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. 2023 Mar 27;20(5):489–511. doi: 10.1038/s41423-023-00989-z

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — BLIMP1-dependent TFH-to-TR1 cell reprogramming. A tSNE plots of 10x Genomics scRNAseq data for sorted BDC2.5 mi/IA^g7 tetramer⁺ (Tet⁺) cells from BDC2.5 mi/IA^g7-NP-treated NOD.Cd4-Cre (n = 3) and NOD.Prdm1^loxP/loxP (n = 3) mice vs. NOD.Cd4-Cre.Prdm1^loxP/loxP (n = 2) mice from 1 experiment. Cell subsets were identified via k-means clustering and prediction using the 10x Genomics scRNAseq data from Fig. 3C as a reference. B Fraction of total cells corresponding to each Tet⁺ subcluster. C Two-dimensional plot of the average log2FC values for the differentially expressed genes in the terminally differentiated TR1 vs. TFH (y-axis) vs. TR1-like vs. TFH (x-axis) comparisons in Prdm1-competent mice. D Trajectory analysis results on UMAP plots generated with 10x Genomics scRNAseq data from BDC2.5 mi/IA^g7 tetramer (Tet⁺) cells isolated from BDC2.5 mi/IA^g7-NP-treated NOD.Cd4-Cre and NOD.Prdm1^loxP/loxP mice. Left, cell cluster identity; right, pseudotime analysis. E Relative expression levels of representative TFH- and TR1-specific genes vs. pseudotime. F Top, tSNE plot for Tet^–CXCR5^–PD-1⁻ (Tconv) and BDC2.5 mi/IA^g7 Tet⁺ splenic CD4⁺ T cells (Tet⁺) from BDC2.5 mi/IA^g7-NP-treated NOD.Cd4-Cre and NOD.Prdm1^loxP/loxP mice stained with the 32-marker CyTOF panel listed in Supplementary Table 4. Bottom, average % of cells ±S.E.M. values in clusters #1 and #2. The data correspond to 2 mice/strain from 1 experiment. G Percentages of BDC2.5 mi/IA^g7 Tet⁺ CD4⁺ T cells in various lymphoid organs from BDC2.5 mi/IA^g7-NP-treated NOD.Cd4-Cre.Tbx21^loxP/loxP vs. NOD.Cd4-Cre mice. The data correspond to 3 mice/strain from 3 experiments. H Average percentages of PD-1^hiCXCR5^hi (TFH) cells within the Tet⁺ and Tet^– subsets of the mice in (G). I Cytokine secretion profiles of splenic Tet⁺ CD4⁺ T cells from the mice in (G) upon stimulation with anti-CD3/anti-CD28 mAb-coated beads. J Left: tSNE plots of 10x Genomics scRNAseq data for sorted BDC2.5 mi/IA^g7 tetramer (Tet⁺) cells from BDC2.5 mi/IA^g7-NP-treated NOD.Cd4-Cre.Tbx21^loxP/loxP mice (n = 3) from 1 experiment. Right: Fraction of total cells corresponding to each Tet⁺ subcluster in BDC2.5 mi/IA^g7-NP-treated NOD.Cd4-Cre.Tbx21^loxP/loxP vs. control (NOD.Cd4-Cre and NOD.Prdm1^loxP/loxP) mice. The data in (G–I) correspond to the mean ± SEM values. The P values in (F) and (G–I) were calculated via two-way ANOVA and the Mann‒Whitney U test, respectively