Diminished IFN signature in splenic immune cells. (A) UMAP embedding of scRNA-seq data colored by cell type. (B) Gene ontology (GO) enrichment analysis of genes differentially expressed across all cell types. Only 15 statistically most significant GO terms are shown. (C) Volcano plots showing changes in expression of tonic-sensitive (red) and tonic-insensitive (blue) ISGs in B cells and macrophages. Fisher’s exact test was performed to quantity enrichment of tonic-sensitive genes among downregulated (LFC > 1, FDR < 0.05) genes. (D) Scatterplots comparing relative gene expression of tonic-sensitive (red) and tonic-insensitive (blue) ISGs in B cells (left) and macrophages (right) of Aire-deficient and Ifnar1-deficient mice. Spearman correlation coefficient R and associated P value are shown in both figures. (E) Heatmap showing relative expression of ISGs in CD4⁺ T cell subpopulations: follicular regulatory (TfR), regulatory (Treg), follicular helper (TfH), and conventional (Tconv) of Aire-deficient rats as compared with control rats. The bar on the right indicates tonic sensitivity of an ISG (SPL, spleen; LN; lymph node). (F) GO enrichment analysis of differentially expressed genes CD4⁺ T cell subpopulations in Aire-deficient rats. Data in A and B are obtained from a single experiment with three Aire-deficient (KO) and three control (HE) rats per group. Data in E and F are obtained from a single experiment with 4 Aire-deficient (KO) and 4 control (HE) rats per group. LFC, log fold change.