Extended Data Fig. 10: scRNA-seq and functional analyses of mouse models.
From: Liver tumour immune microenvironment subtypes and neutrophil heterogeneity
a, Schematic of liver cancer mouse models. Intrahepatic delivery of the transposable vectors pTMC (encoding Myc and ∆90Ctnnb1) or pTMK (encoding Myc and KrasG12D) via HDTV in Alb-Cre × Trp53fl/fl mice. b, Representative photos, H&E, and IHC staining of HCC and ICC mouse models. Rulers in the photo show a minimum unit of mm. Scale bar on the staining slides is 20 μm. c, Survival curve of liver cancer mouse model. Log-rank test. d, UMAP plot showing major cell types of mice with liver cancer. Dots represent individual cells, and colours represent the major cell populations. mILC: innate lymphoid cells, mNeu: neutrophils, mMph: macrophages, mMono: monocytes, mEC: endothelial cells; mFb: fibroblasts, mEpithelial: hepatocytes, biliary cells and progenitors; the first letter m indicates mouse clusters. The two small UMAP plots show the distribution of mouse models (left) and tissue types (right). e, UMAP plot showing myeloid clusters including 5 DC, 2 monocyte and 7 macrophage clusters for liver cancer mouse models. f, Dot heatmap showing the row-scaled expression of typical marker genes for neutrophil clusters in mice. g, Stacked barplot showing the fraction of 12 mouse neutrophil subsets across PB, AL, and tumour. h, The trajectory path of mouse neutrophil clusters inferred by Monocle2. Each dot represents a single cell. Cell orders are inferred from the expression of the most variable genes. The trajectory direction is determined by biological prior. i, Heatmap showing Pearson’s correlations across neutrophil clusters in human and mouse. j, UMAP plots showing the integration of mouse and human neutrophil clusters. k, Sankey plot showing the similarities of the joint clusters, mouse tissue isolated neutrophil clusters, and human sample isolated neutrophil clusters. l, FACS analysis on neutrophil, macrophage, and CD8+ T cell populations in isotype and anti-Ly6G groups. The right barplot shows the decreased neutrophil number in anti-Ly6G group (n = 10). m, FACS analyses and coloured histogram showing reduced PD-L1 expression in TANs and reduced PD-1 and TIM3 expression in tumour-infiltrated CD8+ T cells of the anti-Ly6G group compared with isotype control. The left barplot shows the decreased PD-L1 expression of neutrophils in anti-Ly6G group (n = 8). n, IHC of CD68 in tumour regions of mice treated with isotype control or anti-Ly6G antibody (n = 6). o, FACS analysis showing the expression of surface and intracellular Ly6G in the isotype control and anti-Ly6G treatment groups. p, Bar plot showing the statistical analysis of FACS results (n = 3). In l-p, n denotes biologically independent samples, data are presented as mean values ± SEM, and two-sided Student’s t-test is used.
