MR1-restricted mucosal-associated invariant T (MAIT) cells play a unique role in the immune system. These cells develop intrathymically through a three-stage process, but the events that regulate this are largely unknown. Here, using bulk and single-cell RNA sequencing–based transcriptomic analysis in mice and humans, we studied the changing transcriptional landscape that accompanies transition through each stage. Many transcripts were sharply modulated during MAIT cell development, including SLAM (signaling lymphocytic activation molecule) family members, chemokine receptors, and transcription factors. We also demonstrate that stage 3 “mature” MAIT cells comprise distinct subpopulations including newly arrived transitional stage 3 cells, interferon-γ–producing MAIT1 cells and interleukin-17–producing MAIT17 cells. Moreover, the validity and importance of several transcripts detected in this study are directly demonstrated using specific mutant mice. For example, MAIT cell intrathymic maturation was found to be halted in SLAM-associated protein (SAP)–deficient and CXCR6-deficient mouse models, providing clear evidence for their role in modulating MAIT cell development. These data underpin a model that maps the changing transcriptional landscape and identifies key factors that regulate the process of MAIT cell differentiation, with many parallels between mice and humans.

MR1 限制性粘膜相关不变 T (MAIT) 细胞在免疫系统中发挥着独特的作用。这些细胞通过三个阶段的过程在胸腺内发育，但调节这一过程的事件在很大程度上是未知的。在这里，我们使用基于批量和单细胞 RNA 测序的小鼠和人类转录组分析，研究了伴随每个阶段转变的转录景观的变化。许多转录物在 MAIT 细胞发育过程中受到急剧调节，包括 SLAM（信号淋巴细胞激活分子）家族成员、趋化因子受体和转录因子。我们还证明，3 期“成熟”MAIT 细胞包含不同的亚群，包括新到达的过渡期 3 细胞、产生干扰素 γ 的 MAIT1 细胞和产生白细胞介素 17 的 MAIT17 细胞。此外，本研究中检测到的几个转录本的有效性和重要性是使用特定的突变小鼠直接证明的。例如，在 SLAM 相关蛋白 (SAP) 缺陷和 CXCR6 缺陷小鼠模型中，发现 MAIT 细胞胸腺内成熟停止，这为它们在调节 MAIT 细胞发育中的作用提供了明确的证据。这些数据支撑了一个模型，该模型绘制了不断变化的转录图谱，并确定了调节 MAIT 细胞分化过程的关键因素，小鼠和人类之间有许多相似之处。