Fig. 5: MERFISH reveals conserved zonation and expansion of hepatocyte populations in fibrotic livers that do not follow zonal distribution.

a UMAP of fibrotic tissue measured with MERFISH. Clusters are indicated by color. Portal Hep and Central Hep show similarities to hepatocytes identified as zone 1, 2, and 3 cells from healthy liver, and Fibrotic Hep 1 and Fibrotic Hep 2 contain hepatocyte clusters that emerge with fibrotic injury. The HSC cluster shows similarities to both HSC 1 and HSC 2 cells from healthy liver, and the Mac cluster has similarities to both Mac 1 and Mac 2 clusters from healthy liver. b Relative abundance of each cell type identified in each sample (left to right: healthy donors 1–3 followed by fibrotic donors 4–6). Cell types are colored as in a. Source data are provided as a Source Data file. c–e Spatial distribution of cell populations in the fibrotic liver (donor 4), highlight hepatocytes that are similar to those seen in healthy samples (c), hepatocyte populations that are identified only when including fibrotic liver samples (d), and key non-parenchymal cells (e). Scale bar: 1000 μm. f–h Dot plot quantifying expression of genes differentially expressed in clusters seen in healthy measurements (Healthy zone 1, 2, or 3) or in fibrotic samples (Portal Hep, Central Hep, Fibrotic Hep 1, or Fibrotic Hep 2) for hepatocytes (f), macrophages (g), and HSCs (h). Macs Healthy 1 and Healthy 2 refer to Mac 1 and Mac 2 cells in healthy liver, and HSCs Healthy 1 and Healthy 2 refer to HSC 1 and HSC 2 cells in healthy liver.