Fig 2: A proteogenomic atlas of the healthy murine liver(A) Hepatic cells were isolated from healthy C57B/l6 mice by ex vivo (5 mice, 15 samples) or in vivo (5 mice, 19 samples) enzymatic digestion. Alternatively, nuclei were isolated by tissue homogenization (4 mice, 12 samples). Live cells/intact nuclei were FACS-purified. For cells, total live, live CD45+, live CD45-, live hepatocytes, or myeloid cells (live CD45+, CD3-, CD19-, B220-, NK1.1-) were sorted. 18 samples (7 ex vivo, 11 in vivo) were also stained with a panel of 107–161 barcode-labeled antibodies for CITE-seq analysis. All datasets were pooled together and after QC 185,894 cells/nuclei were clustered using TotalVI.(B) UMAP of sc/snRNA-seq data.(C) Tissue and capsule images from Visium analysis with clusters overlaid.(D) UMAP of zonation of Visium spots (left) and origin of the cells (right).(E) Zonation pattern mapped onto tissue slice.(F and G) Indicated cell signatures from sc/snRNA-seq mapped onto the Visium zonation data.(H) mRNA zonation pattern in Visium highly multiplexed protein analysis and VSIG4-ADT expression pattern (left) and zonated expression patterns of indicated antibodies (right).(I) MICS analysis of indicated proteins.(J) Molecular Cartography of indicated genes and cell types.(K) mRNA (Xcr1, Flt3l, Mafb, and Clec10a) and protein (MHCII and F4/80) expression in the same tissue slice. Scale bars, 50 µm. PV, portal vein; CV, central vein. Arrows indicate specific cell types, colors correspond to cell type/markers. Images are representative of 2–4 mice. See also Figure S2 and Tables S1, S2, S3, and S5.

Fig 3: Combination of CITE-seq, scRNA-seq, snRNA-seq, and spatial analyses enables generation of a human liver atlas, related to Figure 4(A) Murine lymphoid cells (B cells, T cells, NK cells, ILC1s, pDCs; 27,398 cells) were isolated from Figure 1B and re-clustered with TotalVI.(B and C) Top DEGs (B) and DEPs (C) for the cell types from Figure S5A.(D) CITE-seq data from Figure S5A were exported as an FCS file and an in silico gating strategy identified in FlowJo.(E) Human lymphoid cells (B cells, T cells, NK cells, ILC1s, pDCs; 105,790 cells) were isolated from Figure 4B and re-clustered with TotalVI.(F and G) Top DEGs (F) and DEPs (G) for the cell types from Figure S5E.(H) CITE-seq data from Figure S5E were exported as an FCS file and an in silico gating strategy identified in FlowJo.(I) Proportion of indicated cell types arising from patients with <10% (purple) or >10% steatosis (yellow).(J) Hepatic cells were isolated from 22 C57B/l6 mice fed either a standard diet (SD) or a western diet (WD) for 24 or 36 weeks to induce NAFLD and NASH by ex vivo (10 samples) or in vivo (12 samples) enzymatic digestion. Alternatively, livers were snap frozen and nuclei isolated by tissue homogenization (14 samples). Live cells/intact nuclei were purified using FACS. For cells, total live, live CD45+, live CD45-, live hepatocytes or myeloid cells (live CD45+, CD3-, CD19-, B220-, NK1.1-) were sorted. 10 samples were also stained with a panel of 107–161 barcode-labeled antibodies for CITE-seq analysis. All datasets were pooled together and after QC 121,980 cells/nuclei were clustered using TotalVI.(K) Murine lymphoid cells (B cells, T cells, NK cells, ILC1s, pDCs; 21,322 cells) from mice fed the SD or WD for 24 or 36 weeks were isolated from Figure S5J and re-clustered with TotalVI.(L) Proportion of indicated cell types arising from mice fed the SD (purple) or WD (yellow).(M) Top DEGs between CTLs isolated from mice fed the SD (purple) or WD (yellow).