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. 2022 Jul 13;13:4046. doi: 10.1038/s41467-022-31519-6

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© The Author(s) 2022

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 — a Chord diagrams showing the interconnectivity between CD4⁺ T cells sharing the same CDR3 (paired TCRα, and TCRβ chains) amino acid sequences within CD4⁺ T-cell clusters in RA SF (left panel) and between compartments in selected clusters (right panel) (n = 4 ACPA−, n = 4 ACPA+). b Jaccard overlap quantifications for clonal overlap between cell clusters across compartments (n = 4 ACPA−, n = 4 ACPA+). c Percentage of shared expanded clones (n ≥ 2 cells) shared with selected subsets among total cell clones, n = 7 RA patients (n = 4 ACPA+, 3 ACPA−). d Representative flow cytometry dot plots showing the expression of PD-1, GPR56, CXCL13, BLIMP-1, and PRF1 in control (upper panel) or after 48 h CD3/CD28-beads activation of T_PH cell states (lower panel) (PD-1^highGPR56^low and PD-1^highGPR56⁺ from ACPA+ SF), quantified in n = 3 ACPA+ RA patients. d Data are from a pool of three independent experiments where a circle is a single replicate. Line indicates median, two-tailed Wilcoxon paired test, P = 0.0005 (MFI PD-1 on PD-1^highGPR56^low after activation), P = 0.0740 (MFI PD-1 on PD-1^highGPR56⁺ after activation), P = 0.0869 (MFI GPR56 on PD-1^highGPR56^low after activation), P = 0.0276 (MFI GPR56 on PD-1^highGPR56⁺ after activation), P = 0.0563 (% BLIMP-1 on PD-1^highGPR56^low after activation), P = 0.0775 (% BLIMP-1 on PD-1^highGPR56⁺ after activation), P = 0.019 (% PRF1 on PD-1^highGPR56^low after activation). e Velocity plots showing the phenotype directionality between the different CD4⁺ T-cell clusters in RA split in ACPA− (left panel) and ACPA+ (right panel) (n = 4 ACPA−, n = 11 ACPA+, pool PB and SF). f Graphical summary showing the proposed developmental link between the two T_PH subsets, effector and cytotoxic CD4⁺ T cells in SF as well as the identified receptors.