Fig. 1: Single-cell RNA-Seq reveals reactive capillary endothelial cells (rCap) in the lungs 6 h after cancer cell injection.

a B16-F10 melanoma cells or PBS (Ctrl) were intravenously (i.v.) injected into C57BL/6 mice, and endothelial (ECs) and B16-F10 cells were isolated from the lungs after 6 h or after 30 h and subjected for scRNA-Seq. n = 3 independent experiments at 6 h, n = 1 exp at 30 h. Cells from two or three mice were pooled per sample in experiments 1 and 2–3, respectively. b Representative image of a 150 μm thick lung section showing a CellTracker green labeled B16-F10 cell in the lung capillary stained for PECAM1 6 h post-injection. n = 3 mice injected with B16-F10, compared to 3 Ctrl mice. c Uniform Manifold Approximation and Projection (UMAP) of clustered scRNA-Seq data of the lung EC and melanoma subsets. d, e EC cluster markers in the integrated data containing controls and all time points. f Analysis of EC composition per cluster between Ctrl and 6 h post-injection of B16-F10 using scCODA (false discovery rate, FDR > 0.05*). n = 3 independent experiments. The median is indicated by a line, bounds of the box represent the first and third quartiles, and the whiskers the smallest and largest data points within 1.5 interquartile ranges from the bounds. g RNA velocity analysis at 6 h time point. h Fold change of the top 25 rCap cluster markers, ordered based on adjusted p value. i rCap marker expression in EC clusters in control lungs, and at 6 h and 30 h after B16-F10 injection. n = 3 independent experiments (6 h), n = 1 (30 h) (g-i). j RT-qPCR of rCap markers in ECs isolated from control lungs (n = 7 mice for all markers) and 6 h after B16-F10 i.v. injection (n = 10 for Pim3, Inhbb, Tmem252 and Scarb1 each, n = 6 for Bcl3, n = 7 for Osmr, n = 5 for Adamts9). Each dot represents the average from one mouse, values were normalized to Hprt. General capillary, gCap; high interferon EC, hIFN; aerocyte capillary, aCap; lymphatic EC, LEC. Wilcoxon rank-sum test (h, i) (two-sided in i), two-tailed unpaired t-test (j), p < 0.05*, <0.01**, <0.001***. Data are presented as mean values +/- SD. Scale bar, 10 μm (b). Illustration created in Biorender.com (a). Source data are provided as a Source Data file.