Fig. 1: Comprehensive single-cell analysis reveals distinct immune profiles in patients with systemic sclerosis and healthy donors.

a Overview of the experimental workflow. Created in BioRender. Shimagami, H. (2025) https://BioRender.com/jhwa38f. SSc systemic sclerosis, HD healthy donor, PBMC peripheral blood mononuclear cells, scRNA-seq single-cell RNA sequencing, SRC scleroderma renal crisis, ILD interstitial lung disease. b UMAP plots displaying CITE-seq data of PBMCs from SSc patients (SSc; n = 21) and HDs (HD; n = 6), annotated with reference mapping. Each plot shows 30,000 randomly selected cells. Mono monocytes, cDC conventional dendritic cells, ASDC AXL⁺ dendric cells, pDC plasmacytoid dendritic cells, TCM central memory T cells, TEM effector memory T cells, CTL cytotoxic T lymphocytes, Treg regulatory T cells, MAIT mucosal associated invariant T cells, dnT double negative T cells, gdT gamma-delta T cells, PB plasmablasts, NK natural killer cells, ILC innate lymphoid cells, Proliferating proliferating cells, HSPC hematopoietic stem and progenitor cells. Percentages of myeloid (c) and lymphoid (d) cell populations relative to the total PBMCs in SSc patients (n = 21, purple) and HDs (n = 6, black). Values represent means with standard error of the mean (SEM). Statistical analysis was conducted using the two-sided Kolmogorov–Smirnov test with Bonferroni correction for multiple comparisons. e Principal component analysis on the proportion of each cell subset to the total PBMCs. Each subset was defined based on CITE-seq data (Supplementary Figs. 3–8). Vectors represent Principal Component (PC) 1 and PC2 for each cell subset. Red, myeloid cell subset; orange, lymphoid cell subset; gray, HSPC. Vectors with lengths greater than 0.3 are displayed. f Distribution of values of PC1 and PC2 for each study participant. In the left panel, dots represent individuals, with SSc patients shown in purple and HDs in black. In the right panel, each SSc patient is indicated by a colored dot: red for SRC patients, orange for ILD patients without SRC (ILD w/o SRC), and blue for patients without both SRC and ILD (No SRC, No ILD); HDs are represented by black dots. Arrows show the mean vectors for each group, colored to match the dots of corresponding group. Source data are provided as a Source Data file.