Fig. 4

T cell subtypes and their heterogeneity in livers from mice treated with or without OXA. (A) t-SNE visualization of 6 subclusters of the T lineage pooled from mice livers. Each cluster is color-coded according to the cell type. Treg, regulatory T cell; Pro-T, proliferating T cells; CD8 + EM_like T, CD8 + effector memory like T. (B) Bar plot displaying the changes in the percentage of various subclusters of T cells upon OXA administration. (C) Volcano plot showing DEGs of T lineage between unstimulated liver and OXA-treated liver. DEGs were detected by differential expression analysis (two-sided Student’s t-test). Each dot represents a single gene; genes with log2(fold change) (logFC) < -0.25 and logFC > 0.25 were selected and colored in blue and red, respectively. (D) Circle plot displaying enrichment analysis of DEGs in T cells, with top 10 enriched terms showed. (E) Violin plots showing the expression of genes linked to proliferation T cells upon OXA administration. Representative DEGs enriched in positive regulation of lymphocyte proliferation pathway in (D) are displayed. (F) Stacked bar chart showing the constitution of different cell cycle phases of T cells with and without OXA treatment based on the average expression of S and G2/M gene sets. (G) Box plot showing activation score in CD4 + T cells (left), activation score in CD8 + T cells (middle), and immune effector score in CD8 + T cells (right) from mice livers with and without OXA treatment. AddModuleScore function in Seurat R package was used to calculate the average expression with default settings. *P value < 0.05; ****P value < 0.0001