Longitudinal analysis of T-cell receptor repertoires reveals persistence of antigen-driven CD4+ and CD8+ T-cell clusters in Systemic Sclerosis

The T-cell receptor (TCR) is a highly polymorphic surface receptor that allows T-cells to recognize antigenic peptides presented on the major histocompatibility complex (MHC). Changes in the TCR repertoire have been observed in several autoimmune conditions, and these changes are suggested to predispose autoimmunity. Multiple lines of evidence have implied an important role for T-cells in the pathogenesis of Systemic Sclerosis (SSc), a complex autoimmune disease. One of the major questions regarding the roles of T-cells is whether expansion and activation of T-cells observed in the diseases pathogenesis is (auto)antigen driven. To investigate the temporal TCR repertoire dynamics in SSc, we performed high-throughput sequencing of CD4+ and CD8+ TCR{beta} chains on longitudinal samples obtained from four SSc patients collected over a minimum of two years. Repertoire overlap analysis revealed that samples taken from the same individual over time shared a high number of TCR{beta} sequences, indicating a clear temporal persistence of the TCR{beta} repertoire in CD4+ as well as CD8+ T-cells. Moreover, the TCR{beta}s that were found with a high frequency at one time point were also found with a high frequency at the other time points (even after almost four years), showing that frequencies of dominant TCR{beta}s are largely consistent over time. We also show that TCR{beta} generation probability and observed TCR frequency are not related in SSc samples, showing that clonal expansion and persistence of TCR{beta}s is caused by antigenic selection rather than convergent recombination. Moreover, we demonstrate that TCR{beta} diversity is lower in CD4+ and CD8+ T-cells from SSc patients compared to healthy memory T-cells, as SSc TCR{beta} repertoires are largely dominated by clonally expanded persistent TCR{beta} sequences. Lastly, using 'Grouping of Lymphocyte Interactions by Paratope Hotspots' (GLIPH2), we identify clusters of TCR{beta} sequences with homologous sequences that potentially recognize the same antigens and contain TCR{beta}s that are persist in SSc patients. In conclusion, our results show that that CD4+ and CD8+ T-cells are highly persistent in SSc patients over time, and this persistence is likely a result from antigenic selection. Moreover, persistent TCRs form high similarity clusters with other (non-)persistent sequences, that potentially recognize the same epitopes. These data provide evidence for an (auto-)antigen driven expansion of CD4/CD8+ T-cells in SSc.