Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.

SignificanceT cells play a key role in the adaptive immune system. The broad repertoire of unique receptors expressed by T cells is in principle able to recognize a huge diversity of pathogens, but how to extract that information from blood samples remains unclear. By sequencing and analyzing the statistics of T cell receptors of subjects vaccinated against yellow fever, we identified vaccine-specific receptors that expanded following vaccination. We show that each individual has a unique response, which is similar yet across subjects in its sequence composition, with a slightly higher similarity between twins. Our method can be used in the clinic to track disease-specific T cell clones expanding or contracting after infection, vaccination, or therapy.

SARS-CoV-2 mRNA vaccines induce robust anti-spike (S) antibody and CD4 + T cell responses. It is not yet clear whether vaccine-induced follicular helper CD4 + T (T FH ) cell responses contribute to this outstanding immunogenicity. Using fine needle aspiration of draining axillary lymph nodes from individuals who received the BNT162b2 mRNA vaccine, we evaluated the T cell receptor sequences and phenotype of lymph node T FH . Mining of the responding T FH T cell receptor repertoire revealed a strikingly immunodominant HLA-DPB1 ∗ 04-restricted response to S 167-180 in individuals with this allele, which is among the most common HLA alleles in humans. Paired blood and lymph node specimens show that while circulating S-specific T FH cells peak one week after the second immunization, S-specific T FH persist at nearly constant frequencies for at least six months. Collectively, our results underscore the key role that robust T FH cell responses play in establishing long-term immunity by this efficacious human vaccine.