Fig. 5: Characteristics of liver resident Th1-like cells in PBC patients.

a UMAP showing the expression of SELL, KLF2, CD69, CXCR6, ZNF683, and RBPJ in T cells. b UMAP showing the distribution of liver and PBMC T cells. c UMAP showing the distribution of Th1-like and CD8⁺ Trm cells from liver. d Gating strategy showing CD69^-, CD69^INT and CD69^HI populations. Representative flow cytometry plot for CD4⁺ T cell distribution in control liver, PBC liver and summary data showing % CD4⁺ T cells in control and PBC liver (control n = 3, PBC n = 4). Data are presented as means ± s.d. Significance was determined by two-tailed Student’s t-test, *P < 0.05, **P < 0.01. Source data are provided as a Source Data file including exact P values. e Representative flow cytometry plot for CD4⁺ T cell distribution in Liver, PBMC from same PBC patient. f MFI of CXCR6 expressions in the three populations in control and PBC liver (control n = 3, PBC n = 4). The results are presented as the mean with SD, and P values were calculated using one-way ANOVA **P < 0.01, ****P < 0.0001. g Representative immunofluorescent images (n = 5) of DAPI (blue), CD4 (red), CD69 (green), and IFNγ (purple) in the liver of PBC patients. Source data are provided as a Source Data file including exact P values. h Representative immunofluorescent images (n = 5) of DAPI (blue), CD4 (red), CD69 (green), and CXCR6 (purple) in the liver of PBC patients. i Scatter plot with linear regression line showing the correlation between the percentage of CD4⁺CD69⁺ cells in the liver of PBC patients and pathological features (ALP, DBIL, TBIL, Fibrosis level). ALP, alkaline phosphatase. DBIL, direct bilirubin. TBIL, total bilirubin. Grey area represented 95% confidence intervals. n = 32. The line indicates the linear regression fit with the 95% confidence interval as error band. The Pearson correlation analysis was used to assess if there is a significant correlation. j Scatter plot showing the top cell type specific regulons in Th1-like cells. k UMAP showing binarized AUC score of TCF7(+), TBX21(+), RUNX3(+), RUNX1(+), PPARG(+), MAFG(+), STAT1(+), STAT3(+). Black and grey indicate that the activity of a regulon is ‘ON’ and ‘OFF’, respectively. l UMAP showing binarized AUC score of RUNX1(+) and STAT1(+) in control and PBC groups.