Table_1_The T Cell Receptor Immune Repertoire Protects the Liver From Reconsitution.xlsx

Aberrant immune cell infiltrates and microcircumstances represent characteristic features of liver fibrosis. In this study, we profiled the transcriptomes of intrahepatic CD45+ immune cells, from mice, using single-cell RNA sequencing (scRNA-seq) technology to understand the landscape of intrahepatic immune cells during the pathogenesis of fibrosis. Analysis of approximately 10,000 single-cell transcriptomes revealed an increase in dendritic cells (DCs), macrophages, and neutrophils and a decrease in T and natural killer T (NKT) cells. In addition, we report changes in the transcriptomes of diverse immune cell types, implying a deteriorating intrahepatic immune microcircumstance. Furthermore, we uncovered a novel fibrosis-associated CD8 T (Ccl5+, Ccl4+) and CD4 T (mt-Co1+) cell subpopulation, which infiltrates fibrotic liver and is characterized by abnormal activation or inactivation as well as a TCR decline. The results from scRNA-seq and bulk immune repertoire sequencing (IR-seq) revealed an obvious decline in T cell receptor (TCR) clonotypes combined with shrinking VJ and VDJ segment usage, as well as lower complementarity-determining region 3 (CDR3) amino acid (AA) diversity from fibrotic liver. Interestingly, a deficiency of TCR IR (TcrbKO mice) led to a deterioration of liver fibrosis, coupled with activation of hepatic stellate cells (HSCs) induced by the upregulation of macrophage and γδ T cell distribution in fibrotic TcrbKO livers. Our findings reveal the landscape and dynamics of single immune cells in liver fibrosis, and clarify the protective role of TCR IR in response to chronic liver injury.

异常免疫细胞浸润与微环境是肝纤维化的特征性表现。本研究利用单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）技术，对小鼠肝内CD45+免疫细胞开展了转录组谱分析，以解析纤维化发病过程中肝内免疫细胞的全貌。对约1万个单细胞转录组的分析显示，树突状细胞（dendritic cells, DCs）、巨噬细胞与中性粒细胞数量增多，而T细胞及自然杀伤T（natural killer T, NKT）细胞数量减少。此外，本研究还揭示了多种免疫细胞类型的转录组变化，提示肝内免疫微环境出现恶化。进一步，本研究发现了一类新的纤维化相关免疫细胞亚群：表达Ccl5、Ccl4的CD8 T细胞与表达mt-Co1的CD4 T细胞，这类细胞会浸润至纤维化肝脏，其特征为异常激活或失活以及T细胞受体（T cell receptor, TCR）表达下调。单细胞RNA测序与批量免疫组库测序（bulk immune repertoire sequencing, IR-seq）的结果显示，纤维化肝脏中的T细胞受体克隆型显著减少，VJ、VDJ片段的使用范围收缩，且互补决定区3（complementarity-determining region 3, CDR3）的氨基酸（amino acid, AA）多样性降低。有趣的是，TCR免疫组库缺陷（TcrbKO小鼠）会加剧肝纤维化，纤维化TcrbKO肝脏中巨噬细胞与γδ T细胞的分布上调，进而诱导肝星状细胞（hepatic stellate cells, HSCs）激活。本研究揭示了肝纤维化中单个免疫细胞的全貌及动态变化，并阐明了TCR免疫组库在慢性肝损伤应答中的保护作用。