FIGURE 3.

T cell receptor (TCR) profiling from scRNA-seq data identifies clonally expanded subpopulations in pre-expanded Tregs. (A) UMAP plot colored by clonotypes with single occurrences (gray) and multiple occurrences (each clonotype distinctly colored) identifies clusters with expansion (UMAP Components 1 and 2 are the same as those presented in Figure 2). (B) Alpha value (i.e., clonotype frequency) versus evenness value (43) for APB Tregs (orange) and CB Tregs (blue) shows that along the range of the frequency distribution, APB Tregs show decreased evenness at all alpha values, thus exhibiting greater clonal expansion than CB Tregs. (C) When APB Tregs (n = 1, left) and CB Tregs (n = 1, right) are split by cluster (C01-C06, as defined in Figure 2), APB C03 and APB C04 contain expanded subpopulations, while CB C01, C02, C03, and C06 are also moderately expanded. (D) Putative antigen specificity composition of TCRs in each sample show an increased number of clones mapping to known reactivities, including autoimmune clones, in CB Tregs (right) compared to APB Tregs (left).