ALT Peripheral helper T cells are exclusively observed in RA-ILD lungs and have lung specific characteristics. (A) UMAP plots showing scRNA-seq data of T cells from four control lungs, three Non-RA CTD-ILD lungs, and five RA-ILD lungs. From left to right: UMAP plot of all T cells and UMAP plot of T cells colored by disease type. (B) Percentage of each cell subpopulation relative to the number of total T cells derived from four control lungs, three Non-RA CTD-ILD lungs, and five RA-ILD lungs. Data are shown as Box-and-Whisker plots (median, min-max). *p<0.05 by Kruskal−Wallis test. (C) UMAP plots showing scRNA-seq data of Tph cells from five RA-ILD lungs. From left to right: UMAP plots of all Tph cells and feature plots showing the expression of selected genes in Tph cell subclusters. (D) UMAP plots showing scRNA-seq data of T cells from five RA-ILD lungs and five RA synovial tissues. From left to right: Lung and Synovial Tissue. [continues...]