Extended Data Fig. 8: Non-immune populations in irMyocarditis heart tissue.

a, UMAP embedding of 65,409 non-immune cells isolated from the heart, segregated by endothelial cells (top) and non-endothelial cells (bottom), and coloured by the 18 defined cell subsets labeled on the right. b, Dot plot showing top marker genes for each non-immune subset. Dot size represents the percent of cells in the subset with non-zero expression of a given gene. Colour indicates scaled expression across subsets. c, Abundance analysis comparing intramyocardial frequencies of cell populations from pre-steroid irMyocarditis heart samples (n = 12, red) versus controls (n = 8, blue). Left: dots represent logistic regression odds-ratios. Error bars represent 95% confidence intervals. Unadjusted two-sided likelihood-ratio test P values for each subset are shown. Colour and bolded P value indicates FDR < 0.1 Right: box plots display the median (line) and IQR, with whiskers no more than 1.5x IQR. Each dot represents one patient. d, Feature plots using colour to indicate marker gene expression (logCPM) levels of the indicated genes projected onto the heart non-immune UMAP embedding. Cell numbers and percentages represent gene expression across all heart non-immune cells. e, Feature plots showing (top panel) the number of genes expressed by each cell and (bottom panel) percent mitochondrial UMIs on the UMAP of non-immune cells derived from heart scRNA-seq data. f, Embedding of cell density plot displaying the relative proportion of cells from irMyocarditis cases (n = 20,439) and controls (n = 44,970). g, Stacked bar chart depicting the relative contributions of cells in each non-immune cell subset (colour coded to the right) from each pre-corticosteroid irMyocarditis or unenriched control sample. h, Top: the number of DEGs for each cell subset when comparing irMyocarditis cases (up, red) to control (down, blue). Bottom: heatmap showing select DEGs for irMyocarditis versus control heart tissue grouped by biological themes. Colour scale indicates log2FC difference between irMyocarditis cases and controls. Black dots indicate FDR < 0.1 (Wald test). Abbreviations: AP, antigen presentation; CC, co-inhibition or co-stimulation; CS, cytokine signalling; ISG, interferon-stimulated genes; MA, motility and adhesion; TF, transcription factors. Related to Fig. 5.