Fig. 1: Overview of the single-cell transcriptome landscape of circulating immune cells in lupus patients.

A Schematic showing sample collections and sequencing strategy for the discovery cohort (n = 6 per group). B Uniform manifold approximation and projection (UMAP) visualization for the discovery cohort. Bar plot shows the composition of peripheral blood mononuclear cells across systemic lupus erythematosus (SLE), lupus nephritis (LN), and healthy control (HC) groups (n = 6 per group). C Box plots illustrate proportions of major cell types across SLE, LN, and HC groups in the discovery cohort. Box: interquartile range (IQR); line: median; whiskers: 1.5 × IQR range from the quartiles; dots: individual samples (n = 6 per group). Statistical significance of the differences between patients and HC was determined using the Mann–Whitney U test (*P < 0.05, ***P < 0.001; n = 6 per group). D Principal component analysis (PCA) biplot of cell type compositions in the discovery cohort (n = 6 per group). The first two principal components (variance explained indicated in parentheses) are shown. Samples are represented as dots colored by group, and arrows indicate the direction and influence of specific cell types on the component loadings. E Mutation frequency of four reported SLE-related SNPs detected in the discovery cohort (n = 6 per group). Each bar represents the frequency of mutated cells among those with reads covering the respective loci, and the bars are color-coded according to the cell types.