Fig. 3

Comprehensive single-cell transcriptomic analysis reveals myeloid cell heterogeneity and functional dynamics in PAH. A UMAP plot showing the clustering and annotation of myeloid cell subsets, including Monocyte, APOE⁺ Macro, MARCO⁺ Macro, LSAMP⁺ Macro, DC1, DC2, and Mast cells. Each subset represents a functionally distinct population of myeloid cells in PAH and healthy controls. B and C Balloon and bar plots displaying the proportions and counts of myeloid cell subsets in PAH (Case) and healthy controls (Con). APOE⁺ Macro and MARCO⁺ Macro are significantly enriched in PAH, while Monocyte and DC1 proportions decrease, reflecting shifts in myeloid cell composition during disease progression. D Pseudotime trajectories revealing the dynamic differentiation of Monocyte into APOE⁺ Macro, MARCO⁺ Macro, and DC subsets. Bubble plots show the temporal expression patterns of key genes (e.g., APOE, TREM2, and GPNMB), indicating functional evolution during disease progression. E Line plots showing the temporal expression trends of GPNMB in specific subsets (APOE⁺ Macro) between PAH and control groups. Both genes show increased expression along pseudotime in PAH, reflecting their involvement in immune activation and tissue remodeling. F UMAP analysis illustrated the expression levels of GPNMB across myeloid cells in PAH and control group. G Heatmap of differentially expressed genes across myeloid cell subsets, with functional pathway enrichment annotations. APOE⁺ Macro and MARCO⁺ Macro are enriched in lipid metabolism and immune regulation pathways, while DC1 and DC2 are enriched in antiviral response and anti-inflammatory pathways, indicating subset-specific functions in PAH. H Heatmap of transcription factor (TF) activity (AUC scores) in myeloid cell subsets, highlighting key TFs such as SPI1, IRF8, and HIF1A. SPI1 drives inflammation in Monocyte and macrophage subsets, IRF8 regulates antiviral responses in DC subsets, and HIF1A mediates metabolic adaptation in APOE⁺ Macro and MARCO⁺ Macro