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

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 500-1500 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 post-infection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones

The diverse repertoire of T-cell receptors (TCR) plays a key role in the adaptive immune response to infections. Previous studies show that secondary responses to the yellow fever vaccine - the model for acute infection in humans - are weaker than primary ones, but only quantitative measurements can describe the concentration changes and lineage fates for distinct T-cell clones in vivo over time. Using TCR alpha and beta repertoire sequencing for T-cell subsets, as well as single-cell RNAseq and TCRseq, we track the concentrations and phenotypes of individual T-cell clones in response to primary and secondary yellow fever immunization showing their large diversity. We confirm the secondary response is an order of magnitude weaker, albeit $\sim10$ days faster than the primary one. Estimating the fraction of the T-cell response directed against the single immunodominant epitope, we identify the sequence features of TCRs that define the high precursor frequency of the two major TCR motifs specific for this particular epitope. We also show the consistency of clonal expansion dynamics between bulk alpha and beta repertoires, using a new methodology to reconstruct alpha-beta pairings from clonal trajectories

Particle approximation for first order stochastic partial differential equations

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TCR out-of-frame repertoire sharing in monozygous twins is higher than in unrelated individuals, or than predicted by stochastic models of recombination.

<p>The number of shared out-of-frame alpha TCR clonotypes between all 15 pairs among 6 donors consisting of 3 twin pairs (ordinate) is compared to the model prediction (abscissa). To be able to compare pairs of datasets of different sizes, the sharing number was normalized by the product of the cloneset sizes. The three outstanding red circles represent the twin pairs, while the black circles refer to the 12 pairs of unrelated individuals among the 6 twins. The model prediction is based on a generative stochastic model of VJ recombination [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.ref013" target="_blank">13</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.ref014" target="_blank">14</a>], inferred separately for each donor to account for differences between individuals. It agrees well with the data from unrelated individuals up to a common multiplicative factor, but systematically underestimates sharing in twins. Error bars show one standard deviation.</p

Lifetime of abundant in-frame TCR beta clonotypes with zero insertions.

<p>The fraction of zero-insertion clonotypes among the 2000 most abundant clonotypes in the unpartitioned repertoire as a function of age (black circles) is well fitted by an exponentially decaying function of time (black curve). This decay is faster than would be predicted from the decay of the naive compartment alone (red curve), indicating a slow decay of zero-insertion clonotypes of fetal origin. Red diamonds show percentage of naive T-cells measured using flow cytometry (see [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.ref023" target="_blank">23</a>] for details). Scale of red axis was chosen so that the two decay curves start at the same point at age 0, and have the same long-time limit. We present the analysis for different bin sizes in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.s011" target="_blank">S10 Fig</a>.</p

TCR nucleotide sequences shared between twins are statistically different from sequences shared between unrelated individuals.

<p>Distribution of log₁₀ <i>P</i>_gen, with <i>P</i>_gen the probability that a sequence is generated by the VJ recombination process, for shared out-of-frame TCR alpha clonotypes between one individual and the other five. While the distribution of shared sequences between unrelated individuals (red curves) is well explained by coincidental convergent recombination as predicted by our stochastic model (blue), sequences shared between two twins (green) have an excess of low probability sequences: 31 sequences with log₁₀ <i>P</i>_gen < −10. For comparison the distribution of <i>P</i>_gen in regular (not necessarily shared) sequences is shown in black.</p

Sharing of alpha out-of-frame TCR clonotypes as a function of clonal abundance.

<p>The normalized number of shared out-of-frame alpha CDR3 nucleotide sequences between two individuals is showed as a function of clonotype abundance (e.g. normalized sharing for 2000 most abundant clones from both repertoires, 4000 most abundant, etc.), and compared to the amount of sharing that would be expected by chance (blue curve), taking into account the variable fraction of zero-insertion clonotypes as a function of their abundance. Data and predictions show excellent quantitative agreement (inset), with one fitting parameter. Error bars show one standard deviation.</p

The number of inserted nucleotides in in-frame TCR beta clonotypes depends on their abundance.

<p><b>A</b>. Mean numbers of insertions were obtained by analysing groups of 3000 sequences of decreasing abundance. Clonotypes from the cord blood (black) show a strong dependence on abundance, with high-abundance clones having much fewer insertions than low-abundance ones. Clonotypes in a young adult naive repertoire (blue) show a similar but less marked trend. Naive clonotypes in older adults (violet and green) show an even weaker trend. Adult memory samples of all ages show no dependence at all (red, yellow and maroon). Error bars show 2 standard errors. <b>B</b>. Probability distributions of the number of insertions in two rank classes, for young naive and cord-blood samples (ranks 1-3000 on top, ranks 45001-48000 on bottom). For high-ranking sequences, the probability of having zero insertions is high both for adult naive and cord blood samples. For middle-ranking sequences, the probability of 0 insertions is much lower, and the distributions are similar between adult naive and cord-blood samples. <b>C</b>. Fraction of clonotypes with zero insertions for different abundance classes. Error bars show one standard deviation. We present the analysis for independently published cord blood donors and different bin sizes in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.s012" target="_blank">S11</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.s011" target="_blank">S10</a> Figs respectively.</p