Fig 2: Combination of CITE-seq, scRNA-seq, snRNA-seq, and spatial analyses enables generation of a human liver atlas and identification of bona fide human KCs, related to Figure 4(A and B) Top DEGs (A) and DEPs (B) for the cell types from Figure 4B.(C) Distinct profiles of cells or nuclei within the UMAP depending on isolation protocol used; 152,535 cells from ex vivo digestions and 15,063 nuclei.(D) Proportion of each cell type per patient profiled.(E) Proportion of indicated cell types as a % of total CD45+ cells calculated from ex vivo digested samples per surgery type. Ch; cholecystectomy, Re; resection, GB; gastric bypass. ∗p < 0.05; one-way ANOVA with Bonferroni post-test.(F) Mapping of Visium UMAP zonation patterns onto tissue sections from patient H35 and H37.(G) Expression of indicated zonation genes in patients H35–H38 assessed by Molecular Cartography.(H and I) Expression of indicated proteins by MICS 100-plex protein analysis in the healthy (H) and steatotic (I) human liver.(J) Murine myeloid cells (cDC1s, cDC2s, Mig. cDCs, Macs, monocytes, and monocyte-derived cells; 42,922 cells) from mice fed the SD or WD for 24 or 36 weeks were isolated from Figure S5J and re-clustered with TotalVI.(K) Distribution of cells in UMAP originating from SD- (purple) or WD- (yellow) fed mice.(L) Proportion of indicated cell types arising from mice fed the SD (purple) or WD (yellow).(M and N) Flow cytometry analysis of indicated cell populations in SD and WD-fed mice (24 weeks). Representative gating strategies (M) and absolute number of indicated populations (N). ∗p < 0.05, ∗∗p < 0.01 Student’s t test. Data are from 2 independent experiments with n = 5–6 per diet.(O and P) Top DEGs (O) and DEPs (P) for cell types from Figure 4H.(Q) Top 25 Murine KC genes as expressed by the human myeloid cell clusters.(R) Mapping of KC signature onto Visium trajectory for healthy (purple) and steatotic (orange) livers.(S) Expression of VSIG4 mRNA within human myeloid cells.(T) Expression of VSIG4 (red) and CD163 (gray, top) or CD169 (gray, bottom) by MICS analysis in healthy human liver.(U) Representative images showing KC location (red) as assessed by MICS analysis in the healthy (left) and steatotic (right) human liver. PV, portal vein; CV, central Vein, dashed line indicates zones of steatosis.(V) Representative image of CD68 and CD163 staining in 10–15-year-old human liver paraffin sections. Image is representative of 6 different patients.(W) In silico gating strategy to isolate distinct myeloid cell populations identified from CITE-seq data.(X) Expression of VSIG4 and FOLR2 by live CD45+ cells also expressing CD14 in indicated human liver biopsies by flow cytometry. Data are representative of 21 biopsy samples analyzed.