Fig. 3: Assessment of thymic activity in GT patients.
From: Long-term lymphoid progenitors independently sustain naïve T and NK cell production in humans
A T-cell receptor excision circles (TREC) content measured in CD4+ and CD8+ cells in five patients overtime. B Ring plots displaying the relative fractions of TCR rearrangements detected within each T-cell subtype sorted from a healthy donor control (HD) and two patients (P8 and P10) at two timepoints each (months = M) after GT. Numbers inside each ring correspond to the numbers of individual TCR rearrangements retrieved from each sample. C Diversity of TCR rearrangements shown as a 2-dimension t-SNE plot. Coordinates are derived from computing the differences (distance) among clones in sequence composition of a 50 bp window centred on the Complementarity-determining region 3 (CDR3). The size of each dot is proportional to the abundance of the corresponding TCR rearrangement. In these graphical representations the higher it is the spread of dots across the area of the plot the higher it is the diversity of rearrangements observed within the TCR locus. D TCR diversity measured by Shannon Diversity index in each sample and T-cell subtypes of HD, P8 and P10. E Diversity of TCR repertoire in naïve T cells (TN) of HD (grey bar) and Patients (red bars) at different timepoints). F Networks displaying TCR sharing between the four T-cell subtypes from HD or P8 and P10 at each follow up. Nodes represent T-cell subtypes while edges (arrows) represent degree of TCR sharing. Size of each node is proportional to the number of TCR rearrangements detected in each T-cell subtype (Naïve T cells [TN] in light green, other subtypes in light blue). The thickness of the arrows is proportional to the Pearson correlation coefficient calculated on the basis of TCR sharing between each pair of T-cell subtype. G Violin plots showing percent of TCR recaptured within each T-cell subtype isolated from two patients at two independent timepoints.
