Gene regulatory basis of bystander activation in CD8+ T cells (human scRNA-seq)

CD8+ T cells have been categorized as an adaptive lymphocyte, based on their ability to recognize specific foreign antigens and mount memory responses. However, neonatal and adult CD8+ T cells are derived from distinct HSC progenitors, which may alter the roles they play during infection. Here, we demonstrate that neonatal CD8+ T cells can be activated by innate cytokines alone and protect the host from a variety of unrelated pathogens in the absence of TCR signaling. Using a multi-omics approach, we found that neonatal CD8+ T cells are highly responsive to innate cytokines because they can rapidly undergo chromatin remodeling, resulting in the usage of a distinct set of enhancers that are more commonly found in innate-like T cells. We also identified a key gene regulatory axis (Bach2/AP1) that is differentially utilized by neonatal and adult CD8+ T cells to toggle their responsiveness to innate cytokines. Importantly, the developmental switch between innate and adaptive functions in the CD8+ T cell compartment is not mediated by a change in the maturation of individual cells along a linear axis, but rather by changes in the abundance of distinct subsets of cells. Collectively, our findings provide support for the layered immune hypothesis and indicate that the CD8+ T cell compartment is more phenotypically diverse than previously thought. CD8+ cells were magnetically enriched by positive selection (anti-human CD8 microbeads; Miltenyi Biotech) from rested PBMCs or CBMCs. Isolated cells were then treated with IL-2 with or without co-treatment with IL-12 and IL-18 and analyzed using scRNAseq.

CD8+ T细胞曾被归类为适应性淋巴细胞（adaptive lymphocyte），其分类依据为能够识别特异性外来抗原并触发记忆性免疫应答。然而，新生儿与成人CD8+ T细胞源自不同的造血干细胞（Hematopoietic Stem Cell, HSC）祖细胞，这可能会改变二者在感染过程中发挥的功能。本研究证实，仅通过天然细胞因子（innate cytokine）即可激活新生儿CD8+ T细胞，并能在缺乏T细胞受体（T-cell receptor, TCR）信号的情况下，帮助宿主抵御多种不同的外来病原体。我们采用多组学（multi-omics）分析方法发现，新生儿CD8+ T细胞对天然细胞因子具有极高的响应性：其可快速发生染色质重塑（chromatin remodeling），进而启用一组更常见于天然样T细胞（innate-like T cell）的独特增强子（enhancer）。本研究还鉴定出一条关键的基因调控轴（Bach2/AP1），新生儿与成人CD8+ T细胞会差异化利用该轴来调节自身对天然细胞因子的响应能力。值得注意的是，CD8+ T细胞库中天然与适应性功能之间的发育转换，并非由单个细胞沿线性轨迹的成熟状态改变所介导，而是由不同细胞亚群的丰度变化所驱动。综上，本研究结果为分层免疫假说（layered immune hypothesis）提供了支持，并表明CD8+ T细胞库的表型多样性远超此前的认知。CD8+ T细胞通过阳性分选法（抗人CD8磁珠；美天旎生物（Miltenyi Biotech））从静置的外周血单个核细胞（Peripheral Blood Mononuclear Cell, PBMC）或脐带血单个核细胞（Cord Blood Mononuclear Cell, CBMC）中磁珠富集。随后将分离得到的细胞用白细胞介素2（IL-2）单独处理，或联合白细胞介素12（IL-12）与白细胞介素18（IL-18）进行处理，并通过单细胞RNA测序（single-cell RNA sequencing, scRNAseq）完成分析。