Dynamics of the cytotoxic T cell response to a model of acute viral infection

Abstract

A detailed characterization of the dynamics and breadth of the immune response to an acute viral infection, as well as the determinants of recruitment to immunological memory, can greatly contribute to our basic understanding of the mechanics of the human immune system and can ultimately guide the design of effective vaccines. In addition to neutralizing antibodies, T cells have been shown to be critical for the effective resolution of acute viral infections. We report the first in-depth analysis of the dynamics of the CD8(+) T cell repertoire at the level of individual T cell clonal lineages upon vaccination of human volunteers with a single dose of YF-17D. This live attenuated yellow fever virus vaccine yields sterile, long-term immunity and has been previously used as a model to understand the immune response to a controlled acute viral infection. We identified and enumerated unique CD8(+) T cell clones specifically induced by this vaccine through a combined experimental and statistical approach that included high-throughput sequencing of the CDR3 variable region of the T cell receptor β-chain and an algorithm that detected significantly expanded T cell clones. This allowed us to establish that (i) on average, ∼ 2,000 CD8(+) T cell clones were induced by YF-17D, (ii) 5 to 6% of the responding clones were recruited to long-term memory 3 months postvaccination, (iii) the most highly expanded effector clones were preferentially recruited to the memory compartment, and (iv) a fraction of the YF-17D-induced clones could be identified from peripheral blood lymphocytes solely by measuring clonal expansion.

Importance: The exhaustive investigation of pathogen-induced effector T cells is essential to accurately quantify the dynamics of the human immune response. The yellow fever vaccine (YFV) has been broadly used as a model to understand how a controlled, self-resolving acute viral infection induces an effective and long-term protective immune response. Here, we extend this previous work by reporting the identity of activated effector T cell clones that expand in response to the YFV 2 weeks postvaccination (as defined by their unique T cell receptor gene sequence) and by tracking clones that enter the memory compartment 3 months postvaccination. This is the first study to use high-throughput sequencing of immune cells to characterize the breadth of the antiviral effector cell response and to determine the contribution of unique virus-induced clones to the long-lived memory T cell repertoire. Thus, this study establishes a benchmark against which future vaccines can be compared to predict their efficacy.

FIG 1

Selection of FDR thresholds. (A) Number of clones classified as YFV induced for various FDR significance thresholds for all subjects. A threshold of 0.01 was selected. (B) Number of clones classified as putatively reactive clones for various FDR significance thresholds for all subjects. A threshold of 0.05 was selected. Each subject is represented by a different tone of gray, as indicated in the legend.

FIG 2

Identification of YFV-induced clones. The graphs show the abundance of unique clones identified by statistical enrichment on the activated effector CD38⁺ HLA-DR⁺ CD8⁺ T cell compartment on day 14 postvaccination (T_AE-14) versus those present in the corresponding total PBMC sample from the same time point for subject 1 (A) and for subjects 2 to 9 (B). Clones were classified into four categories based both on their presence in the T_AE-14 and the T_M-0 compartments, as indicated in the legend. Red clones are present in the T_AE-14 compartment, whereas gray clones are not; while clones absent in the T_M-0 compartment have a black edge and those present in the T_M-0 compartment do not. Darker colors indicate that multiple data points have been superimposed in that particular position. Regions bound by dashed lines indicate clones present in only one sample. YFV-induced clones were significantly enriched in the CD38⁺ HLA-DR⁺ CD8⁺ T cell-sorted population compared to the corresponding total PBMC sample.

FIG 3

Recruitment of YFV-induced clones to immunological memory compartments. (A) Efficiency of recruitment of YFV-induced clones to the effector (T_EM⁺ T_CM⁻) and central (T_EM⁻ T_CM⁺) memory compartments, or both (T_EM⁺ T_CM⁺), as a percentage of all clones classified as YFV induced. (B) Efficiency of recruitment to the effector and central memory compartments (or both) for YFV-induced clones absent from the day 0 prevaccination total PBMC samples, classified into categories based on their abundance in the day 14 postvaccination total PBMC samples. Clones with a higher degree of expansion are more efficiently recruited to the memory compartment. The aggregated data for all subjects are shown; subject-wise source data can be found in Table SI in the supplemental material.

FIG 4

Composition of the effector and central memory compartments on day 90 postvaccination. (A) Proportion of YFV-induced clones newly recruited to the effector (T_EM-90) and central (T_CM-90) memory compartments on day 90 postvaccination, computed both by clone and template counts. (B) Number of templates per YFV-induced clone identified in the T_EM-90 andT_CM-90 memory compartments. More templates per clone were observed in the T_EM-90 compartment, indicating that these clones were more highly expanded. The aggregated data for all subjects are shown; subject-wise source data can be found in Table SII in the supplemental material.

FIG 5

Identification of YFV putatively reactive clones. The graphs show the abundance of unique clones identified by statistical enrichment in the day 14 postvaccination total PBMC sample compared to the prevaccination day 0 total PBMC sample from subject 1 (A) and for subjects 2 to 9 (B). Putatively reactive clones are enclosed by a blue box. Significant enrichment (or expansion) was defined based on a q value threshold, with 1% and 5% expected false-positive rates for YFV-induced and putatively reactive clones, respectively (see Materials and Methods). Clones were classified into four categories based both on their presence in the T_AE-14 and the T_M-0 compartments, as indicated in the legend. Darker colors indicate that multiple data points are superimposed in that particular position. Regions bound by dashed lines indicate clones present in only one sample.