Fig. 3: Distinct T cell activation and TCR diversity in SLE.

a A UMAP visualization for cell composition by αβT cell subtypes: CD4⁺ naive (CD4 naive), central memory (CD4 Tcm), effector memory (CD4 Tem), regulatory (CD4 Treg), cytotoxic (CD4 CTL), cycling (CD4 cycling), CD8⁺ naive (CD8 naive), GZMK⁺ memory (CD8 GZMK), effector memory (CD8 Tem) and cycling (CD8 cycling) T cells. b The scaled average expression of marker genes across ten αβT cell subtypes, with dot size indicating the expressing cell proportion and the color gradient showing expression levels. c The proportion of αβT cell subtypes by disease state. The lines on the bar indicate the IQR, spanning from Q1 to Q3. Statistically significant increases are marked with orange stars for SLE and green for CTL. d Box plots comparing TCR signaling and T cell cytotoxicity in CD8 Tem cells across controls (CTL) and patients with SLE in three studies. The box represents the IQR, spanning from Q1 to Q3, with the line inside the box indicating the median. The whiskers extend to the smallest and largest values within 1.5 times the IQR. e A UMAP visualization delineates TCR clonotype distribution across αβT cells. Cells are colored based on clonotype expansion status. f Box plots showing TCR diversity (Shannon index) in CD8 T cell subtypes across controls and patients with SLE in two studies: Ota et al.¹⁷ (left) and our study (right). The box represents the IQR, spanning from Q1 to Q3, with the line inside the box indicating the median. The whiskers extend to the smallest and largest values within 1.5 times the IQR. g Heat maps of MHC-I and Galectin signaling strength from myeloid cells to CD8 T cell subtypes. The color gradient represents the relative strength of signaling. h Ligand–receptor communication probability of MHC-I (cM to CD8 T) (left) and Galectin signaling (pDC to CD8 T) (right). The color gradient represents communication probability and the empty dots indicate nonsignificant interactions. **P < 0.01, ***P < 0.001 and ****P < 0.0001.