Fig. 4: Vascular cells exhibit pro-angiogenic, inflammation and immune cell recruitment signatures across disease groups.
a, UMAP embedding delineated nine CM states. b, Upper panel, mean CM state abundances (%) in controls (n = 18). Lower panel, proportional changes of CM states in Non-COVID-19 (n = 8), Post-COVID-19 (n = 10) and Post-Vaccination (n = 4) versus control. Color scale: red (increase) and blue (decrease). Significant P values (FDR ≤ 0.05) are shown. P values were calculated with the two-sided t-test based on CLR-transformed values with Benjamini–Hochberg correction. MIS-C significance was not calculated due to low sample size (n = 2). c, Upper panel, box plots showing HIF1A snRNA-seq pseudo-bulk expression levels in CMs. Boxes depict the interquartile range (IQR); horizontal bars indicte the median; whiskers extend to 1.5× IQR; and dots show the value of each patient. Significant P values (FDR ≤ 0.05) are shown. Lower panel, dot plots showing differential expression of HIF1A in patient groups relative to control across CM states. Dot colors indicate log2-transformed FCs (log2FCs). Dot sizes indicate absolute log2FC. Black circles indicate significance (FDR ≤ 0.05). Upper and lower panel, control: n = 18, Non-COVID-19: n = 8, Post-COVID-19: n = 10, Post-Vaccination: n = 4. P values were calculated using the quasi-likelihood F-test with Benjamini–Hochberg correction. d, VEGFA expression in CMs, shown as described in c. e, UMAP embedding delineated 11 vascular cell states. f, Vascular cell state abundances shown as described in b. g, NFKBIA, JAM2 and JAM3 expression in ECs, shown as described in c. h, Dot plots showing differential expression of IFNγ response genes in patient groups relative to control across vascular cell states. Dot plots, n numbers and P value calculations are as described in c. i, Circle plots showing significant cell–cell communication differences for the indicated pathways (P ≤ 0.05) between patient groups and controls. P values were computed from the one-sided permutation test with Bonferoni correction. Line thickness reflects interaction strength of sending and receiving cells; color indicates changes (orange: increased; blue: decreased); and arrows show signal directionality. j, Dot plot showing FLT1 and KDR expression across EC states. Dot size corresponds to fraction (%) of expressing nuclei; color indicates scaled mean expression levels. k,l, ANGPT1 and ANGPT2 (k) and EFNB2 (l) expression in cell types as described in c. AD, adipocyte; NC, neural cell.
