Extended Data Fig. 7: Immunosuppressive IL-17⁺IL-18R1⁺ neutrophils are enriched in APOE4 female MCI carriers.

a, UMAP of female neutrophils determined by multicolor flow cytometry analysis of MCI patients and neutrophil cluster distribution across APOE ε3/3 and ε3/4 genotypes (n = 4–8/group). b, Donut plots show the percentage of each cluster within each condition. c, Heatmap of normalized Mean Fluorescence Intensity (MFI) for each protein marker in annotated neutrophil clusters. d, UMAP of major identified subclusters of neutrophils from dataset by Schulte-Schrepping et al.²². e, GSEA pathway enrichment according to cluster marker genes (P < 0.05). Permutation-based test. f, Marker genes annotated per neutrophil cluster (Padj < 0.05). g, Circos plot demonstrating predicted top regulatory interactions between neutrophil ligands (this study) and microglia receptors³⁹ upregulated in female CI APOE ε3/4 patients. h, Confocal imaging of degranulating H3Cit⁺ neutrophils (green) coexpressing IL-17 (red) at sites of Ab plaques in the brains of female AD APOE ε3/4 patients, replicated in two independent cohorts. Scale bar, 20μm. i, Confocal images of RNAscope for IL17F (red) and CEACAM8 (CD66b; Cyan) and immunostaining for Aβ-plaques (green) in AD brain sections from 3 different female APOE ε3/4 carriers. Scale bar, 50μm. j, High magnification confocal images of RNAscope for IL17F (red) and CEACAM8 (Cyan) and DAPI (blue). Scale bar, 5μm. Staining was confirmed in three independent experiments. k, Experimental design depicting microglial repopulation in 5xFAD-hCSF1 pups with human APOE ε3/3 iMGs, and brain injection of human neutrophils at 3.5 months of age. Brains were analyzed the next day using immunohistochemistry. Figure created using Biorender.com. Confocal images of LGALS3+IBA+ iMGs in 5xFAD-hCSF1 brains following the injection with MCI female APOE ε3/4 and APOE ε3/3 neutrophils (l) and quantification of Lgals3 immunoreactivity (n = 6/group) (m). Two-tailed student’s t-test. Data were shown as mean ± s.e.m.