Single-cell RNA sequencing of peripheral blood mononuclear cells from acute Kawasaki disease patients

Figures

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  Fig. 1. Two-dimensional representation of cell types identified by scRNA-seq. The dimensional reduction is performed with the uniform manifold approximation and projection (UMAP). Each dot represents a cell, which is colored according to cell type. The cells are pooled across all patients and separated by conditions: a KD before intravenous immunoglobulin (IVIG) therapy; b KD after IVIG therapy; c healthy controls. Percentages of major cell types under each condition are shown on the plot, and percentages of subtypes are shown on Supplementary Fig. 3. mDC, myeloid dendritic cells; pDC, plasmacytoid dendritic cells; HSPC, hematopoietic stem and progenitor cells. Source data are provided in the Source Data file.

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  Fig. 2. Comparison of major cell types across conditions. a Percentage of each cell type in PBMCs revealed by scRNA-seq. The samples are colored according to donors. P-values are calculated between pre- and post-treatment KD patients (n = 7) and healthy controls (n = 3) by using the two-sided t-test. b Percentage of lymphocyte populations by flow cytometric validation on additional KD patients (n = 16) and healthy controls (n = 20). Patients with a decreased percentage after therapy are colored in red, and patients with an increased percentage after therapy are in blue. Healthy controls are colored in green. The gray areas represent the reference ranges of the panel. P-values between conditions are calculated by using the two-sided t-test. c Percentage of monocytes by routine blood test of samples collected for both scRNA-seq (KD patients n = 7) and flow cytometric analysis (KD patients n = 16, healthy controls n = 20). KD patients for scRNA-seq are highlighted with the same color as (a). P-values are calculated by using the two-sided t-test. In (a) and (c), data are represented as boxplots where the middle line is the median, the lower and upper hinges correspond to the first and third…

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  Fig. 3. Characterization of monocytes and transcriptional patterns. a Percentage of CD16+ monocytes across conditions recovered by scRNA-seq (KD patients n = 7, healthy controls n = 3). The middle line of the boxplot is the median, the lower and upper hinges correspond to the first and third quartiles, and the whiskers extend from the hinge to the farthest data point within a maximum of 1.5× interquartile range. The samples are colored according to donors. P-values are calculated by using the two-sided t-test. b Heat map of DEGs with functional enrichment in monocytes. Gene expression on the sample level is measured by the counts per million mapped reads (CPM), which is then scaled across samples. c Expression patterns of cytokines reported to be elevated in KD. The dot plot depicts average expression level and percentage of cells expressing the cytokine genes across PBMC populations. Cytokine genes with higher expression in pre-treatment patients than post-treatment patients or healthy controls (nominal P-value < 0.05 with DESeq231, two-sided) are marked with stars. d Expression level of IL1B and TNF in monocytes across conditions (KD patients n = 7, healthy controls n = 3). The bar…

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  Fig. 4. Characterization of B cells and BCRs. a Percentage of plasma cells across conditions recovered by scRNA-seq (KD patients n = 7, healthy controls n = 3). The samples are colored according to donors. P-values are calculated by using the two-sided t-test. b Percentage of plasma cells (CD19+ CD24−CD38++) by flow cytometric validation on additional KD patients (n = 16) and healthy controls (n = 20). Patients with a decreased percentage after therapy are colored in red, and patients with an increased percentage after therapy are in blue. Healthy controls are colored in green. The gray area represents the reference range of the panel. P-values between conditions are calculated by using the two-sided t-test. c Heat map of DEGs with functional enrichment in B cells. Gene expression on the sample level is measured by the counts per million mapped reads (CPM), which is then scaled across samples. d Percentage of IGHA and IGHG in BCRs across conditions recovered by scBCR-seq (KD patients n = 7, healthy controls n = 3). The samples are in the same colors as (a). P-values are calculated by using the two-sided t-test. In (a) and (d), data are represented as boxplots where the middle line is the…

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  Fig. 5. Characterization of T cells and TCRs. a Percentage of naive and effector memory CD8+ T cells across conditions recovered by scRNA-seq (KD patients n = 7, healthy controls n = 3). The middle line of the boxplot is the median, the lower and upper hinges correspond to the first and third quartiles, and the whiskers extend from the hinge to the farthest data point within a maximum of 1.5× interquartile range. The samples are colored according to donors. P-values are calculated by using the two-sided t-test. b Percentage of naive (CD3+ CD8+ CD27+ CD45RA+) and effector memory (CD3+ CD8+ CD27−) CD8+ T cells by flow cytometric validation on additional KD patients (n = 16) and healthy controls (n = 20). Patients with a decreased percentage after therapy are colored in red, and patients with an increased percentage after therapy are in blue. Healthy controls are colored in green. The gray areas represent the reference ranges of the panel. P-values between conditions are calculated by using the two-sided t-test. The percentage of effector memory CD8+ T cells is plotted and tested on the log scale. c Heat map of DEGs with functional enrichment shared in CD4+ and CD8+ T cells. Gene expression…