Single-cell transcriptomics and TCR repertoire sequencing of T cells of NOD mice

T cells primarily drive the autoimmune destruction of pancreatic beta cells in Type 1 diabetes (T1D). However, the profound yet uncharacterized diversity of the T cell populations in vivo has hindered obtaining a clear picture of the T cell changes that occur longitudinally as T1D onset happens. Here we profiled the transcriptome and TCR repertoire of T cells at single-cell resolution from longitudinally collected peripheral blood and islets of Non-Obese Diabetic (NOD) mice using single-cell RNA sequencing technology. We detected clonal expansion and characterized the transcriptional landscape of "islets-matching" T cell clones in the blood and "blood-matching" T cell clones in islets of diabetic NOD mice using the TCR as a molecular barcode. The clonally matching cells show enriched interferon-gamma response pathways than non-matching cells in blood and islets. In addition, we identified a set of transcriptional markers associated with the matching status of the T cell clones. This study provides a single-cell level transcriptome and TCR repertoire atlas of T cells in NOD mice. The results show that TCR and transcriptional signature can be used combinedly to develop biomarker panels for tracking and investigating islets infiltrating T cells. Overall design: Paired single-cell RNA sequencing (scRNA-seq) and TCR repertoire sequencing on T cells collected from peripheral blood and pancreatic islets of NOD mice were conducted. Six paired islets and blood samples from diabetic mice and four blood samples from non-diabetic mice were used for single-cell RNA-seq and V(D)J repertoire sequencing.

T细胞主要介导1型糖尿病（Type 1 diabetes, T1D）中胰腺β细胞的自身免疫性破坏。然而，体内T细胞群体兼具高度丰富的多样性与未被充分解析的特性，阻碍了我们对1型糖尿病发病过程中T细胞的纵向动态变化形成清晰认知。
本研究利用单细胞RNA测序技术，对纵向采集的非肥胖糖尿病（Non-Obese Diabetic, NOD）小鼠外周血与胰腺胰岛中的T细胞，开展了单细胞分辨率水平的转录组与T细胞受体（TCR）库分析。本研究以TCR作为分子条形码，在糖尿病NOD小鼠的血液中鉴定出了与胰岛匹配的T细胞克隆，在胰岛中鉴定出了与血液匹配的T细胞克隆，检测到克隆扩增现象并解析了此类匹配克隆的转录调控图谱。相较于非匹配细胞，匹配克隆细胞在血液与胰岛中均富集了干扰素-γ应答通路。
此外，本研究还鉴定出了一组与T细胞克隆匹配状态相关的转录标志物。本研究构建了NOD小鼠T细胞的单细胞水平转录组与TCR库图谱，研究结果表明，可将TCR特征与转录特征相结合，开发用于追踪与研究胰岛浸润性T细胞的生物标志物组合。
研究设计概述：本研究对采集自NOD小鼠外周血与胰腺胰岛中的T细胞，开展了配对的单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）与TCR库测序。本研究共使用了来自糖尿病小鼠的6套配对胰岛与血液样本，以及来自非糖尿病小鼠的4份血液样本，用于单细胞RNA测序与V(D)J库测序。