Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins

Abstract

T cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to data from three pairs of identical twins immunized with the yellow fever vaccine. We identified 600 to 1,700 responding TCRs in each donor and validated them using three independent assays. While the responding TCRs were mostly private, albeit with higher overlap between twins, they could be well-predicted using a classifier based on sequence similarity. Our method can also be applied to samples obtained postinfection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic.

Keywords: RepSeq; T cell receptor; high-throughput sequencing; twins; vaccination.

Fig. 1.

(A) Yellow fever vaccination (YFV 17D) study design. (Top) Experimental timeline with the list of samples collected at each timepoint. Unsorted PBMC samples were collected in two biological replicates at each timepoint. (Bottom) Method overview. Peripheral blood samples were subjected to PBMC isolation, synthesis of TCR$\beta$ cDNA libraries, Illumina sequencing, and reconstruction of TCR$\beta$ repertoires. (B) Number of significantly expanded clonotypes in comparison with day 0. The number peaks at day 15 for all donors. The comparison with day −7 corresponds to a contraction reflecting the normal dynamics of a healthy repertoire in absence of vaccination. (C) Activated CD8+CD38+HLA–DR+ subpopulation is enriched with clonotypes expanded between days 0 and 15. Relative abundance of a TCR$\beta$ sequence in the CD8+CD38+HLA–DR+ activated subpopulation (x axis) versus its abundance in the bulk CD8+ population isolated at the same timepoint (y axis). Yellow dots indicate clonotypes that strongly expanded between day 0 and day 15. Brighter shades of blue and yellow indicate clonotypes significantly enriched in the activated subpopulation. Black line shows identity. Red circles indicate sequences found in the A02-NS4b_214−222-dextramer-positive fraction 2 y later.

Fig. 2.

Sharing of YFV-responding TCR$\beta$s across donors. (A) Number of expanded TCR$\beta$ amino acid clonotypes shared between pairs of donors, divided by the product of the numbers of expanded clonotypes in each donor. All three twin pairs (S, P, and Q) show higher numbers of shared expanded clonotype TCR$\beta$s than unrelated individuals and are clustered together by hierarchical clustering (dendrogram on top). (B) The normalized sharing of expanded clonotype TCR$\beta$s (Left) is much higher than the normalized sharing in the whole TCR$\beta$ repertoire (Right). Sharing in twins (red) always exceeds sharing in unrelated individuals (blue).

Fig. 3.

Convergence of amino acid sequences in the YFV-responding TCR$\beta$ repertoire. (A) Number of pairs of similar clones (Left: exact same CDR3 amino acid sequence; Middle: up to one mismatch; Right: up to two mismatches) normalized by the number of possible pairings in each individual (see SI Appendix). The number of similar clones in the data (yellow dots) is larger than the number of similar clones in randomly drawn samples (dark-blue dots) of the same size ($p=0.022,\hspace{0.17em}0.015,\hspace{0.17em}0.008$ for zero, one, and two mismatches; one-sided paired t test). As a reference, the red dots show an example of a restricted and specific repertoire for the yellow fever virus immunodominant epitope NS4b_214−222 [data from VDJdb (20); see Dataset S1]. (B) One thousand most abundant TCRs from donor S1 at day 15. Each vertex corresponds to a TCR$\beta$ amino acid sequence; edges connect sequences differing by two or fewer amino acids in their CDR3. Only vertices with neighbors are plotted. Yellow clonotypes indicate expanded clonotypes, while blue clonotypes were present before immunization at similar frequencies as on day 15. The vast majority of edges (95 out of 103) are formed between TCR$\beta$ clonotypes of the same status (expanded or not expanded).

Fig. 4.

Dynamics of YFV-responding T cells in the CD4+ and CD8+ compartments. Total fraction of (A) CD4+ and (B) CD8+ repertoires occupied by clonotypes significantly expanded from day 0 to day 15 for different timepoints. CD4+ and CD8+ T cell subpopulations show similar dynamics, although the CD8+ response degrades more slowly. Error bars are smaller than one line width.