Fig. 6: Impact of NMP on monocytes/macrophages.

A UMAP-plots of 13,720 monocytes/macrophages, color-coded by time-point [pre (T0) and at the end of (T1) NMP], and of the relative CD68 gene expression level. B Gene expression levels of inflammatory markers (LYZ, FCN1, VCAN, HLA-DRA) and tolerogenic markers (CD163, MARCO, HMOX1, and VSIG4) in monocytes/macrophages pre (T0) and at the end of NMP (T1). Each dot represents the mean of a patient (n = 7). False-discovery rates (FDR) have been determined using pseudo-bulk analysis with DESeq2. The central line denotes the median. Boxes represent the interquartile range (IQR) of the data, whiskers extend to the most extreme data points within 1.5 times the IQR. C Gene expression levels of monocyte/macrophage-specific genes. D UMAP of monocytes/macrophages colored by subclusters (M0, M1, M2, M3). E Expression of selected marker genes in monocyte/macrophage subclusters. F Relative composition of monocyte/macrophage subclusters pre (T0) and at the end of (T1) NMP. G Differential signaling from monocytes/macrophages to other cell-types. Upper panel: Differentially expressed ligands of monocytes/macrophages in T0 vs. T1 (two-sided DESeq2 Wald-test on pseudo-bulk, p-values were adjusted to false-discovery rate (FDR)). Red colors indicate upregulation in T1 compared to T0. Lower panel: Respective receptors and the expression by cell type. Dot sizes and colors refer to the fraction of cells expressing the receptor and gene expression, respectively, averaged over all patients. Dots are only shown for receptors that are expressed in at least 10% of the respective cell types. Only upregulated ligands are shown. The list of downregulated interactions is available in the Source Data file.