The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present TRAPeS, a publicly available tool that can efficiently extract TCR sequence information from short-read scRNA-seq libraries. We apply it to investigate heterogeneity in the CD8⁺ T cell response in humans and mice, and show that it is accurate and more sensitive than existing approaches. Coupling TRAPeS with transcriptome analysis of CD8⁺ T cells specific for a single epitope from Yellow Fever Virus (YFV), we show that the recently described ‘naive-like’ memory population have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype cells. This suggests that TCR usage is associated with the differentiation state of the CD8⁺ T cell response to YFV.

中文翻译：

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从单细胞RNA-seq有针对性地重建T细胞受体序列将CDR3长度连接到T细胞分化状态

T细胞区隔必须在T细胞受体（TCR）库和细胞状态中均包含多样性，以提供针对病原体的有效免疫力。但是，尚不清楚TCR的差异如何导致T细胞状态异质性。单细胞RNA测序（scRNA-seq）可以同时测量TCR序列和单细胞的全局转录谱。但是，目前从scRNA-seq推断TCR的方法的敏感性有限，需要较长的测序读取，因此增加了成本，并减少了可进行分析的细胞数量。在这里，我们介绍TRAPeS，这是一个公开可用的工具，可以从短读scRNA-seq库中有效提取TCR序列信息。我们将其用于研究CD8 ^+中的异质性人类和小鼠的T细胞反应，并表明它比现有方法准确，敏感。将TRAPeS与特异性针对来自黄热病病毒（YFV）的单个表位的CD8 ⁺ T细胞的转录组分析相结合，我们显示，与效应子相比，最近描述的“幼稚样”记忆种群具有更长的CDR3区域和与种系序列的更大差异-记忆表型细胞。这表明TCR的使用与CD8 ⁺ T细胞对YFV的应答的分化状态有关。