Long-term maintenance of human naïve T cells through in situ homeostasis in lymphoid tissue sites

Abstract

Naïve T cells develop in the thymus and coordinate immune responses to new antigens; however, mechanisms for their long-term persistence over the human lifespan remain undefined. Here, we investigated human naïve T cell development and maintenance in primary and secondary lymphoid tissues obtained from individual organ donors aged 3 months-73 years. In the thymus, the frequency of double-positive thymocytes declined sharply in donors over age 40 coincident with reduced recent thymic emigrants (RTE) in lymphoid tissues, while naïve T cells were functionally maintained predominantly in lymph nodes (LN). Analysis of TCR clonal distribution by CDR3 sequencing of naïve CD4+ and CD8+ T cells in spleen and LNs reveal site-specific clonal expansions of naïve T cells from individuals >40 years of age with minimal clonal overlap between lymphoid tissues. We also identified biased naïve T cell clonal distribution within specific lymph nodes based on VJ usage. Together these results suggest prolonged maintenance of naïve T cells through in situ homeostasis and retention in lymphoid tissue.

Quantifying size and diversity of the human T cell alloresponse

“…+ and CD8 + sorted T cells were sent to Adaptive Biotechnologies for β-chain profiling according to protocols and standards for sequencing and error correction that comprise their immunoSEQ Platform (24,43,44). In summary, the Adaptive deep sequencing protocol extracts approximately 1,200 ng of T cell DNA.…”

“…Scatter plots showing the number of individual clones shared between the 2 distinct alloreactive repertoires confirms their disparate nature for both CD4 + and CD8 + T cell repertoires ( Figure 4A). A standard quantitative measure of repertoire overlap is Jensen-Shannon divergence (JSD) (24,25), a tool that accounts for both clone number and frequency and is normalized on a scale of 0 to 1: a JSD of 1 indicates that all clones in 2 populations are distinct. A small group of high frequency shared clones was detected in the CD8 + repertoires of 2 of the 3 pairs (red in Figure 4A).…”

“…Interpopulation differences were determined by the JSD (47), which has previously been applied to TCR repertoire analysis (24,25). Rather than quantifying unevenness within a population, the JSD provides a measure of dissimilarity between the labeled frequencies of 2 populations.…”

“…Similarly, other subpopulations of T cells, such as T regulatory cells, may not proliferate as readily as other subsets in an MLR. Other variables to consider include CMV/EBV exposure history (40)(41)(42) and subject age (24), which likely also play a role in the balance of naive and memory cells and nature of the alloresponse.…”

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

“…We have established a human tissue resource to obtain blood, multiple lymphoid and mucosal tissues from previously healthy organ donors, enabling analysis of T cell compartmentalization and maintenance throughout life (Gordon et al, 2017;Sathaliyawala et al, 2013;Thome et al, 2016a;Thome et al, 2016b;Thome et al, 2014). We present here transcriptional, phenotypic, and functional analyses which define human TRM as a distinct subset in multiple sites.…”