scRNA-seq suggests that dysregulation of TLR signaling pathways begins in CD34⁺/CD16⁺GMPs. (A) Left panel shows UMAP of 11 956 LK cells (Lin⁻, c-Kit⁺) from Giladi et al,²³  with refined cell type labeling. Right panel shows projection of 14 795 LKS⁻ cells from this study onto the same UMAP, with cell type labels transferred from Giladi et al²³  by k-nearest-neighbor algorithm (see supplemental Methods). The control sample includes LKS⁻ cells of pooled BM from 1 Runx1^f/f and 1 Runx1^f/− mouse (ie, with a monoallelic germline Runx1 mutation). (B) Same UMAP from panel A, colored by genotype. (C) Top upregulated pathways in Runx1 KO neutrophil HPs compared with control cells. Color indicates pathway activity score computed using the AUCell package.⁴⁶  Cells were down-sampled so that Runx1 KO and control have equal cell numbers across stages. (D) Significance level computed by 2-tailed unpaired Student t test of pathways shown in panel C. (E) Activity score of “Toll Like Receptor 4 Cascade” between Runx1 KO and control cells across stages. Two-tailed unpaired Student t tests were performed between genotypes for each stage. **q value ≤ 0.01; ***q value ≤ 0.001; ****q value ≤ 0.0001. AD, Alzheimer disease.