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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. 8 — Single-cell multiomic analysis of pMHCII-NP-induced TFH-TR1 cells vs. KLH-induced TFH cells. A tSNE plot of weighted nearest neighbor-integrated scRNAseq and scATACseq data from BDC2.5 mi/IA^g7 Tet⁺, KLH-induced TFH and TH0 cells. The colors represent the different K-means and their predicted identity. BDC2.5 mi/IA^g7 Tet⁺ subclustered into TFH, TR1-like and TR1 cells, while KLH-induced cells subclustered into TFH.1, TFH.2 and TFH.3 cells. BDC2.5 mi/IA^g7 Tet⁺ TFH and KLH-induced TFH.1 cells clustered together. The data are from 4 (BDC2.5 mi/IA^g7 Tet⁺) and 8 mice (KLH-induced TFH and TH0) from 2 experiments. B Two-dimensional plot of the average log2FC values for the differentially expressed genes (adjusted P value <0.05) among KLH-DNP-induced TFH cell subtypes (TFH.1, TFH.2 and TFH.3) from (A). The data were obtained from 10X Genomics scRNAseq for CD4⁺CD44^hiPD-1^hiCXCR5^hi T cells sorted from KLH-DNP-immunized NOD mice (n = 5). The X-axis shows the TFH.2 vs. TFH.1 comparison; the Y-axis, the TFH.3 vs. TFH.1 comparison. The dot color represents the subset specificity of differential gene expression. C Heatmap and dendrogram showing the average relative gene expression levels in BDC2.5 mi/IA^g7 Tet⁺ TFH cells and the three clusters within the KLH-induced TFH cell pool (TFH.1, TFH.2 and TFH.3). D Single-cell resolution heatmap showing the relative expression levels of TFH-related genes in BDC2.5 mi/IA^g7 Tet⁺ TFH cells and the three clusters within the KLH-induced TFH pool (TFH.1, TFH.2 and TFH.3)