TCR repertoire: size, diversity, and function

胸腺调节性T细胞（tTreg）在维持正常T细胞免疫和耐受中至关重要。TCR在tTreg细胞选择中的作用仍不完全清楚。在此，我们通过高通量测序评估了小鼠tTreg和常规胸腺CD 4 + T（Tconv）细胞的TCR和TCR序列。 我们鉴定了tTreg或Tconv细胞所特有的TCR序列，并发现这些序列是不同的，如机器学习（ML）算法和tTreg细胞的CDR 3中优先使用的氨基酸三聚体所识别的。此外，在Tconv细胞中也发现了一部分由tTreg表达的TCR序列，ML将这些共享的TCR序列中的绝大多数归类为Tconv细胞而不是tTreg细胞的特征。这些发现鉴定了两个tTreg群体，其中一个群体中Treg命运与TCR的独特性质相关，另一个群体中Treg命运与Tconv细胞的TCR性质特征相关，其中tTreg命运由TCR序列以外的因素决定。 多样的TCR库被认为是T细胞免疫提供宿主抵抗所有潜在病原体的保护所必需的。然而，TCR库的大小和内容及其随年龄的变化仍然难以捉摸。在这里，我们报告了对30名年龄在25岁至85岁的健康成年人的人CD 4+和CD 8 + T细胞以及幼稚和记忆亚群的TCR库的纵向分析，第一次访问和平均9年的随访作为RNAseq的第二次访问。通过分析组合的1.9 X IO 8个⑶ 4+和⑶ 8 + T细胞，我们分别鉴定了总共1.1 X IO 6个和2.8 X IO 6个独特的TCR和TCR序列。我们预测成人具有4 X IO 8的TCR库丰富度。 通过循环T细胞的实际数量估计的TCR库变化显示以下关键的年龄相关变化：1）在CD 4+和CD 8 + T细胞中的TCR和TCR库丰富度降低，其中幼稚CD 8 + T细胞的减少最大; 2）在所有T细胞亚群中TCR库的克隆扩增增加，其中记忆CD 8 + T细胞的扩增最大; 3）显著降低了CD 4+和CD 8 + TCR库的含量变化，因为TCR和TCR序列的保留在两次访问之间增加，其中记忆性CD 8 + T细胞显示最高;和4）降低了原始T细胞和记忆性T细胞之间以及CD 4+和CD 8 + T细胞之间的TCR和TCR序列的区别。这些发现预测了人类TCR库的大小，并描述了CD 4+和CD 8 + T细胞及其亚群中TCR库随年龄的精确变化。总的来说，我们的研究结果表明，与年龄相关的T细胞免疫下降是更严重的CD 8 + T细胞介导的细胞毒性比CD 4 + T辅助功能。

Thymic regulatory T cells (tTreg) are critical in maintenance of normal T cell immunity and tolerance. The role of TCR in tTreg cell selection remains incompletely understood. Here we assessed TCR and TCR sequences of mouse tTreg and conventional thymic CD4+ T (Tconv) cells by high throughput sequencing. We identified TCR sequences that were unique to either tTreg or Tconv cells and found that these were distinct as recognized by machine learning (ML) algorithm and by preferentially used amino acid trimers in CDR3 of tTreg cells. In addition, a proportion of TCR sequences expressed by tTreg were also found in Tconv cells, and ML classified the great majority of these shared TCR sequences as characteristic of Tconv and not tTreg cells. These findings identify two populations of tTreg, one in which Treg fate is associated with unique properties of the TCR, and another with TCR properties characteristic of Tconv cells for which tTreg fate is determined by factors beyond TCR sequence. A diverse TCR repertoire is considered essential for T cell immunity to provide protection of the host against all potential pathogens. However, the size and content of the TCR repertoire and its changes with age remains elusive. Here, we report a longitudinal analysis of TCR repertoire of human CD4+ and CD8+ T cells and nave and memory subsets from 30 healthy adults aged from 25 to 85 at first visit and an average of 9-year follow-up as second visit by RNAseq. Through analysis of combined 1.9 x 108 CD4+ and CD8+ T cells, we identified a total of 1.1 x 106 and 2.8 x 106 unique TCR and TCR sequences, respectively. We predicted that an adult has TCR repertoire richness of 4 x 108. TCR repertoire changes estimated by the actual number of circulating T cells displayed the following key age-associated changes: 1) reduction of TCR and TCR repertoire richness in both CD4+ and CD8+ T cells, with the greatest reduction in nave CD8+ T cells; 2) increased clonal expansion of TCR repertoire in all T cell subsets, with the greatest expansion in memory CD8+ T cells; 3) profoundly reduced content changes of CD4+ and CD8+ TCR repertoire, as retention of TCR and TCR sequences increased between two visits, with memory CD8+ T cells showing the highest; and 4) decreased distinction of TCR and TCR sequences between nave and memory T cells, as well as between CD4+ and CD8+ T cells. These findings predicted the size of TCR repertoire in human and described the precise alterations of TCR repertoire in CD4+ and CD8+ T cells and their subsets with age. Collectively, our results suggested that age-related decline of T cell immunity is more severe in CD8+ T cell mediated cytotoxicity than in CD4+ T helper function.