Figure 7. Expanded SF CD4⁺ T cell clones primarily concentrate in clusters of Tph-like cells.

Sorted Tregs (CD4⁺CD25⁺CD127^lo) and Teffs (CD4⁺CD25^–) from the SF of 2 patients with oligo JIA were evaluated at the single-cell level for T cell receptor (TCR) repertoire analysis with 10x Genomics. (A) UMAP projection split by patient, highlighting clones with 3 copies or more across the data set (expanded). A clone is defined by its paired TCRα and TCRβ chain; cells with missing sequencing data for the α and/or β chain were excluded. (B) Percentage (mean ± SD) of expanded clones (≥3 copies) per cluster and study subject. (C) Similarity in clonotypic composition across clusters for each patient measured with the Morisita-Horn index expressed as a percentage. Clusters are defined as follows: 1) Th1-like Treg, 2) classical Treg, 3) activated/HLA-DR^hi Treg, 4) CD25^intCD161⁺ Treg, 5) IFN-induced Treg, 6) activated/HLA-DR^hi Tph-like, 7) Tph-like, 8) CD4⁺ CTLs, 9) Th1 effector memory, 10) Th17 effector memory, 11) CXCR3^hi central memory, 12) CXCR3^lo central memory. JIA, juvenile idiopathic arthritis; SF, synovial fluid; Tph, T peripheral helper T lymphocytes; CTLs, cytotoxic T lymphocytes; UMAP, uniform manifold approximation and projection.