Extended Data Fig. 6: Liver metastasis alters the liver immune microenvironment.

a UMAP plot of all hepatic immune cell clusters on all samples merged. b Table identifying immune cell clusters and listing key genes. c Frequency of all immune cell clusters in mice with a subcutaneous tumour (S.C.) and mice with subcutaneous and liver tumours (S.C. + liver). d Apoptosis gene set enrichment analysis of in activated T-cell clusters in mice with a subcutaneous tumour and mice with subcutaneous and liver tumours. Activated T cells were identified by expression of Cd44. Unpaired two-tailed Student’s t-test, min to max, S.C. n = 157 cells, S.C. + liver n = 38 cells. e UMAP plot of Lgal3 on all samples merged. f UMAP plot of residential and migratory macrophages on all samples merged. g Violin plot of residential and migratory macrophage gene signatures in mice with a subcutaneous tumour and mice with subcutaneous and liver tumours. Unpaired two-tailed Student’s t-test, min to max. h Violin plot of residential macrophage M2-like and M1-like gene set enrichment in mice with a subcutaneous tumour and mice with subcutaneous and liver tumours. Unpaired two-tailed Student’s t-test, NS, not significant, min to max. S.C. n = 543 cells, S.C. + liver n = 936 cells. i Violin plot of cross-presentation gene set enrichment in resident (n = 1479 cells) and mono-derived (n = 6698 cells) macrophages. Unpaired two-tailed Student’s t-test, min to max. j Violin plot of M2-like and M1-like signatures within monocyte-derived macrophage cell subsets in mice with a subcutaneous tumour and mice with subcutaneous and liver tumours. Unpaired two-tailed Student’s t-test, min to max. k Pseudotime analysis overlying time with monocyte-derived macrophage cell states. l Pseudotime analysis overlaying monocyte-derived macrophage clusters and states.