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. 2020 Feb 21;9:e53704. doi: 10.7554/eLife.53704

Figure 2. Diversity of individual clonal trajectories in primary and secondary responses.

(A, B) Frequency of each YF-responding clonotype in bulk TCR repertoire as a function of time. Individual clones show remarkable expansion after the primary response (A, left panel) and secondary response both 18 months (A, right panel) and 30 years (B) after the primary vaccination. The ten most abundant (by peak frequency) CD4+ and CD8+ YF-responding clonotypes are shown for each vaccination. Clonal traces for all YF-responding clonotypes are shown in Figure 2—figure supplement 1. Color indicates the time of the response peak for each clonotype: blue for a peak at day 5, pink at day 10, green at day 15 and purple at day 21. Despite overall heterogeneity in clonal traces, more clones peak at early timepoints during the secondary response. Heterogeneity in clonal traces allows for expanded clones identification and computational alpha-beta TCR pairing (Figure 2—figure supplement 4).

Figure 2—source data 1. Concentrations of YF-responding clonotypes for donor M1 on all timepoints.
elife-53704-fig2-data1.xlsx (604.4KB, xlsx)
Figure 2—source data 2. Concentrations of YF-responding clonotypes for donor P30 on all timepoints.

Figure 2.

Figure 2—figure supplement 1. Time traces of all YF-responding clonotypes.

Figure 2—figure supplement 1.

Individual clonal trajectories of all YF-responding clonotypes. Frequency of each YF-responding clonotype in bulk TCR repertoire as a function of time. Individual clones show remarkable expansion after the primary response (A, left panel) and secondary response both 18 months (A, right panel) and 30 years (B) after the primary vaccination. Color indicates the time of the response peak for each clonotype: blue for a peak at day 5, pink at day 10, green at day 15 and purple at day 21.
Figure 2—figure supplement 2. Decay of YF-responding clonotypes between primary and secondary immunization.

Figure 2—figure supplement 2.

Decay of YF-responding clonotypes between primary and secondary immunization. Frequencies of YF-responding clones on day 45 of the primary immunization of donor M1 versus their frequencies 18 months later, before the second immunization). Diagonal line shows identity.
Figure 2—figure supplement 3. Frequencies of CD8+ and CD4+ YF-responding clonotypes before and after secondary immunization.

Figure 2—figure supplement 3.

Frequencies of CD8+ (A) and CD4+ (B) clonotypes having responded to the primary YFV17D immunization in bulk before (x-axis) versus at the peak of the response to booster immunization (y-axis). Diagonal line shows identity.
Figure 2—figure supplement 4. Clustering of time traces allows for expanded clones identification and computational TCR alpha-beta chain pairing.

Figure 2—figure supplement 4.

(A) YF-responding clones identified using hierarchical clustering of clonal time traces with and without biological replicates. The plot shows two first principal components (x and y-axis) of the matrix, where rows are clonotypes and columns are normalized frequencies of these clonotypes on timepoints before and after primary immunization of donor M1. The frequency of each clonotype was normalized by its peak concentration. Pink color shows expanded clonotypes identified with edgeR. Two clusters (circles and crosses) were identified using hierarchical clustering. Similar results were obtained for both TCR alpha (left column) and TCR beta (right column) sequencing, with (top row) and without (bottom row) biological replicates for every timepoint. (B) Dynamics of YF-responding clonotypes after primary vaccination data from Pogorelyy et al. (2018). The cumulative frequency of YF-responding clonotypes defined as significantly expanded by edgeR is shown in blue. The green line indicates the cumulative frequency of responding clonotypes identified by hierarchical clustering of individual clonal trajectories. For the clustering procedure, only frequencies of biological replicate 1 of the bulk repertoire were used. (C) Examples of time traces for two YF-responding (purple and green) and one non-responding (blue) clonotypes in the TCR alpha repertoire (left), and their associated chain in TCR beta repertoire (right). The similarity of the alpha and beta traces of the same clone allows for computational alpha-beta pairing prediction. .