TCR repertoire: size, diversity, and function

如何理解TCR蛋白的大小和内容以及它们随年龄的变化仍然是免疫生物学中的一个关键挑战。在这里，我们报告了RNAseq对30名年龄从25岁到85岁的健康成年人的TCR谱及其亚群的纵向分析，并在第二次访问时进行了平均9年的随访。通过对2.0x108的NAVE和记忆性的CD4+和CD8+T细胞的分析，我们确定了1.1x106和2.8x106独特的TCR和TCR序列。我们发现，尽管随着年龄的增长，NAVE TCR谱系的大小普遍减少，但研究对象的NAVE TCR谱系(物种丰富度和D50指数)在体内的变化是高度个性化的。幼稚的CD8+和CD8+T细胞在30-90岁的所有成人中都有减少，但改变了晚年发现的幼稚CD8+T细胞的扩张，这可能是由于多年来积累的不平衡的体内平衡扩张所致。一个显著的年龄变化是NAVE与记忆性CD4+和CD8+T细胞的TCR谱系的相似性增加，这表明也可以选择NAVE TCR谱系。这些发现提供了TCR和TCR多样性的框架，以及它们随年龄的变化在CD4+和CD8+初始T细胞和记忆性T细胞中的变化。 胸腺调节性T细胞(TTreg)是维持正常T细胞免疫和耐受的关键。TCR在tTreg细胞选择中的作用尚不完全清楚。在这里，我们通过高通量测序评估了tTreg和传统胸腺CD4+T(Tconv)细胞的TCR和TCR序列。我们鉴定了tTreg或Tconv细胞特有的TCR序列，并发现这些序列与机器学习(ML)算法识别的不同，并且在tTreg细胞的CDR3中优先使用氨基酸三聚体。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细胞的特征而不是tTreg细胞的特征。这些发现鉴定了两个tTreg群体，其中一个群体的Treg命运与TCR的独特属性有关，另一个群体与Tconv细胞的TCR属性有关，其中tTreg的命运由TCR序列以外的因素决定。

Understanding how the size and content of TCR reprotire and their changes with age remains a critical challenge in immunobiology. Here, we report a longitudinal analysis of TCR repertoire of human T cells and 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. From analysis of combined 2.0 x 108 nave and memory CD4+ and CD8+ T cells, we identified 1.1 x 106 and 2.8 x 106 unique TCR and TCR sequences. We found despite a general reduction of nave TCR repertoire size with age, the in vivo change of nave TCR repertoire (species richness and D50 index) in the study subjects was highly individualized. Reduction of nave CD4+ and CD8+ TCR repertoires occurred at all adult age from 30-90 but altered expansion of naive CD8+ T cells found in later years, probably due to cumulated unbalanced homeostatic expansion over the years of life. A striking age change is increased similarity of TCR repertoire between nave and memory CD4+ and CD8+ T cells, suggesting nave TCR repertoires may be also selected. These findings provide a framework of TCR and TCR diversity and their changes with age in CD4+ and CD8+ nave and memory T cells. 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 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.