Developmental regulation by miR-29 specifies age-related differences in the CD8+ T cell immune response (Mouse scRNA-Seq)

Neonates are highly susceptible to repeat infection and respond poorly to vaccination; these attributes derive from intrinsic differences between neonatal and adult naïve CD8+ T cells. In contrast to adult cells, naïve neonatal cells exhibit a greatly limited ability to differentiate into memory cells, a fundamental property of their adult counterparts. Here, we describe the role of the miR-29 microRNA in naïve T cells, focusing on age-related differences in miR-29 expression and the consequences of these differences in adult and neonatal cells, from mice and humans. In adults, high expression of miR-29 licenses naïve cells towards eventual memory cell fates; whereas neonatal naïve cells, which lack high expression of miR-29, are predisposed towards effector cell fates in response to an infection. Multiple lines of evidence support this model, including analysis of a mouse model deficient in miR-29, which we examine with adoptive transfer experiments to define the functional consequences of reduction of miR-29, together with genomic assays to define the regulatory impact of miR-29. Adult miR 29 deficient naïve CD8+ T cells cell are primed for activation and therefore secrete elevated levels of cytolytic molecules, and express transcription factors at levels associated with effector cell differentiation; moreover, these cells exhibit an altered CD8+ T cell memory repertoire, akin to that of neonatal CD8+ T cells. Importantly, we use a method that exploits extracellular vesicles as a delivery vehicle with which to modulate levels of miR-29 in neonatal and adult naïve T cells, examining both human and mouse cells. For example, increasing miR 29 expression in mouse naïve neonatal CD8+ T cells significantly improved the memory response during infection, concomitant with alterations to the chromatin landscape characteristic of cells primed for memory differentiation. Delivery of miR-29 antagomirs to human adult naïve CD8+ T cells was sufficient to induce the adult cells to adopt phenotypes and gene expression signatures normally found in cells present in newborns. This study establishes miR-29 as a key conserved regulator in naïve CD8+ T cells, and by adjusting levels of miR-29, has the potential to underlie therapeutic strategies for controlling the balance of effector versus memory fates in human T cells. single cell mRNA profiles of adult CD8+ T cells, neonatal CD8+ T cells and adult CD8+ T cells with miR-29 gene knocked out.

新生儿极易发生重复感染，且疫苗应答效果不佳；这一特性源于新生与成年初始CD8+ T细胞（naïve CD8+ T cells）之间的内在差异。与成年细胞不同，新生初始T细胞向记忆细胞分化的能力极为有限——而这正是成年初始T细胞的核心特性之一。本研究聚焦微小RNA miR-29（miR-29 microRNA）在初始T细胞中的作用，重点探讨miR-29表达的年龄相关差异，以及该差异在小鼠与人类的成年、新生T细胞中产生的影响。在成年个体中，高表达的miR-29可赋予初始细胞向记忆细胞命运分化的潜能；而新生初始T细胞因缺乏miR-29的高表达，更倾向于在感染应答中走向效应细胞命运。多条实验证据支持这一模型，包括利用miR-29缺陷小鼠模型开展的研究：我们通过过继转移实验明确了miR-29表达下调的功能后果，并结合基因组学实验解析了miR-29的调控作用。成年miR-29缺陷型初始CD8+ T细胞已被激活启动，因此会分泌更高水平的细胞溶解分子，并表达与效应细胞分化相关的转录因子；此外，这些细胞的CD8+ T细胞记忆库发生改变，与新生CD8+ T细胞的特征类似。重要的是，我们开发了一种以细胞外囊泡（extracellular vesicles）作为递送载体的方法，用以调控新生与成年初始T细胞中的miR-29水平，并同时检测了人类与小鼠细胞。例如，提升小鼠新生初始CD8+ T细胞中的miR-29表达水平，可显著改善感染过程中的记忆应答，同时伴随记忆分化启动细胞特有的染色质景观改变。向人类成年初始CD8+ T细胞递送miR-29拮抗剂（antagomirs），即可诱导成年细胞呈现新生儿T细胞特有的表型与基因表达特征。本研究确立了miR-29作为初始CD8+ T细胞中关键保守调控因子的地位，通过调整miR-29的表达水平，有望为调控人类T细胞效应与记忆命运平衡的治疗策略提供理论基础。本数据集包含成年CD8+ T细胞、新生CD8+ T细胞以及miR-29基因敲除的成年CD8+ T细胞的单细胞mRNA转录组图谱。