Fig. 4: CODEX analysis of liver tissue.

a–d, Images of liver tissue from patient CVR35 (b,d) and a liver sample from an unaffected individual (control; a,c) show differences in cellular composition (c,d). a, Regularly structured bile ducts in the liver biopsy from the control are highlighted by asterisks, and epithelial cells are stained green using cytokeratin (CK). Scattered macrophages (CD68, red), T cells (CD3, cyan) and activated T cells (CD44, yellow) are also present. b, By contrast, the explant liver from patient CVR35 shows prominent proliferation of epithelial cells throughout the liver tissue (green), with increased macrophages (red), T cells (cyan) and activated T cells (yellow). c, The control liver shows scattered cytotoxic T cells (CD8, red), CD107a-positive cells (brown) and CD4-positive cells (yellow) cells and low expression of the interferon-induced GTP-binding protein MX1 (green). d, High numbers of all cell types and high MX1 expression are observed in the explant liver from patient CVR35. One section of liver was stained per individual, and the entire area was manually outlined. Cells were segmented to identify the nuclei and cytoplasm, and the algorithm was tuned to detect the colour signal in the cells. All samples were analysed using the same algorithm for each stain. Scale bars, 50 μm.