Transcriptome dynamics of HSPCs and T cells and their crosstalk after immunosuppressive therapy. (A) Diagram of tracking patients with non-SAA (n = 5) responsive to immunosuppressive treatment. Characteristics of each patient are shown on the left table; days of follow-up relative to diagnosis and the time points for sample collection are shown on the right accordingly. (B) UMAP display of HSPCs based on single-cell transcriptomes. Each dot represents a single cell; colors indicate cell clusters (left) and source of donors (right) (untreated, n = 12; treated, n = 5). (C) Bar plot showing the ratio of observed to expected cell numbers of each cell type in patients with both untreated and treated samples (n = 5). Dots indicate individual patients and dot sizes indicate logarithmic transformed P values (χ² test). Error bars represent ± standard error of the mean. Student t test was used for differential comparison between untreated and treated. (D) Volcano plot showing the DEGs of MD2 in treatment-naïve patients (n = 12) compared with control (Ctrl). Each dot represents a single gene; the black dots represent DEGs (fold change using default parameters in Seurat with Bonferroni adjusted P ≤ .05). Selected enriched GO terms of downregulated and upregulated genes in treatment-naïve patients are shown on the top. Genes with blue and red colors are related to response to steroid hormone and IFN-γ–mediated signaling pathway, respectively. (E) Bar plot displays the number of DEGs between different donor groups in HSPCs (untreated, n = 12; treated, n = 5). (F) Line chart showing the expression dynamics of 4 gene sets in Ctrl and different time points of patients with non-SAA illustrating milder hematopoietic improvement after treatment (left) (untreated, n = 12; treated, n = 5). The number in the middle means the number of genes sharing the same expression pattern in each cluster. Enriched GO terms in each cluster were shown on the right. (G) Molecular interaction states of 55 ligand-receptor pairs (rows) between HSPCs and T cells (columns) in non-SAA after immunosuppressive treatment (n = 5). Molecules in gray indicate that they were downregulated in T cells or HSPCs. Dot sizes and colors represent logarithmic transformed P values (permutation test) and mean expression of interacting molecules in corresponding cell subsets.