Figure 6. Gene expression in Th1-polarized Tregs and Teffs from oligo JIA SF.

Sorted Tregs (CD4⁺CD25⁺CD127^lo) and Teffs (CD4⁺CD25^–) from the SF of 2 oligo JIA patients were studied with 10x Genomics. (A) Cluster-level expression of markers from key immune cell types (Treg, Th1, Th17, CTLs, Tph/B cell helper T cells), states (activation, exhaustion, naive/memory), and pathways (IFN signaling, viral sensing) used to characterize clusters. For each gene and cluster, the size of the dot is proportional to the percentage of cells expressing the gene in that cluster, and the color code illustrates the average level of expression of all cells in the cluster. (B) Expression levels of key Treg-, Th1-, Th17-, and Tph-related genes across the 6190 cells. The global UMAP color-coded by cluster is shown again for reference. For each gene, cells in the top 95% quantile of expression level are color-coded; the bottom 5% appear in gray. Additional genes can be browsed at https://amjule.shinyapps.io/oligo-JIA/ Clusters were defined as 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 T peripheral helper–like (Tph-like), 7) Tph-like, 8) CD4⁺ cytotoxic T lymphocytes (CTLs), 9) Th1 effector memory, 10) Th17 effector memory, 11) CXCR3^hi central memory, 12) CXCR3^lo central memory, 13) cells undergoing OXPHOS metabolism, 14) mitotic cells.