Fig. 3.

Identification of the tetramer⁺ TFH-like and TR1-like subclusters via mass cytometry and 10x Genomics scRNAseq. A tSNE plot for Tet⁻CXCR5⁻PD-1⁻ (Tconv), Tet⁻PD-1^hiCXCR5^hi (TFH) and BDC2.5 mi/IA^g7 Tet⁺ splenic CD4⁺ T cells stained with the 32-marker CyTOF panel listed in Supplementary Table 4. The data correspond to n = 4 samples each from 2 experiments. B t-SNE plot of 10x Genomics-based scRNAseq data for sorted Tet⁺ and Tet^– cells from NOD mice treated with BDC2.5 mi or InsB_9-23/IA^g7-NPs (from n = 5 mice for Tet⁺ cells and 15 mice for Tet⁻ cells; aliquots of the sorted cells were also used for other experiments). The data are from 4 experiments. C Volcano plots showing the Tet⁺ vs. Tconv comparison (from C), with representative TR1-associated and non-TR1-associated genes identified. Red, upregulated genes; blue, downregulated genes. D K-means clustering of the cells from (B). E Venn diagram comparing differentially expressed genes between bulk TFH and Tconv cells from KLH-immunized mice and between Tet⁺ TFH-like and Tet^– Tconv cells from pMHCII-NP-treated mice. F Representative feature plots for genes enriched in the Tconv, Tet⁺ TFH and Tet⁺ TR1 subclusters or shared between the latter two. The P values in (B) were calculated by the Mann‒Whitney U test