Extended Data Fig. 9: Prolonged ATF6α activation in hepatocytes is associated with an immunosuppressive liver microenvironment in mice, Related to Fig. 5.
From: Activated ATF6α is a hepatic tumour driver restricting immunosurveillance
(a) Gene signatures predicting poor survival and Immune-mediated Cancer Field (ICF) signature analysed in livers of 3-month-old TGAlb-cre− (n = 5) and TGAlb-cre+ (n = 7) mice, as shown in Fig. 5a. (b) Heatmap of immune features and signatures related to immune checkpoint blockade (ICB) response in HCC patients (n = 17119) divided into two groups by high and low enrichment of the mouse-derived ATF6α-activation signature established from RNA-seq data of DEN/HFD-treated TGAAV-cre and TGAAV-gfp mice (see Methods). (c) Representative immunoblot analysis and quantification of PD-L1 expression from livers of 6-month-old TGAlb-cre− (n = 4) and TGAlb-cre+ (n = 9) mice. GAPDH as loading control, ran on PD-L1 blot. kDa: kilodalton. (d-e) Representative IHC (d; scale bar = 100 µm) with quantification (e) from livers of 6-month-old TGAlb-cre− (n = 6) and TGAlb-cre+ (n = 7) mice. (f) Liver CD45+ lymphocytes count (per gram of liver) in 6-month-old TGAlb-cre− (n = 6) and TGAlb-cre+ (n = 7) mice by FACS. (g-h) The proportion of CD4+ T-cells (g) and macrophages, monocytes, monocytic- or polymorphonuclear myeloid-derived suppressor cells (M/PMN-MDSC, h) in livers of TGAlb-cre− (n = 6) and TGAlb-cre+ (n = 7) mice. (i) Quantification of immunofluorescence staining in Fig. 5d of livers from TGAlb-cre− (n = 3) and TGAlb-cre+ (n = 4) mice. (j-k) scRNA-seq UMAP representations of immune cell populations from FACS-sorted CD45+ cells (j) and respective cell-type distribution (k) from livers of 6-month-old TGAlb-cre− and TGAlb-cre+ mice (n = 4/group). (l) scRNA-seq cell-type distribution of subclustered CD8+ T-cells (Fig. 5e) from livers of 6-month-old TGAlb-cre− and TGAlb-cre+ mice (n = 4/group). Scatter dot plot data are presented as mean values ± SEM. Data in 9a were analysed using the nonparametric Wilcoxon and Kruskal-Wallis tests. Data in 9b with continuous variables were analysed by two-tailed Student’s t-test, and categorical variables were analysed by Fisher’s exact test. Data in 9c,e-i were analysed by two-tailed unpaired t-test or Mann-Whitney test based on data normality distribution.
