Fig. 5: Citrullinated antigens induce clonal expansion of ACPA+ RA blood CD8⁺ T cells that express cytotoxic and synovial-trafficking markers.

a, b UMAP plots showing clonal size of ACPA+ RA CD8⁺ T cells (n = 3284) stimulated by vimentin or citrullinated vimentin (a) and H3 or citrullinated H3 (b). c Cytotoxicity and RA synovial-trafficking scores in CD8⁺ T cells stimulated by native or citrullinated antigens. d, e Comparison of TCR repertoire in CD8⁺ T cells stimulated by native or citrullinated proteins (Vimentin; d or H3; e). Bar graphs representing changes of proportion in each top 5 clonotype between native and citrullinated antigens (left), UMAP depicting the selected 5 expanded clones labeled by different color (right). f Expression level of GZMB, GNLY, IFNG, GZMK or MKI67 in the selected 5 clonotypes stimulated by native vimentin (n = 9) or citrullinated vimentin (n = 67). The boxplot represents the median shown as a line in the center of the box, the boundaries are the first and third quartile, and whiskers represent the minimum and maximum values in the data. g, h Integrated analysis of paired blood and synovial tissue using single cell RNA seq datasets to identify whether RA synovial cytotoxic CD8⁺ T cells express transcriptional programs shared with those expressed by the citrullinated antigen-reactive clonally expanded GZMB⁺GNLY⁺ CD8⁺ T cells in RA blood. Circos plot depicting shared expanded clonal families in PBMCs (red) or synovium (blue) from two representative ACPA+ RA patients distinguished by brown and gray colors (g). Heatmap showing expression level of cytotoxic markers such as GZMB, GNLY or GZMK in each expanded clone of blood or synovium (h). In f, ^*P < 0.05, or ^***P < 0.001 by two-tailed unpaired t-test (GZMB; ^***P = 0.00054, GNLY; ^*P = 0.024, IFNG; ^*P = 0.014, GZMK; P = 0.3209, MKI67; ^*P = 0.016). ns, not significant. Source data are provided as a Source Data file. ACPA anti-citrullinated protein antibodies, RA rheumatoid arthritis.