Fig. 4: scRNA-seq of BM immune cells from PNH patients and healthy donors.

A A Uniform Manifold Approximation and Projection (UMAP) plot of 190,032 BM immune cells from all subjects. Leiden clusters based on 3’ gene expression are shown, colored by major cell types. B Differential abundance analysis of BM immune cells using Milo. The neighborhood graph (left) shows neighborhoods (Nhoods) within BM immune cells, with node colors indicating log2FC between GPI(+) and GPI(−) cell populations in PNH. Significant changes are colored in blue and red. Nondifferential abundance Nhoods (false discovery rate [FDR] ≥ 0.10) are shown in white. A Beeswarm and box plot (right) shows the distribution of log2FC differences in different cell type clusters as in Fig. 2B. C Percentages of GPI(−) cell populations relative to the total number of cells in each immune cell type derived from PNH patients (n = 6). P-values were calculated using the Wilcoxon matched-pairs signed rank test. D A dot plot showing gene set enrichment scores across BM immune cell subtypes in PNH patients by GSEA. A color scale indicates mean normalized enrichment score (NES) differences between PNH patients and healthy donors, and dot sizes indicate FDR values. Non-significant pathways (FDR ≥ 0.20) are shown in grey. E A dot plot showing gene set enrichment scores across BM immune cell subtypes comparing patients with large and small PNH cell fractions by GSEA. The color scale indicates mean NES differences between the two groups, and dot sizes indicate FDR values. Non-significant pathways (FDR ≥ 0.20) are shown in grey. DCs dendritic cells, Mono monocytes, Neut neutrophils, NK natural killer cells, Plasma plasma cells.