Extended Data Fig. 4: Annotating human liver MPs.
From: Resolving the fibrotic niche of human liver cirrhosis at single-cell level
a, Clustering and selected genes expressed in 10,737 MPs from healthy (n = 5) and cirrhotic (n = 5) human livers. b, Scaled gene expression of KC cluster markers across MP cells from healthy (n = 5) and cirrhotic (n = 5) livers. c, Representative immunofluorescence images (n ≥ 3) of TIMD4 (red), CD163 (white), MARCO (green) and DAPI (blue) in healthy and cirrhotic liver; arrows denote CD163+MARCO+TIMD4− cells. d, Immunohistochemistry (left) and cell counts (right) of TIMD4 expression in healthy (n = 12) and cirrhotic (n = 9) human liver. e, Immunohistochemistry (left) and cell counts (right) of MARCO expression in healthy (n = 8) and cirrhotic (n = 8) liver. f, Flow cytometry gating strategy for identifying KCs, TMs and SAMacs in healthy (n = 2) and cirrhotic (n = 3) liver. SAMacs are detected as TREM2+CD9+ cells within the TM and SAMac gate (see Fig. 2f). g, Representative immunofluorescence images (n ≥ 3) of TREM2 (red), MNDA (white), collagen 1 (green) and DAPI (blue) in cirrhotic liver. h, Representative images (n = 2) of TREM2 (smFISH; red), MNDA (immunofluorescence; green) and DAPI (blue) in cirrhotic liver. i, Representative immunofluorescence images (n ≥ 3) of CD9 (red), MNDA (white), collagen 1 (green) and DAPI (blue) in cirrhotic liver. j, Immunohistochemistry (top) and cell counts (bottom) of TREM2 expression in healthy (n = 10) and cirrhotic (n = 9) liver. k, Immunohistochemistry (top) and cell counts (bottom) of CD9 expression in healthy (n = 12) and cirrhotic (n = 10) liver. l, Top, exemplar tissue segmentation of cirrhotic liver section into fibrotic septae (orange) and parenchymal nodules (purple). Bottom, cell counts based on immunohistochemistry analysis of TREM2 (n = 9), CD9 (n = 11), TIMD4 (n = 9) and MARCO (n = 7) in parenchymal nodules and fibrotic septae. m, Top, clustering and annotation of 208 cycling MP cells from healthy (n = 5) and cirrhotic (n = 5) livers, with scaled gene expression of MP subpopulation markers across four clusters of cycling MP cells. Bottom, fractions of cycling MP subpopulations in healthy (n = 5) and cirrhotic (n = 5) livers. All scale bars, 50 μm. Data are mean ± s.e.m. P values determined by two-tailed Mann–Whitney (e, j, k), two-tailed Wilcoxon test (l) or Wald test (m).
