Fig. 4: Impact of NMP on neutrophils.

A Gene expression levels of neutrophil-specific genes in individual cell types. B CXCR2 gene expression levels in individual cell types. Each dot represents the mean of a patient (n = 8). C UMAP plots of 41,177 neutrophils, color-coded by timepoint and the CXCR2, CXCR1, and CXCR4 gene expression levels. D CXCR2, CXCR1, and CXCR4 gene expression levels in neutrophils pre (T0) and at the end of (T1) NMP. Each dot represents the mean of a patient (n = 7). False-discovery rates (FDR) have been determined using pseudo-bulk analysis with DESeq2. E Immunofluorescent staining of CXCR2 and CD15 pre (T0) NMP. Images are displayed at ×20 magnification (scale bar: 100 µm, n = 10, for each sample 4 representative images were taken). F Cell density (number of cells/mm2) of CXCR2⁺ cells pre (T0) and at the end of (T1) NMP. The upper graph presents the values for each individual liver, the lower graph is a column statistical analysis (n = 10, paired t-test, two-tailed, mean ± SEM, *p = 0.02). G CXCL8 gene expression level in neutrophils pre (T0) and at the end of (T1) NMP. Each dot represents the mean of a patient (n = 7). False-discovery rates (FDR) have been determined using pseudo-bulk analysis with DESeq2. H UMAP plot of 90,404 single cells (only T0 and T1 samples), colored by CXCL8 gene expression. The monocyts/macrophage (1) and neutrophil (2) clusters are highlighted. I Differential signaling from neutrophils to other cell types. Upper panel: Differentially expressed ligands of neutrophils 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. In all boxplots, 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.