue), and ARMic (red). G, H Visualization of all subtypes of microglia on the evolutionary trajectory UMAP plot according to G neurofibrillary tangle (NFT) burden or H neuritic plaque burden of the samples. I. Detailed definition of microglial subtypes defined by our analysis, particularly the female-enriched and disease-associated microglia (FDAMic). J Single-cell trajectory analysis with the Monocle 3 algorithm identified an evolutionary relationship among all microglia in the Morabito et al. cohort. The expression intensities of the VSIG4, SPP1, RPS19 and C1QB genes are indicated on the right. K Sex- and status-specific cell ratio distribution among all subclusters of microglia identified in the Marabito et al. study. L Ratios of nuclei in samples of different Braak stages belonging to different subclusters of the Marabito et al. cohort. M Relative cell ratio changes in Cluster 13 of the Mathys et al. cohort after selective removal of FDAMic nuclei from the analysis. N Relative expression levels of the DEGs curated from the comparison between Cluster 13 nuclei originating from female LOAD versus ND samples (Fig. 1M, top panel) in different subtypes of microglia of the Mathys et al. cohort