Identification of two transitional stem-like memory CD8+ T cell states during viral infection and vaccination

Stem-like CD8+ T cells are a key feature of chronic conditions and long-lived memory. Currently stem-like CD8+ T cells are named according to their environment, where precursors of exhausted (TPEX) cells arise in chronic viral infections, autoimmunity and cancer, while stem cell-like memory (TSCM) cells are associated with acute infection and vaccination. Here, we established and validated a method to monitor the transition between transcriptionally distinct TPEX and TSCM cell states. We reveal a linear and reversible developmental trajectory that is concomitant with viral clearance. Further, we demonstrate that TPEX to TSCM cell conversion is observed during acute viral infection and vaccination, aligning the processes that establish stem-like CD8+ T cells in acute and chronic settings. This work supports the potential to monitor stem-like CD8+ T cell conversion as biomarkers of disease in patients with chronic infection, cancer, and autoimmunity and broadens the importance of this transition during the establishment of vaccine-induced long-lived immune protection. Overall design: Paired single cell RNA sequencing (scRNAseq) and surface protein sequencing (CITEseq) analysis compared P14 cells from day 8 acute LCMV Armstrong infection (4499 cells) and chronic LCMV Docile infection (4967 cells) with days 0-1 IFNAR blocked LCMV Armstrong at both day 8 (5061 cells) and day 14 (3102 cells).

干细胞样CD8+ T细胞（Stem-like CD8+ T cells）是慢性疾病与长效免疫记忆形成的关键特征。目前，该类细胞根据其所处微环境进行命名：耗竭前体（TPEX）细胞的前体产生于慢性病毒感染、自身免疫病及癌症情境中，而干细胞样记忆（TSCM）细胞则与急性感染及疫苗接种密切相关。本研究建立并验证了一种可监测转录特征迥异的TPEX与TSCM细胞状态间转化的方法。我们揭示了一条伴随病毒清除的线性且可逆的发育轨迹。进一步研究证实，在急性病毒感染与疫苗接种过程中均可观测到TPEX向TSCM细胞的转化，这统一了急性与慢性环境中干细胞样CD8+ T细胞的形成机制。本研究支持将干细胞样CD8+ T细胞转化作为慢性感染、癌症及自身免疫病患者的疾病生物标志物的潜在应用价值，并拓展了该转化过程在疫苗诱导的长效免疫保护建立过程中的重要意义。总体实验设计：通过配对的单细胞RNA测序（scRNAseq）与表面蛋白测序（CITEseq）分析，对比了四类样本中的P14细胞：急性淋巴细胞脉络丛脑膜炎病毒（LCMV）Armstrong株感染第8天的样本（含4499个细胞）、慢性LCMV Docile株感染样本（含4967个细胞），以及于感染第0-1天阻断I型干扰素受体（IFNAR）的LCMV Armstrong株感染样本，分别在感染第8天（含5061个细胞）与第14天（含3102个细胞）采集。