Extended Data Fig. 5: Phenotypic characterization of mononuclear phagocytes in healthy and cirrhotic human livers.
From: Resolving the fibrotic niche of human liver cirrhosis at single-cell level
a, Top, self-organizing map (60 × 60 grid) of smoothed scaled metagene expression of 10,737 MPs from healthy (n = 5) and cirrhotic (n = 5) livers. In total, 20,952 genes, 3,600 metagenes and 44 signatures were identified. A–F denote metagene signatures overexpressed in one or more MP subpopulations. Bottom, smoothed mean metagene expression profile for each MP subpopulation. b, Radar plots (left), exemplar genes (middle) and selected GO enrichment (right) of metagene signatures A–F showing distribution of signature expression across MP subpopulations from 10,737 MP cells. c, Diffusion map (DM) visualization of blood monocytes and liver-resident MP lineages (23,075 cells from healthy (n = 5) and cirrhotic (n = 5) liver samples and PBMCs (n = 5)), annotating monocle pseudotemporal dynamics (purple to yellow). Top, RNA velocity field (red arrows) visualized using Gaussian smoothing on regular grid. Bottom, annotation of MPs by subpopulation and injury condition. d, Unspliced–spliced phase portraits (top); 23,075 cells coloured and visualized as in Fig. 3a; monocyte (MNDA), SAMac (CD9) and KC (TIMD4) marker genes. Cells plotted above or below the steady-state (black dashed line) indicate increasing or decreasing expression of gene, respectively. Spliced expression profile for stated genes (middle row; red, high, blue, low). Unspliced residuals for stated genes (bottom row), positive (red) indicating expected upregulation, negative (blue) indicating expected downregulation. MNDA displays negative velocity in SAMacs; CD9 displays positive velocity in monocytes and SAMacs; TIMD4 velocity is restricted to KCs. e, Cubic smoothing spline curve fitted to averaged expression of all genes in module 2 from the blood monocyte-to-SAMac pseudotemporal trajectory (see Fig. 3c), with selected GO enrichment (right). f, Cubic smoothing spline curve fitted to averaged expression of all genes in module 3 from the blood monocyte-to-cDC pseudotemporal trajectory (see Fig. 3c), with selected GO enrichment (right). g, Luminex assay showing quantification of levels of stated proteins in culture medium from FACS-isolated SAMacs (n = 3), TMs (n = 2) and KCs (n = 2). Control denotes medium alone (n = 2). Data are mean ± s.e.m. h, Heat map of transcription factor regulons across MP pseudotemporal trajectory and in KCs (colour-coded by MP cluster, condition and pseudotime), with selected regulons labelled (right). Columns denote cells; rows denote genes. i, Scaled regulon expression of selected regulons across MP clusters from healthy (n = 5) and cirrhotic (n = 5) livers. All P values determined by Fisher’s exact test.
