Fig. 1: AD microglia have lipid transcriptional state defined by ACSL1.

a, Schematic of snRNA-seq cohort and workflow (Methods). b, UMAP representation of all cells (n = 100,317) from snRNA-seq, coloured by annotated cell type. Data are shown after quality control and batch correction. c,d, Volcano plot representing MAST-based single-cell differential gene expression results (see section on ‘Single-cell differential gene expression’) of microglia from control individuals compared to microglia from individuals with AD and the APOE3/3 genotype (c) and from individuals with AD and the APOE4/4 genotype (d). Selected lipid- and metabolism-associated genes highlighted in red. e, Pathway diagram showing placement of differentially expressed gene ACSL1 in pathway starting from free fatty acid to LD formation. f, Violin plots showing ACSL1 expression across the cell types in the snRNA-seq dataset. Significance results indicate MAST-based adjusted P values (see section on ‘Single-cell differential gene expression’). g, Normalized and z-scored gene expression amounts of HOMEOSTATIC, DAM, LDAM and MACRO (macrophage) marker genes across the 11 subclusters identified in the microglia. HOMEOSTATIC, DAM and LDAM signature scores are shown across the 11 identified subclusters at the bottom. h, UMAP representation of microglia cells indicating the marker gene-based cell state annotation (bottom right) and the signature scores per cell for HOMEOSTATIC (top left), DAM (top right) and LDAM (bottom left) states. Contour lines indicate kernel density estimates of the signatures across the UMAP space. i, Bar plots indicating the percentage of cells from the three different cellular states (HOMEOSTATIC, DAM and LDAM) across microglia from control, AD-APOE3/3 and AD-APOE4/4 groups. Chi-square test results indicate the significance of the percentage differences between the groups (***P < 0.0001). j, Representative immunofluorescence images of human frontal cortex adjacent to the tissue used in snRNA-seq experiments stained for microglia marker IBA1 (green), ACSL1 (red) and DAPI (blue) in an aged-matched healthy control subject (left), an AD-APOE3/3 subject (middle) and an AD-APOE4/4 subject. Scale bars, 20 μm. k, Quantification of percentage of IBA1⁺ microglia positive for ACSL1. n = 5 per group; each dot represents individual subject; one-way analysis of variance (ANOVA); mean ± s.e.m. Schematics in a created with BioRender.com.