Single T Cell Sequencing Demonstrates the Functional Role αβ TCR Pairing in Cell Lineage and Antigen Specificity
Single T Cell Sequencing Demonstrates the Functional Role αβ TCR Pairing in Cell Lineage and Antigen Specificity
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DOI：
10.3389/fimmu.2019.01516
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发表时间：
2019-07-31
影响因子：
7.3
通讯作者：
Atwal, Gurinder S.
中科院分区：
文献类型：
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作者：
Carter, Jason A.;Preall, Jonathan B.;Atwal, Gurinder S.
尽管对单个T细胞受体（TCRs）的结构研究已经揭示了α链和β链在指导MHC和抗原识别中的重要作用，但从历史上看，全谱水平的免疫基因组分析只研究了β链。为了确定在α - β配对中编码的TCR库功能的有用信息的数量，我们分析了使用两种不同的高通量单细胞测序方法捕获的近100,000个独特CD4+和CD8+ T细胞的配对TCR序列。我们的研究结果表明，在健康的CD4+和CD8+基因库中几乎没有重叠，共享的TCR序列具有明显较短的CDR3序列，对应于更高的生成概率。我们进一步利用信息论和机器学习的工具表明，虽然α链和β链与谱系仅微弱相关，但配对似乎协同驱动TCR-MHC相互作用。V α β基因配对被发现是T细胞谱系中最具信息量的TCR特征，支持种系编码配对α β TCR- mhc相互作用基序的存在。最后，使用已知抗原特异性序列数据库注释我们的TCR对，我们证明大约三分之一的T细胞拥有α和β链，它们各自识别不同的已知抗原，这表明α - β配对对于准确推断库功能至关重要。总之，这些发现为α - β配对的功能意义提供了生物学见解，并突出了单细胞测序在免疫基因组学中的实用性。
Although structural studies of individual T cell receptors (TCRs) have revealed important roles for both the alpha and beta chain in directing MHC and antigen recognition, repertoire-level immunogenomic analyses have historically examined the beta chain alone. To determine the amount of useful information about TCR repertoire function encoded within alpha beta pairings, we analyzed paired TCR sequences from nearly 100,000 unique CD4+ and CD8+ T cells captured using two different high-throughput, single-cell sequencing approaches. Our results demonstrate little overlap in the healthy CD4+ and CD8+ repertoires, with shared TCR sequences possessing significantly shorter CDR3 sequences corresponding to higher generation probabilities. We further utilized tools from information theory and machine learning to show that while alpha and beta chains are only weakly associated with lineage, of pairings appear to synergistically drive TCR-MHC interactions. V alpha beta gene pairings were found to be the TCR feature most informative of T cell lineage, supporting the existence of germline-encoded paired alpha beta TCR-MHC interaction motifs. Finally, annotating our TCR pairs using a database of sequences with known antigen specificities, we demonstrate that approximately a third of the T cells possess alpha and beta chains that each recognize different known antigens, suggesting that alpha beta pairing is critical for the accurate inference of repertoire functionality. Together, these findings provide biological insight into the functional implications of alpha beta pairing and highlight the utility of single-cell sequencing in immunogenomics.