Environmental conditioning by type I interferons poises naive CD4+ T cells for transition to precursor central memory cells

Upon antigenic stimulation, naïve CD4+ T cells differentiate into phenotypically distinct T helper cells. Naïve T cells are considered homogenous save for their unique T cell receptor (TCR), thought to confer distinct differentiation potential according to its affinity for cognate antigen. Here we show that naïve T cells are transcriptionally heterogeneous and identify a role for type I interferon (IFN) in shaping this heterogeneity. Using complementary single cell analyses, we show that T cell fate is independent of TCR and identify a role for type I IFN signaling in regulating the early differentiation of naïve CD4 T cells towards central memory precursors. Thus, naïve CD4 T cell differentiation potential is determined by environmental cues both prior to and during priming. IFN-conditioned naïve CD4 T cells are expanded in human viral infection and autoimmunity highlighting the relevance of this pathway to beneficial and maladaptive T cell responses, as well as its therapeutic potential for enhanced T cell memory formation. Overall design: Single-cell RNA sequencing was performed on mouse splenic CD4 T cells. Naïve CD4 T cells from transgenic TCR (tgTCR) Smarta and C7 mice (two replicates each) were adoptively transferred into congenic recipients and profiled at steady state along with host naïve CD4 T cells. To study in vivo C7 differentiation, adoptively transferred tgTCR C7 T cells were profiled 16hr (two replicates) and 40hr post L. monocytogenes-ESAT infection. Additionally, gp66:I-Ab tetramer+ T cells were sorted from an Lm-gp66 infected mouse 7 days post intravenous infection (two replicates) and profiled with single-cell 5' RNA-seq + TCR-seq.

当受到抗原刺激时，初始CD4+ T细胞（naïve CD4+ T cells）会分化为表型各异的辅助性T细胞。既往观点认为，初始T细胞（naïve T cells）除携带独特的T细胞受体（T cell receptor, TCR）外均具有均一性，且该受体通过与同源抗原的亲和力赋予细胞不同的分化潜能。本研究证实，初始T细胞在转录层面存在异质性，并揭示了I型干扰素（type I interferon, IFN）在塑造该异质性中的作用。通过互补式单细胞分析手段，本研究证明T细胞命运与TCR无关，并明确了I型干扰素信号通路在调控初始CD4+ T细胞向中枢记忆前体细胞早期分化中的功能。由此可见，初始CD4+ T细胞的分化潜能由致敏前及致敏过程中的环境信号共同决定。经干扰素预处理的初始CD4+ T细胞在人类病毒感染与自身免疫疾病中发生扩增，这提示该通路与有益及病理性T细胞应答均密切相关，同时也为增强T细胞记忆形成提供了治疗潜力。

实验设计概述：本研究对小鼠脾脏CD4+ T细胞开展单细胞RNA测序（single-cell RNA sequencing）。将来自转基因T细胞受体（transgenic TCR, tgTCR）Smarta与C7小鼠的初始CD4+ T细胞（每组各设2个生物学重复）过继转移至同系受体小鼠体内，并在稳态下对其与宿主初始CD4+ T细胞一同进行转录组表征分析。为探究C7细胞的体内分化过程，本研究在李斯特菌（L. monocytogenes）-ESAT感染后16小时（2个生物学重复）与40小时，对过继转移的tgTCR C7 T细胞进行转录组表征分析。此外，本研究在静脉注射Lm-gp66感染7天后，从感染小鼠体内分选得到gp66:I-Ab四聚体阳性T细胞（2个生物学重复），并通过单细胞5'端RNA测序（single-cell 5' RNA-seq）与TCR测序（TCR-seq）联合分析完成转录组表征。